Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD0116c_(-)_140265_141020
DateTue Jul 23 14:50:15 BST 2019
Unique Job IDa126ae3df323137e
SequenceMRRVVRYLSV ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:53.787 Y:47.161 Z:50.309
Model (left) based on template c3u1qB_
Top template information
PDB header:peptidoglycan binding protein
Chain: B: PDB Molecule:mycobacteria tuberculosis ld-transpeptidase type 2;
PDBTitle: crystal structure of m. tuberculosis ld-transpeptidase type 2 with 2-2 mercaptoethanol
Confidence and coverage
Confidence:100.0% Coverage: 85%
214 residues ( 85% of your sequence) have been modelled with 100.0% confidence by the single highest scoring template.
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Sequence analysis 

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Domain analysis [Show] 

Detailed template information [Hide] 

 

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Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3u1qB_
100.0 44
PDB header:peptidoglycan binding protein
Chain: B: PDB Molecule:mycobacteria tuberculosis ld-transpeptidase type 2;
PDBTitle: crystal structure of m. tuberculosis ld-transpeptidase type 2 with 2-2 mercaptoethanol
2c4xvoB_
100.0 62
PDB header:transferase
Chain: B: PDB Molecule:l,d-transpeptidase;
PDBTitle: l,d-transpeptidase from mycobacterium smegmatis
3c4jmxA_
100.0 100
PDB header:transferase/transferase inhibitor
Chain: A: PDB Molecule:probable l,d-transpeptidase ldta;
PDBTitle: structure of ld transpeptidase ldtmt1 in complex with imipenem
4c3vynB_
100.0 41
PDB header:transferase
Chain: B: PDB Molecule:probable conserved lipoprotein lpps;
PDBTitle: crystal structure of mycobacterium tuberculosis l,d-transpeptidase2 ldtmt2 n55 truncation mutant (resideus 55-408)
5c4z7aA_
100.0 30
PDB header:transferase
Chain: A: PDB Molecule:mycobacterium tuberculosis (3,3)l,d-transpeptidase type 5;
PDBTitle: structural and biochemical characterization of a non-functionally2 redundant m. tuberculosis (3,3) l,d-transpeptidase, ldtmt5.
6c4k73A_
100.0 57
PDB header:transferase
Chain: A: PDB Molecule:l,d-transpeptidase;
PDBTitle: x-ray crystal structure of an l,d-transpeptidase from mycobacterium2 tuberculosis h37rv
7c2hklB_
100.0 22
PDB header:transferase
Chain: B: PDB Molecule:l,d-transpeptidase;
PDBTitle: crystal structure of enterococcus faecium l,d-2 transpeptidase c442s mutant
8c5bmqA_
100.0 21
PDB header:hydrolase
Chain: A: PDB Molecule:erfk/ybis/ycfs/ynhg family protein;
PDBTitle: crystal structure of l,d-transpeptidase (yku) from stackebrandtia2 nassauensis
9d1zata1
100.0 29
Fold:L,D-transpeptidase catalytic domain-like
Superfamily:L,D-transpeptidase catalytic domain-like
Family:L,D-transpeptidase catalytic domain-like
10d1y7ma1
100.0 24
Fold:L,D-transpeptidase catalytic domain-like
Superfamily:L,D-transpeptidase catalytic domain-like
Family:L,D-transpeptidase catalytic domain-like
11c1y7mB_
100.0 21
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:hypothetical protein bsu14040;
PDBTitle: crystal structure of the b. subtilis ykud protein at 2 a2 resolution
12c4lzhA_
100.0 15
PDB header:transferase
Chain: A: PDB Molecule:l,d-transpeptidase;
PDBTitle: l,d-transpeptidase from klebsiella pneumoniae
13c4lpqA_
99.9 18
PDB header:transferase
Chain: A: PDB Molecule:erfk/ybis/ycfs/ynhg family protein;
PDBTitle: crystal structure of the l,d-transpeptidase (residues 123-326) from2 xylanimonas cellulosilytica dsm 15894
14c4y4vB_
99.9 16
PDB header:hydrolase
Chain: B: PDB Molecule:conserved hypothetical secreted protein;
PDBTitle: structure of helicobacter pylori csd6 in the d-ala-bound state
15c4xxtA_
99.9 24
PDB header:hydrolase
Chain: A: PDB Molecule:fusion of predicted zn-dependent amidase/peptidase (cell
PDBTitle: crystal structure of fused zn-dependent2 amidase/peptidase/peptodoglycan-binding domain-containing protein3 from clostridium acetobutylicum atcc 824
16c4hu2A_
99.8 35
PDB header:unknown function
Chain: A: PDB Molecule:probable conserved lipoprotein lpps;
PDBTitle: crystal structure of ldtmt2, a l,d-transpeptidase from mycobacterium2 tuberculosis: domain a and b
17c6ntwA_
99.4 18
PDB header:transferase/transferase inhibitor
Chain: A: PDB Molecule:probable l,d-transpeptidase ycbb;
PDBTitle: crystal structure of e. coli ycbb
18d1cz5a1
56.9 15
Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
19d1ix2a_
54.3 18
Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:Copper resistance protein C (CopC, PcoC)
20c1eqqD_
51.2 16
PDB header:replication/rna
Chain: D: PDB Molecule:single stranded dna binding protein;
PDBTitle: single stranded dna binding protein and ssdna complex
21c6rteB_
not modelled 48.8 17
PDB header:oxidoreductase
Chain: B: PDB Molecule:cytochrome c;
PDBTitle: dihydro-heme d1 dehydrogenase nirn in complex with dhe
22c2vw9B_
not modelled 45.7 16
PDB header:dna-binding protein
Chain: B: PDB Molecule:single-stranded dna binding protein;
PDBTitle: single stranded dna binding protein complex from2 helicobacter pylori
23c3lgjA_
not modelled 44.2 18
PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of single-stranded binding protein (ssb) from2 bartonella henselae
24c5xgtA_
not modelled 39.7 16
PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of the n-terminal domain of staphylococcus aureus2 single-stranded dna-binding protein ssba at 1.82 angstrom resolution
25c1z9fA_
not modelled 39.2 24
PDB header:dna binding protein
Chain: A: PDB Molecule:single-strand binding protein;
PDBTitle: crystal structure of single stranded dna-binding protein (tm0604) from2 thermotoga maritima at 2.60 a resolution
26c5gqoB_
not modelled 37.9 28
PDB header:dna binding protein
Chain: B: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: structure of the second single stranded dna binding protein (ssbb)2 from mycobacterium smegmatis
27d1eyga_
not modelled 36.9 14
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
28c3tqyA_
not modelled 35.1 20
PDB header:transferase
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: structure of a single-stranded dna-binding protein (ssb), from2 coxiella burnetii
29c5odnG_
not modelled 34.3 8
PDB header:dna binding protein
Chain: G: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: salinibacter ruber single-strand binding protein
30c3pe9D_
not modelled 33.0 11
PDB header:unknown function
Chain: D: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
31d2piaa1
not modelled 32.8 29
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
32d1qvca_
not modelled 32.7 16
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
33c1qvcA_
not modelled 32.7 16
PDB header:dna binding protein
Chain: A: PDB Molecule:single stranded dna binding protein monomer;
PDBTitle: crystal structure analysis of single stranded dna binding protein2 (ssb) from e.coli
34d3ulla_
not modelled 32.5 21
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
35c6nfqC_
not modelled 32.0 24
PDB header:metal binding protein
Chain: C: PDB Molecule:copc;
PDBTitle: copc from pseudomonas fluorescens
36c4damA_
not modelled 31.4 35
PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein 1;
PDBTitle: crystal structure of small single-stranded dna-binding protein from2 streptomyces coelicolor
37c1ue7A_
not modelled 31.2 24
PDB header:dna binding protein
Chain: A: PDB Molecule:single-strand binding protein;
PDBTitle: crystal structure of the single-stranded dna-binding2 protein from mycobacterium tuberculosis
38c3pgzB_
not modelled 30.2 14
PDB header:dna binding protein
Chain: B: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of a single strand binding protein (ssb) from2 bartonella henselae
39c3vdyA_
not modelled 27.3 20
PDB header:dna binding protein/dna
Chain: A: PDB Molecule:single-stranded dna-binding protein ssbb;
PDBTitle: b. subtilis ssbb/ssdna
40d2c9qa1
not modelled 27.2 18
Fold:Immunoglobulin-like beta-sandwich
Superfamily:E set domains
Family:Copper resistance protein C (CopC, PcoC)
41c3eivB_
not modelled 26.3 15
PDB header:dna binding protein
Chain: B: PDB Molecule:single-stranded dna-binding protein 2;
PDBTitle: crystal structure of single-stranded dna-binding protein2 from streptomyces coelicolor
42d3btaa1
not modelled 26.1 15
Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Clostridium neurotoxins, the second last domain
43c5ch7E_
not modelled 23.5 16
PDB header:oxidoreductase
Chain: E: PDB Molecule:dmso reductase family type ii enzyme, molybdopterin
PDBTitle: crystal structure of the perchlorate reductase pcrab - phe164 gate2 switch intermediate - from azospira suillum ps
44c4p9lA_
not modelled 22.9 26
PDB header:transport protein
Chain: A: PDB Molecule:ryanodine receptor 2;
PDBTitle: crystal structure of mouse ryanodine receptor 2 spry2 domain (1080-2 1253) disease mutant a1107m
45d1gawa1
not modelled 22.4 25
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
46d1ue1a_
not modelled 21.6 24
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
47c3ulpC_
not modelled 21.2 14
PDB header:dna binding protein/dna
Chain: C: PDB Molecule:single-strand binding protein;
PDBTitle: plasmodium falciparum ssb complex with ssdna
48c2xc8B_
not modelled 20.7 23
PDB header:viral protein
Chain: B: PDB Molecule:gene 22 product;
PDBTitle: crystal structure of the gene 22 product of the bacillus subtilis spp12 phage
49c5zktA_
not modelled 20.6 29
PDB header:transcription
Chain: A: PDB Molecule:putative transcription factor pcf6;
PDBTitle: crystal structure of tcp domain of pcf6 in oryza sativa
50d2slia1
not modelled 19.7 16
Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Leech intramolecular trans-sialidase, N-terminal domain
51c5icuA_
not modelled 19.5 18
PDB header:chaperone
Chain: A: PDB Molecule:copc;
PDBTitle: the crystal structure of copc from methylosinus trichosporium ob3b
52d1cqxa2
not modelled 19.1 29
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
53d2bmwa1
not modelled 18.9 13
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
54d1gvha2
not modelled 18.4 29
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
55c1h5nC_
not modelled 18.3 21
PDB header:oxidoreductase
Chain: C: PDB Molecule:dmso reductase;
PDBTitle: dmso reductase modified by the presence of dms and air
56d1fnda1
not modelled 18.2 19
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
57d1tvca1
not modelled 17.4 22
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
58c5zktB_
not modelled 17.1 29
PDB header:transcription
Chain: B: PDB Molecule:putative transcription factor pcf6;
PDBTitle: crystal structure of tcp domain of pcf6 in oryza sativa
59d1e1oa1
not modelled 15.7 25
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
60c2mnuB_
not modelled 15.2 13
PDB header:cell adhesion
Chain: B: PDB Molecule:apt;
PDBTitle: backbone and side chain 1h, 13c, and 15n chemical shift assignments2 for edb and specific binding aptide
61c4qt6A_
not modelled 15.2 31
PDB header:transport protein
Chain: A: PDB Molecule:probable e3 ubiquitin-protein ligase herc1;
PDBTitle: crystal structure of the spry domain of human herc1
62c3flpJ_
not modelled 15.1 24
PDB header:sugar binding protein
Chain: J: PDB Molecule:sap-like pentraxin;
PDBTitle: crystal structure of native heptameric sap-like pentraxin2 from limulus polyphemus
63c6er3B_
not modelled 14.5 17
PDB header:sugar binding protein
Chain: B: PDB Molecule:bnr/asp-box repeat protein;
PDBTitle: ruminococcus gnavus it-sialidase cbm40 bound to alpha2,3 sialyllactose
64c4ywkA_
not modelled 14.4 31
PDB header:cell cycle
Chain: A: PDB Molecule:cell division control protein 21;
PDBTitle: pyrococcus furiosus mcm n-terminal domain with zinc-binding subdomain2 b deleted
65c4obiA_
not modelled 14.3 6
PDB header:structural genomics, unknown function
Chain: A: PDB Molecule:uncharacterized protein;
PDBTitle: crystal structure of a duf1312 family protein (ef3258) from2 enterococcus faecalis v583 at 1.73 a resolution
66d1sm4a1
not modelled 14.2 19
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
67c2iheA_
not modelled 14.0 27
PDB header:dna binding protein
Chain: A: PDB Molecule:single-stranded dna-binding protein;
PDBTitle: crystal structure of wild-type single-stranded dna binding protein2 from thermus aquaticus
68d1krha1
not modelled 13.6 17
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
69d1eg7a_
not modelled 13.4 39
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
70c3pe9B_
not modelled 13.3 12
PDB header:unknown function
Chain: B: PDB Molecule:fibronectin(iii)-like module;
PDBTitle: structures of clostridium thermocellum cbha fibronectin(iii)-like2 modules
71d1wjja_
not modelled 13.3 24
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Single strand DNA-binding domain, SSB
72c5a4jC_
not modelled 13.2 44
PDB header:ligase
Chain: C: PDB Molecule:formate--tetrahydrofolate ligase;
PDBTitle: crystal structure of fthfs1 from t.acetoxydans re1
73c4p9jC_
not modelled 13.0 26
PDB header:transport protein
Chain: C: PDB Molecule:ryanodine receptor 1;
PDBTitle: crystal structure of rabbit ryanodine receptor 1 spry2 domain (1070-2 1246)
74d1e32a1
not modelled 12.9 22
Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Cdc48 N-terminal domain-like
75d1bbua1
not modelled 12.6 21
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:Anticodon-binding domain
76c3do6B_
not modelled 12.4 33
PDB header:ligase
Chain: B: PDB Molecule:formate--tetrahydrofolate ligase;
PDBTitle: crystal structure of putative formyltetrahydrofolate synthetase2 (tm1766) from thermotoga maritima at 1.85 a resolution
77c5n1tM_
not modelled 12.0 21
PDB header:oxidoreductase
Chain: M: PDB Molecule:copc;
PDBTitle: crystal structure of complex between flavocytochrome c and copper2 chaperone copc from t. paradoxus
78d1y5ia1
not modelled 12.0 21
Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
79d1a8da1
not modelled 11.8 11
Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Clostridium neurotoxins, the second last domain
80d1k78a1
not modelled 11.8 71
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
81c2v73B_
not modelled 11.7 12
PDB header:sugar-binding protein
Chain: B: PDB Molecule:putative exo-alpha-sialidase;
PDBTitle: the structure of the family 40 cbm from c. perfringens nanj2 in complex with a sialic acid containing molecule
82c4pogC_
not modelled 11.5 33
PDB header:replication, dna binding protein/dna
Chain: C: PDB Molecule:cell division control protein 21;
PDBTitle: mcm-ssdna co-crystal structure
83c2vl6C_
not modelled 10.9 38
PDB header:dna binding protein
Chain: C: PDB Molecule:minichromosome maintenance protein mcm;
PDBTitle: structural analysis of the sulfolobus solfataricus mcm2 protein n-terminal domain
84c2vdaB_
not modelled 10.8 26
PDB header:protein transport
Chain: B: PDB Molecule:maltoporin;
PDBTitle: solution structure of the seca-signal peptide complex
85c4owtB_
not modelled 10.8 28
PDB header:dna binding protein
Chain: B: PDB Molecule:soss complex subunit b1;
PDBTitle: structural basis of soss1 complex assembly
86d1lkta_
not modelled 10.6 17
Fold:Head-binding domain of phage P22 tailspike protein
Superfamily:Head-binding domain of phage P22 tailspike protein
Family:Head-binding domain of phage P22 tailspike protein
87d1ogya1
not modelled 10.4 16
Fold:Double psi beta-barrel
Superfamily:ADC-like
Family:Formate dehydrogenase/DMSO reductase, C-terminal domain
88d1qfza1
not modelled 10.3 20
Fold:Reductase/isomerase/elongation factor common domain
Superfamily:Riboflavin synthase domain-like
Family:Ferredoxin reductase FAD-binding domain-like
89d6paxa1
not modelled 10.1 57
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:Homeodomain-like
Family:Paired domain
90c4me3A_
not modelled 10.1 20
PDB header:replication
Chain: A: PDB Molecule:dna replication licensing factor mcm related protein;
PDBTitle: 1.8 angstrom crystal structure of the n-terminal domain of an archaeal2 mcm
91c1ltlE_
not modelled 9.9 40
PDB header:replication
Chain: E: PDB Molecule:dna replication initiator (cdc21/cdc54);
PDBTitle: the dodecamer structure of mcm from archaeal m.2 thermoautotrophicum
92c6cqoH_
not modelled 9.6 11
PDB header:dna binding protein
Chain: H: PDB Molecule:single-stranded dna-binding protein rim1, mitochondrial;
PDBTitle: crystal structure of mitochondrial single-stranded dna binding2 proteins from s. cerevisiae (semet labeled), rim1 (form2)
93c6hinA_
not modelled 9.5 15
PDB header:membrane protein
Chain: A: PDB Molecule:5-hydroxytryptamine receptor 3a;
PDBTitle: mouse serotonin 5-ht3 receptor, serotonin-bound, f conformation
94c4azzB_
not modelled 9.5 9
PDB header:hydrolase
Chain: B: PDB Molecule:levanase;
PDBTitle: carbohydrate binding module cbm66 from bacillus subtilis
95d1qksa2
not modelled 9.4 20
Fold:8-bladed beta-propeller
Superfamily:C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
Family:C-terminal (heme d1) domain of cytochrome cd1-nitrite reductase
96d1c1la_
not modelled 9.2 17
Fold:Concanavalin A-like lectins/glucanases
Superfamily:Concanavalin A-like lectins/glucanases
Family:Galectin (animal S-lectin)
97c2kd2A_
not modelled 9.2 32
PDB header:apoptosis
Chain: A: PDB Molecule:fas apoptotic inhibitory molecule 1;
PDBTitle: nmr structure of faim-ctd
98c5jiaH_
not modelled 9.1 25
PDB header:ran-binding protein
Chain: H: PDB Molecule:ran-binding protein 10;
PDBTitle: the crystal structure of ius-spry domain from ranbp10
99d1ltla_
not modelled 8.9 40
Fold:OB-fold
Superfamily:Nucleic acid-binding proteins
Family:DNA replication initiator (cdc21/cdc54) N-terminal domain

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