Phyre Home Retrieve Phyre Job Id
Emailmdejesus@rockefeller.edu
DescriptionRVBD2906c_(trmD)_3215675_3216367
DateThu Aug 8 16:20:06 BST 2019
Unique Job ID7f1c5de52a34165b
SequenceVRIDIVTIFP ... Download FASTA
Job Typenormal
Job Expiry

Summary 

Top model
Image coloured by rainbow N → C terminus
Model dimensions (Å):X:50.711 Y:48.923 Z:76.257
Model (left) based on template c3quvB_
Top template information
PDB header:transferase
Chain: B: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure of a trna-guanine-n1-methyltransferase from2 mycobacterium abscessus
Confidence and coverage
Confidence:100.0% Coverage: 96%
221 residues ( 96% 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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#
Template Alignment Coverage3D Model Confidence
% i.d. Template Information
1c3quvB_
100.0 76
PDB header:transferase
Chain: B: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure of a trna-guanine-n1-methyltransferase from2 mycobacterium abscessus
2c4h3zA_
100.0 42
PDB header:transferase
Chain: A: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure of a symmetric dimer of a trna (guanine-(n(1)-)-2 methyltransferase from burkholderia phymatum bound to s-adenosyl3 homocystein in both half-sites
3c5wyrA_
100.0 46
PDB header:transferase
Chain: A: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure and catalytic mechanism of the essential m1g37 trna2 methyltransferase trmd from pseudomonas aeruginosa
4d1uala_
100.0 42
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:tRNA(m1G37)-methyltransferase TrmD
5d1p9pa_
100.0 44
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:tRNA(m1G37)-methyltransferase TrmD
6c3iefA_
100.0 45
PDB header:transferase, rna binding protein
Chain: A: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure of trna guanine-n1-methyltransferase from bartonella2 henselae using mpcs.
7c3ky7A_
100.0 45
PDB header:transferase
Chain: A: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: 2.35 angstrom resolution crystal structure of a putative trna2 (guanine-7-)-methyltransferase (trmd) from staphylococcus aureus3 subsp. aureus mrsa252
8c1oy5B_
100.0 38
PDB header:transferase
Chain: B: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure of trna (m1g37) methyltransferase from aquifex2 aeolicus
9d1oy5a_
100.0 38
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:tRNA(m1G37)-methyltransferase TrmD
10c3knuD_
100.0 50
PDB header:transferase
Chain: D: PDB Molecule:trna (guanine-n(1)-)-methyltransferase;
PDBTitle: crystal structure of trna (guanine-n1)-methyltransferase from2 anaplasma phagocytophilum
11d1to0a_
95.2 23
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YbeA-like
12d1vh0a_
94.9 22
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YbeA-like
13d1ns5a_
94.1 13
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YbeA-like
14c2v3jA_
94.0 8
PDB header:ribosomal protein
Chain: A: PDB Molecule:essential for mitotic growth 1;
PDBTitle: the yeast ribosome synthesis factor emg1 alpha beta knot2 fold methyltransferase
15d2v3ka1
93.2 8
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:EMG1/NEP1-like
16d1o6da_
92.8 13
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YbeA-like
17c3o7bA_
82.0 15
PDB header:transferase
Chain: A: PDB Molecule:ribosome biogenesis nep1 rna methyltransferase;
PDBTitle: crystal structure of archaeoglobus fulgidus nep1 bound to s-2 adenosylhomocysteine
18c6aytD_
45.4 16
PDB header:hydrolase, transferase
Chain: D: PDB Molecule:5'-methylthioadenosine/s-adenosylhomocysteine nucleosidase;
PDBTitle: crystal structure of campylobacter jejuni 5'-methylthioadenosine/s-2 adenosyl homocysteine nucleosidase (mtan) complexed with3 pyrazinylthio-dadme-immucillin-a
19c5faiA_
40.8 13
PDB header:transferase
Chain: A: PDB Molecule:ribosomal rna small subunit methyltransferase nep1;
PDBTitle: emg1 n1-specific pseudouridine methyltransferase
20c3d3rA_
40.7 54
PDB header:chaperone
Chain: A: PDB Molecule:hydrogenase assembly chaperone hypc/hupf;
PDBTitle: crystal structure of the hydrogenase assembly chaperone hypc/hupf2 family protein from shewanella oneidensis mr-1
21d3d3ra1
not modelled 38.7 54
Fold:OB-fold
Superfamily:HupF/HypC-like
Family:HupF/HypC-like
22c4k30B_
not modelled 31.6 11
PDB header:transferase
Chain: B: PDB Molecule:n-acetylglutamate synthase, mitochondrial;
PDBTitle: structure of the n-acetyltransferase domain of human n-acetylglutamate2 synthase
23c3ai9X_
not modelled 31.5 14
PDB header:transferase
Chain: X: PDB Molecule:upf0217 protein mj1640;
PDBTitle: crystal structure of duf358 protein reveals a putative spout-class2 rrna methyltransferase
24c6hnuA_
not modelled 31.1 8
PDB header:transferase
Chain: A: PDB Molecule:aromatic amino acid aminotransferase i;
PDBTitle: crystal structure of the aminotransferase aro8 from c. albicans with2 ligands
25c5zyoD_
not modelled 29.6 17
PDB header:transferase
Chain: D: PDB Molecule:ribosomal rna large subunit methyltransferase h;
PDBTitle: crystal structure of domain-swapped circular-permuted ybea (cp74) from2 escherichia coli
26d2ot2a1
not modelled 29.5 27
Fold:OB-fold
Superfamily:HupF/HypC-like
Family:HupF/HypC-like
27c1zosE_
not modelled 29.0 18
PDB header:hydrolase
Chain: E: PDB Molecule:5'-methylthioadenosine / s-adenosylhomocysteine
PDBTitle: structure of 5'-methylthionadenosine/s-adenosylhomocysteine2 nucleosidase from s. pneumoniae with a transition-state inhibitor mt-3 imma
28c5n9mA_
not modelled 27.9 17
PDB header:transferase
Chain: A: PDB Molecule:cobyric acid synthase;
PDBTitle: crystal structure of gatd - a glutamine amidotransferase from2 staphylococcus aureus involved in peptidoglycan amidation
29c4m38A_
not modelled 27.0 13
PDB header:transferase/transferase substrate
Chain: A: PDB Molecule:protein arginine n-methyltransferase 7;
PDBTitle: crystal structure of trypanosoma brucei protein arginine2 methyltransferase 7 complex with adohcy and histone h4 peptide
30d2z1ca1
not modelled 25.9 27
Fold:OB-fold
Superfamily:HupF/HypC-like
Family:HupF/HypC-like
31c1rcuB_
not modelled 23.6 9
PDB header:structural genomics, unknown function
Chain: B: PDB Molecule:conserved hypothetical protein vt76;
PDBTitle: x-ray structure of tm1055 northeast structural genomics2 consortium target vt76
32c4l69A_
not modelled 23.4 19
PDB header:transferase
Chain: A: PDB Molecule:ribosomal rna small subunit methyltransferase e;
PDBTitle: rv2372c of mycobacterium tuberculosis is rsme like methyltransferse
33d1rcua_
not modelled 23.0 9
Fold:MCP/YpsA-like
Superfamily:MCP/YpsA-like
Family:MoCo carrier protein-like
34c3kw2A_
not modelled 21.2 15
PDB header:transferase
Chain: A: PDB Molecule:probable r-rna methyltransferase;
PDBTitle: crystal structure of probable rrna-methyltransferase from2 porphyromonas gingivalis
35d1fdja_
not modelled 21.0 22
Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
36c6h4kA_
not modelled 21.0 29
PDB header:immune system
Chain: A: PDB Molecule:ubiquitin carboxyl-terminal hydrolase 25;
PDBTitle: structure of the usp25 c-terminal domain
37c3bl6A_
not modelled 20.7 13
PDB header:hydrolase
Chain: A: PDB Molecule:5'-methylthioadenosine nucleosidase/s-
PDBTitle: crystal structure of staphylococcus aureus 5'-2 methylthioadenosine/s-adenosylhomocysteine nucleosidase in3 complex with formycin a
38c4ljkA_
not modelled 20.0 27
PDB header:dna binding protein
Chain: A: PDB Molecule:dna processing chain a (dpra);
PDBTitle: structural insights into the unique single-stranded dna binding mode2 of dna processing protein a from helicobacter pylori
39c3r7tA_
not modelled 19.9 18
PDB header:ligase
Chain: A: PDB Molecule:adenylosuccinate synthetase;
PDBTitle: crystal structure of adenylosuccinate synthetase from campylobacter2 jejuni
40c5vm8A_
not modelled 19.3 25
PDB header:transferase
Chain: A: PDB Molecule:ribosomal rna small subunit methyltransferase e;
PDBTitle: crystal structure of a ribosomal rna small subunit methyltransferase e2 from neisseria gonorrhoeae bound to s-adenosyl methionine
41c1zggA_
not modelled 19.0 36
PDB header:hydrolase
Chain: A: PDB Molecule:putative low molecular weight protein-tyrosine-
PDBTitle: solution structure of a low molecular weight protein2 tyrosine phosphatase from bacillus subtilis
42c2mxfA_
not modelled 18.8 23
PDB header:transcription regulator/dna
Chain: A: PDB Molecule:mvat;
PDBTitle: structure of the dna complex of the c-terminal domain of mvat
43c1egpA_
not modelled 18.7 27
PDB header:proteinase inhibitor
Chain: A: PDB Molecule:eglin-c;
PDBTitle: proteinase inhibitor eglin c with hydrolysed reactive center
44c5t87D_
not modelled 18.2 35
PDB header:toxin
Chain: D: PDB Molecule:cdii immunity protein;
PDBTitle: crystal structure of cdi complex from cupriavidus taiwanensis lmg2 19424
45d2z1aa2
not modelled 17.9 17
Fold:Metallo-dependent phosphatases
Superfamily:Metallo-dependent phosphatases
Family:5'-nucleotidase (syn. UDP-sugar hydrolase), N-terminal domain
46c6acvA_
not modelled 17.5 18
PDB header:dna binding protein
Chain: A: PDB Molecule:methyl-cpg-binding domain-containing protein 11;
PDBTitle: the solution nmr structure of mbd domain
47c4etiA_
not modelled 17.4 36
PDB header:hydrolase
Chain: A: PDB Molecule:low molecular weight protein-tyrosine-phosphatase ywle;
PDBTitle: crystal structure of ywle from bacillus subtilis
48c2xhzC_
not modelled 16.7 16
PDB header:isomerase
Chain: C: PDB Molecule:arabinose 5-phosphate isomerase;
PDBTitle: probing the active site of the sugar isomerase domain from e. coli2 arabinose-5-phosphate isomerase via x-ray crystallography
49c3fxaA_
not modelled 16.7 11
PDB header:sugar binding protein
Chain: A: PDB Molecule:sis domain protein;
PDBTitle: crystal structure of a putative sugar-phosphate isomerase2 (lmof2365_0531) from listeria monocytogenes str. 4b f2365 at 1.60 a3 resolution
50c1w4zA_
not modelled 16.3 18
PDB header:antibiotic biosynthesis
Chain: A: PDB Molecule:ketoacyl reductase;
PDBTitle: structure of actinorhodin polyketide (actiii) reductase
51c3uqzB_
not modelled 16.1 23
PDB header:dna binding protein
Chain: B: PDB Molecule:dna processing protein dpra;
PDBTitle: x-ray structure of dna processing protein a (dpra) from streptococcus2 pneumoniae
52c4dowA_
not modelled 16.0 30
PDB header:replication
Chain: A: PDB Molecule:origin recognition complex subunit 1;
PDBTitle: structure of mouse orc1 bah domain bound to h4k20me2
53d1p9ba_
not modelled 15.5 16
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
54d1ixrc1
not modelled 15.4 34
Fold:DNA/RNA-binding 3-helical bundle
Superfamily:"Winged helix" DNA-binding domain
Family:Helicase DNA-binding domain
55c5i34B_
not modelled 15.3 16
PDB header:ligase
Chain: B: PDB Molecule:adenylosuccinate synthetase;
PDBTitle: adenylosuccinate synthetase from cryptococcus neoformans complexed2 with gdp and imp
56c2pyhB_
not modelled 15.3 13
PDB header:isomerase
Chain: B: PDB Molecule:poly(beta-d-mannuronate) c5 epimerase 4;
PDBTitle: azotobacter vinelandii mannuronan c-5 epimerase alge4 a-module2 complexed with mannuronan trisaccharide
57c2ky8A_
not modelled 15.1 27
PDB header:transcription/dna
Chain: A: PDB Molecule:methyl-cpg-binding domain protein 2;
PDBTitle: solution structure and dynamic analysis of chicken mbd2 methyl binding2 domain bound to a target methylated dna sequence
58d1zcza1
not modelled 15.0 26
Fold:Methylglyoxal synthase-like
Superfamily:Methylglyoxal synthase-like
Family:Inosicase
59c4txkA_
not modelled 14.9 21
PDB header:oxidoreductase
Chain: A: PDB Molecule:protein-methionine sulfoxide oxidase mical1;
PDBTitle: construct of mical-1 containing the monooxygenase and calponin2 homology domains
60c3vxvA_
not modelled 14.9 27
PDB header:hydrolase/dna
Chain: A: PDB Molecule:methyl-cpg-binding domain protein 4;
PDBTitle: crystal structure of methyl cpg binding domain of mbd4 in complex with2 the 5mcg/tg sequence
61c5z3mB_
not modelled 14.9 18
PDB header:hydrolase
Chain: B: PDB Molecule:phosphotyrosine protein phosphatase;
PDBTitle: crystal structure of low molecular weight phosphotyrosine phosphatase2 (vclmwptp-2) from vibrio choleraeo395
62d1m2ka_
not modelled 14.7 15
Fold:DHS-like NAD/FAD-binding domain
Superfamily:DHS-like NAD/FAD-binding domain
Family:Sir2 family of transcriptional regulators
63c4xruE_
not modelled 14.4 30
PDB header:protein binding
Chain: E: PDB Molecule:rnl;
PDBTitle: structure of pnkp1/rnl/hen1 complex
64d1dj3a_
not modelled 14.2 18
Fold:P-loop containing nucleoside triphosphate hydrolases
Superfamily:P-loop containing nucleoside triphosphate hydrolases
Family:Nitrogenase iron protein-like
65c1xi4O_
not modelled 14.1 22
PDB header:endocytosis/exocytosis
Chain: O: PDB Molecule:clathrin light chain a;
PDBTitle: clathrin d6 coat
66c3a8tA_
not modelled 13.9 20
PDB header:transferase
Chain: A: PDB Molecule:adenylate isopentenyltransferase;
PDBTitle: plant adenylate isopentenyltransferase in complex with atp
67d3dl3a1
not modelled 13.9 21
Fold:Double-stranded beta-helix
Superfamily:Clavaminate synthase-like
Family:TehB-like
68d1a5ca_
not modelled 13.8 19
Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
69d1nxza2
not modelled 13.6 13
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:YggJ C-terminal domain-like
70c2ehdB_
not modelled 13.5 21
PDB header:oxidoreductase
Chain: B: PDB Molecule:oxidoreductase, short-chain dehydrogenase/reductase family;
PDBTitle: crystal structure analysis of oxidoreductase
71d3bb6a1
not modelled 13.5 8
Fold:Double-stranded beta-helix
Superfamily:Clavaminate synthase-like
Family:TehB-like
72c5agqA_
not modelled 13.5 18
PDB header:transcription
Chain: A: PDB Molecule:bromodomain adjacent to zinc finger domain protein 2a;
PDBTitle: solution structure of the tam domain of human tip5 baz2a2 involved in epigenetic regulation of rrna genes
73c3h7aC_
not modelled 13.3 23
PDB header:oxidoreductase
Chain: C: PDB Molecule:short chain dehydrogenase;
PDBTitle: crystal structure of short-chain dehydrogenase from rhodopseudomonas2 palustris
74c4p6iD_
not modelled 13.2 19
PDB header:hydrolase
Chain: D: PDB Molecule:crispr-associated endonuclease cas1;
PDBTitle: crystal structure of the cas1-cas2 complex from escherichia coli
75c1zmrA_
not modelled 13.0 5
PDB header:transferase
Chain: A: PDB Molecule:phosphoglycerate kinase;
PDBTitle: crystal structure of the e. coli phosphoglycerate kinase
76c2pc4B_
not modelled 12.9 19
PDB header:lyase
Chain: B: PDB Molecule:fructose-bisphosphate aldolase;
PDBTitle: crystal structure of fructose-bisphosphate aldolase from plasmodium2 falciparum in complex with trap-tail determined at 2.4 angstrom3 resolution
77c4da9C_
not modelled 12.9 8
PDB header:oxidoreductase
Chain: C: PDB Molecule:short-chain dehydrogenase/reductase;
PDBTitle: crystal structure of putative short-chain dehydrogenase/reductase from2 sinorhizobium meliloti 1021
78c4dg5A_
not modelled 12.8 7
PDB header:transferase
Chain: A: PDB Molecule:phosphoglycerate kinase;
PDBTitle: crystal structure of staphylococcal phosphoglycerate kinase
79c4e6nC_
not modelled 12.5 67
PDB header:protein binding
Chain: C: PDB Molecule:metallophosphoesterase;
PDBTitle: crystal structure of bacterial pnkp-c/hen1-n heterodimer
80c4go1A_
not modelled 12.5 14
PDB header:transcription
Chain: A: PDB Molecule:transcriptional regulator lsrr;
PDBTitle: crystal structure of full length transcription repressor lsrr from e.2 coli.
81d1gxha_
not modelled 12.4 30
Fold:Acyl carrier protein-like
Superfamily:Colicin E immunity proteins
Family:Colicin E immunity proteins
82d2qmma1
not modelled 12.4 18
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:AF1056-like
83c2k1lB_
not modelled 12.4 55
PDB header:signaling protein
Chain: B: PDB Molecule:ephrin type-a receptor 1;
PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3
84c2k1kA_
not modelled 12.4 55
PDB header:signaling protein
Chain: A: PDB Molecule:ephrin type-a receptor 1;
PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3
85c2k1kB_
not modelled 12.4 55
PDB header:signaling protein
Chain: B: PDB Molecule:ephrin type-a receptor 1;
PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 4.3
86c2k1lA_
not modelled 12.4 55
PDB header:signaling protein
Chain: A: PDB Molecule:ephrin type-a receptor 1;
PDBTitle: nmr structures of dimeric transmembrane domain of the2 receptor tyrosine kinase epha1 in lipid bicelles at ph 6.3
87c5b7pB_
not modelled 12.4 23
PDB header:hydrolase
Chain: B: PDB Molecule:mta/sah nucleosidase;
PDBTitle: structures and functional analysis of periplasmic 5-2 methylthioadenosine/s-adenosylhomocysteine nucleosidase from3 aeromonas hydrophila
88c2no8A_
not modelled 12.3 30
PDB header:immune system
Chain: A: PDB Molecule:colicin-e2 immunity protein;
PDBTitle: nmr structure analysis of the colicin immuntiy protein im2
89c6ixjK_
not modelled 12.2 18
PDB header:cytosolic protein
Chain: K: PDB Molecule:sulfoacetaldehyde reductase;
PDBTitle: the crystal structure of sulfoacetaldehyde reductase from klebsiella2 oxytoca
90c4qkoA_
not modelled 12.2 20
PDB header:antimicrobial protein
Chain: A: PDB Molecule:pyocin-s2 immunity protein;
PDBTitle: the crystal structure of the pyocin s2 nuclease domain, immunity2 protein complex at 1.8 angstroms
91d1xfba1
not modelled 12.1 22
Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
92c6fqbE_
not modelled 12.1 15
PDB header:ligase
Chain: E: PDB Molecule:cobyric acid synthase;
PDBTitle: murt/gatd peptidoglycan amidotransferase complex from streptococcus2 pneumoniae r6
93d2vlqa1
not modelled 12.0 20
Fold:Acyl carrier protein-like
Superfamily:Colicin E immunity proteins
Family:Colicin E immunity proteins
94c3ty8A_
not modelled 12.0 67
PDB header:transferase
Chain: A: PDB Molecule:polynucleotide 2',3'-cyclic phosphate phosphodiesterase /
PDBTitle: crystal structure of c. thermocellum pnkp ligase domain apo form
95c5fwaA_
not modelled 11.8 14
PDB header:transferase
Chain: A: PDB Molecule:protein arginine n-methyltransferase 2;
PDBTitle: crystal structure of mus musculus protein arginine methyltransferase 22 with cp1
96d3bbda1
not modelled 11.8 12
Fold:alpha/beta knot
Superfamily:alpha/beta knot
Family:EMG1/NEP1-like
97d1ayia_
not modelled 11.8 30
Fold:Acyl carrier protein-like
Superfamily:Colicin E immunity proteins
Family:Colicin E immunity proteins
98d1zaia1
not modelled 11.7 22
Fold:TIM beta/alpha-barrel
Superfamily:Aldolase
Family:Class I aldolase
99c1gshA_
not modelled 11.5 20
PDB header:glutathione biosynthesis ligase
Chain: A: PDB Molecule:glutathione biosynthetic ligase;
PDBTitle: structure of escherichia coli glutathione synthetase at ph 7.5

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