Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	E	L	P	E	V	E	T	S	R	R	G	I	E	P	H	L	V	G	A	T	I	L	H	A	V	V	R	N	G	R	L	R	W	P	V	S	E	E	I	Y	R	L	S	D	Q	P	V	L	S	V	Q	R	R	A	K	Y	L	L
Secondary structure
SS confidence
Disorder		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	E	L	P	E	G	W	I	I	I	H	L	G	M	S	G	S	L	R	I	L	P	E	E	L	P	P	E	K	H	D	H	V	D	L	V	M	S	N	G	K	V	L	R	Y	T	D	P	R	R	F	G	A	W	L	W	T	K	E	L
Secondary structure
SS confidence
Disorder																										?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		E	G	H	N	V	L	T	H	L	G	P	E	P	L	S	D	D	F	N	G	E	Y	L	H	Q	K	C	A	K	K	K	T	A	I	K	P	W	L	M	D	N	K	L	V	V	G	V	G	N	I	Y	A	S	E	S	L	F	A	A	G
Secondary structure
SS confidence
Disorder			?	?																										?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		I	H	P	D	R	L	A	S	S	L	S	L	A	E	C	E	L	L	A	R	V	I	K	A	V	L	L	R	S	I	E	Q	G	G	T	T	L	K	D	F	L	Q	S	D	G	K	P	G	Y	F	A	Q	E	L	Q	V	Y	G	R	K
Secondary structure
SS confidence
Disorder																																											?			?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.
Sequence		G	E	P	C	R	V	C	G	T	P	I	V	A	T	K	H	A	Q	R	A	T	F	Y	C	R	Q	C	Q	K
Secondary structure
SS confidence
Disorder																												?	?	?
Disorder confidence

Confidence Key
High(9)											Low (0)

?	Disordered
	Alpha helix
	Beta strand

Domain analysis

Hover over an aligned region to see model and summary info

Please note, only up to the top 20 hits are modelled to reduce computer load

Rank Aligned region

PDB 2f5q chain A Region: 2 - 269 Aligned: 268 Modelled: 268 Confidence: 100.0% Identity: 40% PDB header:hydrolase/dna Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase; PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2 Phyre2 PDB 1k82 chain D Region: 2 - 269 Aligned: 260 Modelled: 268 Confidence: 100.0% Identity: 100% PDB header:hydrolase/dna Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna Phyre2 PDB 1nnj chain A Region: 3 - 269 Aligned: 261 Modelled: 267 Confidence: 100.0% Identity: 37% PDB header:hydrolase Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna Phyre2 PDB 1ee8 chain A Region: 2 - 269 Aligned: 258 Modelled: 268 Confidence: 100.0% Identity: 41% PDB header:dna binding protein Chain: A: PDB Molecule:mutm (fpg) protein; PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8 Phyre2 PDB 2opf chain A Region: 2 - 268 Aligned: 247 Modelled: 255 Confidence: 100.0% Identity: 24% PDB header:hydrolase/dna Chain: A: PDB Molecule:endonuclease viii; PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate Phyre2 PDB 3a46 chain B Region: 2 - 269 Aligned: 260 Modelled: 268 Confidence: 100.0% Identity: 27% PDB header:hydrolase Chain: B: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of mvnei1/thf complex Phyre2 PDB 1tdh chain A Region: 2 - 263 Aligned: 244 Modelled: 262 Confidence: 100.0% Identity: 25% PDB header:hydrolase Chain: A: PDB Molecule:nei endonuclease viii-like 1; PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1) Phyre2 PDB 1k82 chain A domain 2 Region: 2 - 129 Aligned: 128 Modelled: 128 Confidence: 100.0% Identity: 100% Fold: N-terminal domain of MutM-like DNA repair proteins Superfamily: N-terminal domain of MutM-like DNA repair proteins Family: N-terminal domain of MutM-like DNA repair proteins Phyre2 PDB 1r2z chain A domain 1 Region: 130 - 223 Aligned: 94 Modelled: 94 Confidence: 100.0% Identity: 41% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1r2z chain A domain 2 Region: 2 - 129 Aligned: 128 Modelled: 128 Confidence: 100.0% Identity: 34% Fold: N-terminal domain of MutM-like DNA repair proteins Superfamily: N-terminal domain of MutM-like DNA repair proteins Family: N-terminal domain of MutM-like DNA repair proteins Phyre2 PDB 1k82 chain A domain 1 Region: 130 - 217 Aligned: 88 Modelled: 88 Confidence: 100.0% Identity: 100% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1ee8 chain A domain 1 Region: 130 - 218 Aligned: 89 Modelled: 89 Confidence: 100.0% Identity: 42% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1tdz chain A domain 1 Region: 130 - 217 Aligned: 88 Modelled: 88 Confidence: 100.0% Identity: 38% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1tdz chain A domain 2 Region: 3 - 126 Aligned: 123 Modelled: 124 Confidence: 99.9% Identity: 33% Fold: N-terminal domain of MutM-like DNA repair proteins Superfamily: N-terminal domain of MutM-like DNA repair proteins Family: N-terminal domain of MutM-like DNA repair proteins Phyre2 PDB 1k3x chain A domain 1 Region: 129 - 214 Aligned: 86 Modelled: 86 Confidence: 99.9% Identity: 22% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1ee8 chain A domain 2 Region: 2 - 129 Aligned: 118 Modelled: 128 Confidence: 99.9% Identity: 39% Fold: N-terminal domain of MutM-like DNA repair proteins Superfamily: N-terminal domain of MutM-like DNA repair proteins Family: N-terminal domain of MutM-like DNA repair proteins Phyre2 PDB 1k3x chain A domain 2 Region: 2 - 128 Aligned: 119 Modelled: 127 Confidence: 99.9% Identity: 22% Fold: N-terminal domain of MutM-like DNA repair proteins Superfamily: N-terminal domain of MutM-like DNA repair proteins Family: N-terminal domain of MutM-like DNA repair proteins Phyre2 PDB 1tdh chain A domain 2 Region: 2 - 121 Aligned: 116 Modelled: 120 Confidence: 99.9% Identity: 27% Fold: N-terminal domain of MutM-like DNA repair proteins Superfamily: N-terminal domain of MutM-like DNA repair proteins Family: N-terminal domain of MutM-like DNA repair proteins Phyre2 PDB 1tdh chain A domain 1 Region: 129 - 219 Aligned: 91 Modelled: 91 Confidence: 99.8% Identity: 29% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1ee8 chain A domain 3 Region: 218 - 269 Aligned: 52 Modelled: 52 Confidence: 99.6% Identity: 42% Fold: Glucocorticoid receptor-like (DNA-binding domain) Superfamily: Glucocorticoid receptor-like (DNA-binding domain) Family: C-terminal, Zn-finger domain of MutM-like DNA repair proteins Phyre2 1 c2f5qA_ 2 c1k82D_ 3 c1nnjA_ 4 c1ee8A_ 5 c2opfA_ 6 c3a46B_ 7 c1tdhA_ 8 d1k82a2 9 d1r2za1 10 d1r2za2 11 d1k82a1 12 d1ee8a1 13 d1tdza1 14 d1tdza2 15 d1k3xa1 16 d1ee8a2 17 d1k3xa2 18 d1tdha2 19 d1tdha1 20 d1ee8a3 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156

Detailed template information

# Template Alignment Coverage 3D Model Confidence % i.d. Template Information

1 c2f5qA_ 100.0 40 PDB header:hydrolase/dna Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase; PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2 2 c1k82D_ 100.0 100 PDB header:hydrolase/dna Chain: D: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of e.coli formamidopyrimidine-dna2 glycosylase (fpg) covalently trapped with dna 3 c1nnjA_ 100.0 37 PDB header:hydrolase Chain: A: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure complex between the lactococcus lactis fpg and an2 abasic site containing dna 4 c1ee8A_ 100.0 41 PDB header:dna binding protein Chain: A: PDB Molecule:mutm (fpg) protein; PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8 5 c2opfA_ 100.0 24 PDB header:hydrolase/dna Chain: A: PDB Molecule:endonuclease viii; PDBTitle: crystal structure of the dna repair enzyme endonuclease-viii (nei)2 from e. coli (r252a) in complex with ap-site containing dna substrate 6 c3a46B_ 100.0 27 PDB header:hydrolase Chain: B: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of mvnei1/thf complex 7 c1tdhA_ 100.0 25 PDB header:hydrolase Chain: A: PDB Molecule:nei endonuclease viii-like 1; PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1) 8 d1k82a2 100.0 100 Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins 9 d1r2za1 100.0 41 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 10 d1r2za2 100.0 34 Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins 11 d1k82a1 100.0 100 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 12 d1ee8a1 100.0 42 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 13 d1tdza1 100.0 38 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 14 d1tdza2 99.9 33 Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins 15 d1k3xa1 99.9 22 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 16 d1ee8a2 99.9 39 Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins 17 d1k3xa2 99.9 22 Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins 18 d1tdha2 99.9 27 Fold:N-terminal domain of MutM-like DNA repair proteins Superfamily:N-terminal domain of MutM-like DNA repair proteins Family:N-terminal domain of MutM-like DNA repair proteins 19 d1tdha1 99.8 29 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 20 d1ee8a3 99.6 42 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 21 d2hkja1 not modelled 99.6 19 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Topoisomerase VI-B subunit middle domain 22 d1tdza3 not modelled 99.6 46 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 23 d1r2za3 not modelled 99.6 52 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 24 d1k82a3 not modelled 99.5 100 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 25 d1l1ta3 not modelled 99.5 55 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 26 d1k3xa3 not modelled 99.3 39 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:C-terminal, Zn-finger domain of MutM-like DNA repair proteins 27 c3doaA_ not modelled 97.3 13 PDB header:protein binding Chain: A: PDB Molecule:fibrinogen binding protein; PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus 28 d2uubm1 not modelled 96.8 25 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 29 d2gy9m1 not modelled 96.6 27 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 30 c3iz6M_ not modelled 96.5 27 PDB header:ribosome Chain: M: PDB Molecule:40s ribosomal protein s18 (s13p); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 31 c2zkqm_ not modelled 96.4 25 PDB header:ribosomal protein/rna Chain: M: PDB Molecule: PDBTitle: structure of a mammalian ribosomal 40s subunit within an2 80s complex obtained by docking homology models of the rna3 and proteins into an 8.7 a cryo-em map 32 c2xznM_ not modelled 96.4 22 PDB header:ribosome Chain: M: PDB Molecule:rps18e; PDBTitle: crystal structure of the eukaryotic 40s ribosomal2 subunit in complex with initiation factor 1. this file3 contains the 40s subunit and initiation factor for4 molecule 2 33 d1i94m_ not modelled 96.3 25 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 34 c1mx0D_ not modelled 95.3 23 PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit 35 d2i0za2 not modelled 92.4 26 Fold:HI0933 insert domain-like Superfamily:HI0933 insert domain-like Family:HI0933 insert domain-like 36 c3fuxB_ not modelled 92.0 21 PDB header:transferase Chain: B: PDB Molecule:dimethyladenosine transferase; PDBTitle: t. thermophilus 16s rrna a1518 and a1519 methyltransferase (ksga) in2 complex with 5'-methylthioadenosine in space group p212121 37 c3fteA_ not modelled 89.3 31 PDB header:transferase/rna Chain: A: PDB Molecule:dimethyladenosine transferase; PDBTitle: crystal structure of a. aeolicus ksga in complex with rna 38 d1qyra_ not modelled 89.2 25 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:rRNA adenine dimethylase-like 39 c2gb5B_ not modelled 86.1 21 PDB header:hydrolase Chain: B: PDB Molecule:nadh pyrophosphatase; PDBTitle: crystal structure of nadh pyrophosphatase (ec 3.6.1.22) (1790429) from2 escherichia coli k12 at 2.30 a resolution 40 c2zbkB_ not modelled 85.5 22 PDB header:isomerase Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b; PDBTitle: crystal structure of an intact type ii dna topoisomerase:2 insights into dna transfer mechanisms 41 c3uzuA_ not modelled 84.6 15 PDB header:transferase Chain: A: PDB Molecule:ribosomal rna small subunit methyltransferase a; PDBTitle: the structure of the ribosomal rna small subunit methyltransferase a2 from burkholderia pseudomallei 42 c3tqsB_ not modelled 78.9 6 PDB header:transferase Chain: B: PDB Molecule:ribosomal rna small subunit methyltransferase a; PDBTitle: structure of the dimethyladenosine transferase (ksga) from coxiella2 burnetii 43 c2h1rA_ not modelled 78.8 11 PDB header:transferase Chain: A: PDB Molecule:dimethyladenosine transferase, putative; PDBTitle: crystal structure of a dimethyladenosine transferase from2 plasmodium falciparum 44 c3bbnM_ not modelled 76.4 17 PDB header:ribosome Chain: M: PDB Molecule:ribosomal protein s13; PDBTitle: homology model for the spinach chloroplast 30s subunit2 fitted to 9.4a cryo-em map of the 70s chlororibosome. 45 d2jnea1 not modelled 71.9 21 Fold:Rubredoxin-like Superfamily:YfgJ-like Family:YfgJ-like 46 c2jneA_ not modelled 71.9 21 PDB header:metal binding protein Chain: A: PDB Molecule:hypothetical protein yfgj; PDBTitle: nmr structure of e.coli yfgj modelled with two zn+2 bound.2 northeast structural genomics consortium target er317. 47 c2jrpA_ not modelled 71.2 21 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative cytoplasmic protein; PDBTitle: solution nmr structure of yfgj from salmonella typhimurium2 modeled with two zn+2 bound, northeast structural genomics3 consortium target str86 48 d2fiya1 not modelled 70.5 20 Fold:FdhE-like Superfamily:FdhE-like Family:FdhE-like 49 d2gqfa2 not modelled 67.2 17 Fold:HI0933 insert domain-like Superfamily:HI0933 insert domain-like Family:HI0933 insert domain-like 50 c3u50C_ not modelled 65.2 26 PDB header:dna binding protein Chain: C: PDB Molecule:telomerase-associated protein 82; PDBTitle: crystal structure of the tetrahymena telomerase processivity factor2 teb1 ob-c 51 c1dvbA_ not modelled 63.4 21 PDB header:electron transport Chain: A: PDB Molecule:rubrerythrin; PDBTitle: rubrerythrin 52 c3grrA_ not modelled 59.2 12 PDB header:transferase Chain: A: PDB Molecule:dimethyladenosine transferase; PDBTitle: crystal structure of the complex between s-adenosyl homocysteine and2 methanocaldococcus jannaschi dim1. 53 d1qf8a_ not modelled 59.2 27 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 54 c2lcqA_ not modelled 58.9 20 PDB header:metal binding protein Chain: A: PDB Molecule:putative toxin vapc6; PDBTitle: solution structure of the endonuclease nob1 from p.horikoshii 55 d1l1oc_ not modelled 57.9 24 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 56 c2q2eB_ not modelled 57.9 16 PDB header:isomerase Chain: B: PDB Molecule:type 2 dna topoisomerase 6 subunit b; PDBTitle: crystal structure of the topoisomerase vi holoenzyme from2 methanosarcina mazei 57 d1pfta_ not modelled 57.4 20 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 58 c1dgsB_ not modelled 56.1 30 PDB header:ligase Chain: B: PDB Molecule:dna ligase; PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis 59 c2owoA_ not modelled 55.5 29 PDB header:ligase/dna Chain: A: PDB Molecule:dna ligase; PDBTitle: last stop on the road to repair: structure of e.coli dna ligase bound2 to nicked dna-adenylate 60 c2kpiA_ not modelled 55.4 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein sco3027; PDBTitle: solution nmr structure of streptomyces coelicolor sco30272 modeled with zn+2 bound, northeast structural genomics3 consortium target rr58 61 d1vd4a_ not modelled 54.6 42 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 62 d2f4ma1 not modelled 51.8 31 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 63 c3fydA_ not modelled 51.6 12 PDB header:transferase Chain: A: PDB Molecule:probable dimethyladenosine transferase; PDBTitle: crystal structure of dim1 from the thermophilic archeon,2 methanocaldococcus jannaschi 64 d1odha_ not modelled 51.1 17 Fold:GCM domain Superfamily:GCM domain Family:GCM domain 65 d2akla2 not modelled 51.0 26 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:PhnA zinc-binding domain 66 c2js4A_ not modelled 49.8 22 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0434 protein bb2007; PDBTitle: solution nmr structure of bordetella bronchiseptica protein2 bb2007. northeast structural genomics consortium target3 bor54 67 c3na7A_ not modelled 49.4 14 PDB header:gene regulation, chaperone Chain: A: PDB Molecule:hp0958; PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874 68 d2avue1 not modelled 49.2 28 Fold:FlhC-like Superfamily:FlhC-like Family:FlhC-like 69 c1yuzB_ not modelled 48.8 30 PDB header:oxidoreductase Chain: B: PDB Molecule:nigerythrin; PDBTitle: partially reduced state of nigerythrin 70 c2hr5B_ not modelled 48.3 40 PDB header:metal binding protein Chain: B: PDB Molecule:rubrerythrin; PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form 71 c3kp9A_ not modelled 47.4 30 PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase 72 c2jr6A_ not modelled 46.6 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:upf0434 protein nma0874; PDBTitle: solution structure of upf0434 protein nma0874. northeast structural2 genomics target mr32 73 d1jwhc_ not modelled 46.3 27 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 74 c2avuF_ not modelled 45.4 28 PDB header:transcription activator Chain: F: PDB Molecule:flagellar transcriptional activator flhc; PDBTitle: structure of the escherichia coli flhdc complex, a2 prokaryotic heteromeric regulator of transcription 75 c3eswA_ not modelled 41.7 19 PDB header:hydrolase Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine PDBTitle: complex of yeast pngase with glcnac2-iac. 76 d1ctla1 not modelled 41.5 25 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 77 c2ba1B_ not modelled 41.4 23 PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core 78 d1twfi2 not modelled 40.8 31 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 79 d2jnya1 not modelled 40.7 9 Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like 80 c2qkdA_ not modelled 39.9 24 PDB header:signaling protein, cell cycle Chain: A: PDB Molecule:zinc finger protein zpr1; PDBTitle: crystal structure of tandem zpr1 domains 81 c2riqA_ not modelled 39.3 24 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: crystal structure of the third zinc-binding domain of human parp-1 82 d1ibia1 not modelled 38.8 40 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 83 c1nypA_ not modelled 38.6 23 PDB header:cell adhesion Chain: A: PDB Molecule:pinch protein; PDBTitle: 4th lim domain of pinch protein 84 d1i4wa_ not modelled 38.6 14 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:rRNA adenine dimethylase-like 85 c1i4wA_ not modelled 38.6 14 PDB header:transcription Chain: A: PDB Molecule:mitochondrial replication protein mtf1; PDBTitle: the crystal structure of the transcription factor sc-mttfb2 offers intriguing insights into mitochondrial transcription 86 c3eg9B_ not modelled 38.0 15 PDB header:protein transport Chain: B: PDB Molecule:sec24 related gene family, member d; PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23/24 bound to the transport signal sequence of membrin 87 d1x3za1 not modelled 37.6 19 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 88 d2k4xa1 not modelled 37.2 36 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein S27a 89 d1dl6a_ not modelled 36.6 17 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 90 c3egxB_ not modelled 36.1 42 PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24a; PDBTitle: crystal structure of the mammalian copii-coat protein2 sec23a/24a complexed with the snare protein sec22b and3 bound to the transport signal sequence of the snare protein4 bet1 91 d2pk7a1 not modelled 36.1 17 Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like 92 c2jvnA_ not modelled 35.4 35 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: domain c of human parp-1 93 d2hf1a1 not modelled 35.2 22 Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like 94 c1pd0A_ not modelled 35.1 27 PDB header:transport protein Chain: A: PDB Molecule:protein transport protein sec24; PDBTitle: crystal structure of the copii coat subunit, sec24,2 complexed with a peptide from the snare protein sed53 (yeast syntaxin-5) 95 c1mpgB_ not modelled 35.1 19 PDB header:hydrolase Chain: B: PDB Molecule:3-methyladenine dna glycosylase ii; PDBTitle: 3-methyladenine dna glycosylase ii from escherichia coli 96 d1qypa_ not modelled 35.0 25 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 97 d2ct7a1 not modelled 34.1 21 Fold:RING/U-box Superfamily:RING/U-box Family:IBR domain 98 c1m2vB_ not modelled 33.6 27 PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24; PDBTitle: crystal structure of the yeast sec23/24 heterodimer 99 d2cu8a1 not modelled 33.2 30 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 100 c2yg8B_ not modelled 33.2 26 PDB header:hydrolase Chain: B: PDB Molecule:dna-3-methyladenine glycosidase ii, putative; PDBTitle: structure of an unusual 3-methyladenine dna glycosylase ii (2 alka) from deinococcus radiodurans 101 c3a44D_ not modelled 33.1 23 PDB header:metal binding protein Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa; PDBTitle: crystal structure of hypa in the dimeric form 102 c2jr7A_ not modelled 32.4 33 PDB header:metal binding protein Chain: A: PDB Molecule:dph3 homolog; PDBTitle: solution structure of human desr1 103 c3eh2B_ not modelled 30.9 19 PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24c; PDBTitle: crystal structure of the human copii-coat protein sec24c 104 d2b9da1 not modelled 30.4 26 Fold:E7 C-terminal domain-like Superfamily:E7 C-terminal domain-like Family:E7 C-terminal domain-like 105 d1woua_ not modelled 30.4 23 Fold:Thioredoxin fold Superfamily:Thioredoxin-like Family:Txnl5-like 106 d1e29a_ not modelled 29.2 13 Fold:Cytochrome c Superfamily:Cytochrome c Family:monodomain cytochrome c 107 c2h56C_ not modelled 28.7 11 PDB header:hydrolase Chain: C: PDB Molecule:dna-3-methyladenine glycosidase; PDBTitle: crystal structure of dna-3-methyladenine glycosidase (10174367) from2 bacillus halodurans at 2.55 a resolution 108 d1x3ha1 not modelled 28.3 16 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 109 c2jhnB_ not modelled 27.8 26 PDB header:hydrolase Chain: B: PDB Molecule:3-methyladenine dna-glycosylase; PDBTitle: 3-methyladenine dna-glycosylase from archaeoglobus fulgidus 110 d1pcfa_ not modelled 27.7 26 Fold:ssDNA-binding transcriptional regulator domain Superfamily:ssDNA-binding transcriptional regulator domain Family:Transcriptional coactivator PC4 C-terminal domain 111 d1ywsa1 not modelled 27.6 25 Fold:Rubredoxin-like Superfamily:CSL zinc finger Family:CSL zinc finger 112 c1m2oA_ not modelled 27.6 12 PDB header:protein transport/signaling protein Chain: A: PDB Molecule:protein transport protein sec23; PDBTitle: crystal structure of the sec23-sar1 complex 113 c2nn6I_ not modelled 26.5 8 PDB header:hydrolase/transferase Chain: I: PDB Molecule:3'-5' exoribonuclease csl4 homolog; PDBTitle: structure of the human rna exosome composed of rrp41, rrp45,2 rrp46, rrp43, mtr3, rrp42, csl4, rrp4, and rrp40 114 c1x3hA_ not modelled 26.2 16 PDB header:metal binding protein Chain: A: PDB Molecule:leupaxin; PDBTitle: solution structure of the lim domain of human leupaxin 115 d1wd2a_ not modelled 26.1 21 Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4 116 c3f6qB_ not modelled 26.0 19 PDB header:signaling protein/signaling protein Chain: B: PDB Molecule:lim and senescent cell antigen-like-containing PDBTitle: crystal structure of integrin-linked kinase ankyrin repeat2 domain in complex with pinch1 lim1 domain 117 d1wgea1 not modelled 25.9 33 Fold:Rubredoxin-like Superfamily:CSL zinc finger Family:CSL zinc finger 118 d2ct1a1 not modelled 25.7 40 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 119 c2eloA_ not modelled 25.6 30 PDB header:transcription Chain: A: PDB Molecule:zinc finger protein 406; PDBTitle: solution structure of the 12th c2h2 zinc finger of human2 zinc finger protein 406 120 d1u5ka2 not modelled 25.4 21 Fold:ArfGap/RecO-like zinc finger Superfamily:ArfGap/RecO-like zinc finger Family:RecO C-terminal domain-like

Binding site prediction

Due to computational demand, binding site predictions are not run for batch jobs

If you want to predict binding sites, please manually submit your model of choice to 3DLigandSite

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Phyre is for academic use only

Please cite: Protein structure prediction on the web: a case study using the Phyre server
Kelley LA and Sternberg MJE. Nature Protocols 4, 363 - 371 (2009) [pdf] [Import into BibTeX]
If you use the binding site predictions from 3DLigandSite, please also cite:
3DLigandSite: predicting ligand-binding sites using similar structures.
Wass MN, Kelley LA and Sternberg MJ Nucleic Acids Research 38, W469-73 (2010) [PubMed]
© Structural Bioinformatics Group Imperial College London Lawrence Kelley, Benjamin Jefferys Disclaimer Terms and Conditions	Component software Template detection: HHpred 1.51 Secondary structure prediction: Psi-pred 2.5 Disorder prediction: Disopred 2.4 Transmembrane prediction: Memsat_SVM Multi-template modelling and ab initio: Poing 1.0