Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	P	E	G	P	E	I	R	R	A	A	D	N	L	E	A	A	I	K	G	K	P	L	T	D	V	W	F	A	F	P	Q	L	K	P	Y	Q	S	Q	L	I	G	Q	H	V	T	H	V	E	T	R	G	K	A	L	L	T	H	F	S
Secondary structure
SS confidence
Disorder		?	?	?																														?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		N	D	L	T	L	Y	S	H	N	Q	L	Y	G	V	W	R	V	V	D	T	G	E	E	P	Q	T	T	R	V	L	R	V	K	L	Q	T	A	D	K	T	I	L	L	Y	S	A	S	D	I	E	M	L	T	P	E	Q	L	T	T	H
Secondary structure
SS confidence
Disorder																							?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	F	L	Q	R	V	G	P	D	V	L	D	P	N	L	T	P	E	V	V	K	E	R	L	L	S	P	R	F	R	N	R	Q	F	A	G	L	L	L	D	Q	A	F	L	A	G	L	G	N	Y	L	R	V	E	I	L	W	Q	V	G
Secondary structure
SS confidence
Disorder																											?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		L	T	G	N	H	K	A	K	D	L	N	A	A	Q	L	D	A	L	A	H	A	L	L	E	I	P	R	F	S	Y	A	T	R	G	Q	V	D	E	N	K	H	H	G	A	L	F	R	F	K	V	F	H	R	D	G	E	P	C	E	R
Secondary structure
SS confidence
Disorder																																				?		?	?	?	?	?												?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.
Sequence		C	G	S	I	I	E	K	T	T	L	S	S	R	P	F	Y	W	C	P	G	C	Q	H
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 2opf chain A Region: 2 - 263 Aligned: 256 Modelled: 256 Confidence: 100.0% Identity: 98% 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 2f5q chain A Region: 2 - 262 Aligned: 255 Modelled: 261 Confidence: 100.0% Identity: 30% 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 1nnj chain A Region: 3 - 262 Aligned: 255 Modelled: 260 Confidence: 100.0% Identity: 24% 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 1k82 chain D Region: 2 - 262 Aligned: 253 Modelled: 261 Confidence: 100.0% Identity: 24% 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 1ee8 chain A Region: 2 - 262 Aligned: 251 Modelled: 261 Confidence: 100.0% Identity: 27% 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 3a46 chain B Region: 2 - 262 Aligned: 247 Modelled: 261 Confidence: 100.0% Identity: 26% PDB header:hydrolase Chain: B: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of mvnei1/thf complex Phyre2 PDB 1tdh chain A Region: 2 - 257 Aligned: 238 Modelled: 249 Confidence: 100.0% Identity: 22% PDB header:hydrolase Chain: A: PDB Molecule:nei endonuclease viii-like 1; PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1) Phyre2 PDB 1k3x chain A domain 1 Region: 126 - 214 Aligned: 89 Modelled: 89 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 1k3x chain A domain 2 Region: 2 - 125 Aligned: 124 Modelled: 124 Confidence: 100.0% Identity: 98% 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: 127 - 222 Aligned: 93 Modelled: 96 Confidence: 100.0% Identity: 27% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1k82 chain A domain 1 Region: 127 - 217 Aligned: 88 Modelled: 91 Confidence: 100.0% 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 1 Region: 127 - 218 Aligned: 89 Modelled: 92 Confidence: 100.0% Identity: 28% 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: 127 - 216 Aligned: 87 Modelled: 90 Confidence: 100.0% Identity: 25% 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 - 126 Aligned: 122 Modelled: 125 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 1ee8 chain A domain 2 Region: 2 - 126 Aligned: 117 Modelled: 125 Confidence: 99.9% Identity: 25% 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 1tdz chain A domain 2 Region: 3 - 126 Aligned: 122 Modelled: 124 Confidence: 99.9% Identity: 20% 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 2 Region: 2 - 126 Aligned: 122 Modelled: 122 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 1 Region: 126 - 207 Aligned: 82 Modelled: 82 Confidence: 99.8% Identity: 30% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Middle domain of MutM-like DNA repair proteins Phyre2 PDB 1tdh chain A domain 2 Region: 2 - 108 Aligned: 106 Modelled: 107 Confidence: 99.8% Identity: 20% 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 2hkj chain A domain 1 Region: 126 - 205 Aligned: 75 Modelled: 80 Confidence: 99.6% Identity: 20% Fold: S13-like H2TH domain Superfamily: S13-like H2TH domain Family: Topoisomerase VI-B subunit middle domain Phyre2 1 c2opfA_ 2 c2f5qA_ 3 c1nnjA_ 4 c1k82D_ 5 c1ee8A_ 6 c3a46B_ 7 c1tdhA_ 8 d1k3xa1 9 d1k3xa2 10 d1r2za1 11 d1k82a1 12 d1ee8a1 13 d1tdza1 14 d1r2za2 15 d1ee8a2 16 d1tdza2 17 d1k82a2 18 d1tdha1 19 d1tdha2 20 d2hkja1 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 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 121 122 123 124 125 126 127 128 129 130 131 132 133 134 135 136 137 138 139 140 141 142 143 144 145 146 147 148 149 150 151 152 153 154 155 156 157 158 159 160

Detailed template information

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

1 c2opfA_ 100.0 98 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 2 c2f5qA_ 100.0 30 PDB header:hydrolase/dna Chain: A: PDB Molecule:formamidopyrimidine-dna glycosidase; PDBTitle: catalytically inactive (e3q) mutm crosslinked to oxog:c2 containing dna cc2 3 c1nnjA_ 100.0 24 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 c1k82D_ 100.0 24 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 5 c1ee8A_ 100.0 27 PDB header:dna binding protein Chain: A: PDB Molecule:mutm (fpg) protein; PDBTitle: crystal structure of mutm (fpg) protein from thermus thermophilus hb8 6 c3a46B_ 100.0 26 PDB header:hydrolase Chain: B: PDB Molecule:formamidopyrimidine-dna glycosylase; PDBTitle: crystal structure of mvnei1/thf complex 7 c1tdhA_ 100.0 22 PDB header:hydrolase Chain: A: PDB Molecule:nei endonuclease viii-like 1; PDBTitle: crystal structure of human endonuclease viii-like 1 (neil1) 8 d1k3xa1 100.0 100 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 9 d1k3xa2 100.0 98 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 10 d1r2za1 100.0 27 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 11 d1k82a1 100.0 22 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 12 d1ee8a1 100.0 28 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 13 d1tdza1 100.0 25 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 14 d1r2za2 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 15 d1ee8a2 99.9 25 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 16 d1tdza2 99.9 20 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 d1k82a2 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 d1tdha1 99.8 30 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Middle domain of MutM-like DNA repair proteins 19 d1tdha2 99.8 20 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 20 d2hkja1 99.6 20 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Topoisomerase VI-B subunit middle domain 21 d1k3xa3 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 22 d1ee8a3 not modelled 99.5 32 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 d1tdza3 not modelled 99.5 34 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 d1r2za3 not modelled 99.5 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 25 d1k82a3 not modelled 99.5 36 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 d1l1ta3 not modelled 99.4 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 27 d2uubm1 not modelled 96.8 24 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 28 c2zkqm_ not modelled 96.6 14 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 29 c3iz6M_ not modelled 96.5 20 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 30 d1i94m_ not modelled 96.4 27 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 31 d2gy9m1 not modelled 96.4 24 Fold:S13-like H2TH domain Superfamily:S13-like H2TH domain Family:Ribosomal protein S13 32 c2xznM_ not modelled 96.3 20 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 c3doaA_ not modelled 96.1 19 PDB header:protein binding Chain: A: PDB Molecule:fibrinogen binding protein; PDBTitle: the crystal structure of the fibrinogen binding protein from2 staphylococcus aureus 34 d2i0za2 not modelled 94.0 21 Fold:HI0933 insert domain-like Superfamily:HI0933 insert domain-like Family:HI0933 insert domain-like 35 c1mx0D_ not modelled 93.6 18 PDB header:isomerase Chain: D: PDB Molecule:type ii dna topoisomerase vi subunit b; PDBTitle: structure of topoisomerase subunit 36 d1qyra_ not modelled 90.9 28 Fold:S-adenosyl-L-methionine-dependent methyltransferases Superfamily:S-adenosyl-L-methionine-dependent methyltransferases Family:rRNA adenine dimethylase-like 37 c2gb5B_ not modelled 88.3 20 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 38 c3uzuA_ not modelled 88.1 24 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 39 c3fuxB_ not modelled 85.3 20 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 40 c3fteA_ not modelled 85.3 15 PDB header:transferase/rna Chain: A: PDB Molecule:dimethyladenosine transferase; PDBTitle: crystal structure of a. aeolicus ksga in complex with rna 41 c1yuzB_ not modelled 85.0 17 PDB header:oxidoreductase Chain: B: PDB Molecule:nigerythrin; PDBTitle: partially reduced state of nigerythrin 42 c3tqsB_ not modelled 82.1 9 PDB header:transferase Chain: B: PDB Molecule:ribosomal rna small subunit methyltransferase a; PDBTitle: structure of the dimethyladenosine transferase (ksga) from coxiella2 burnetii 43 c3bbnM_ not modelled 78.7 23 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. 44 d2fiya1 not modelled 78.1 23 Fold:FdhE-like Superfamily:FdhE-like Family:FdhE-like 45 c1dvbA_ not modelled 77.4 20 PDB header:electron transport Chain: A: PDB Molecule:rubrerythrin; PDBTitle: rubrerythrin 46 d1twfi2 not modelled 74.7 29 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 47 d2gqfa2 not modelled 74.4 15 Fold:HI0933 insert domain-like Superfamily:HI0933 insert domain-like Family:HI0933 insert domain-like 48 c2jneA_ not modelled 74.0 17 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. 49 d2jnea1 not modelled 74.0 17 Fold:Rubredoxin-like Superfamily:YfgJ-like Family:YfgJ-like 50 c2jrpA_ not modelled 73.5 17 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 51 d2f4ma1 not modelled 73.4 16 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 52 c3u50C_ not modelled 70.8 27 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 53 d2akla2 not modelled 70.5 42 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:PhnA zinc-binding domain 54 d1qypa_ not modelled 69.9 32 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 55 c2owoA_ not modelled 65.1 38 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 56 c2hr5B_ not modelled 62.7 29 PDB header:metal binding protein Chain: B: PDB Molecule:rubrerythrin; PDBTitle: pf1283- rubrerythrin from pyrococcus furiosus iron bound form 57 d1pfta_ not modelled 61.8 28 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 58 c3eg9B_ not modelled 61.7 23 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 59 c2kpiA_ not modelled 61.6 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 60 d1l1oc_ not modelled 61.4 23 Fold:OB-fold Superfamily:Nucleic acid-binding proteins Family:Single strand DNA-binding domain, SSB 61 c3egxB_ not modelled 61.2 29 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 62 c2h1rA_ not modelled 61.0 11 PDB header:transferase Chain: A: PDB Molecule:dimethyladenosine transferase, putative; PDBTitle: crystal structure of a dimethyladenosine transferase from2 plasmodium falciparum 63 c1dgsB_ not modelled 60.8 35 PDB header:ligase Chain: B: PDB Molecule:dna ligase; PDBTitle: crystal structure of nad+-dependent dna ligase from t.2 filiformis 64 c1pd0A_ not modelled 60.7 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) 65 c2lcqA_ not modelled 60.1 30 PDB header:metal binding protein Chain: A: PDB Molecule:putative toxin vapc6; PDBTitle: solution structure of the endonuclease nob1 from p.horikoshii 66 d1tfia_ not modelled 59.7 30 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 67 d1qf8a_ not modelled 59.5 30 Fold:Rubredoxin-like Superfamily:Casein kinase II beta subunit Family:Casein kinase II beta subunit 68 d1odha_ not modelled 57.7 13 Fold:GCM domain Superfamily:GCM domain Family:GCM domain 69 c3h0gI_ not modelled 57.6 28 PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii subunit rpb9; PDBTitle: rna polymerase ii from schizosaccharomyces pombe 70 c3eh2B_ not modelled 55.8 19 PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24c; PDBTitle: crystal structure of the human copii-coat protein sec24c 71 c1m2vB_ not modelled 54.9 27 PDB header:protein transport Chain: B: PDB Molecule:protein transport protein sec24; PDBTitle: crystal structure of the yeast sec23/24 heterodimer 72 c1i3qI_ not modelled 53.4 29 PDB header:transcription Chain: I: PDB Molecule:dna-directed rna polymerase ii 14.2kd PDBTitle: rna polymerase ii crystal form i at 3.1 a resolution 73 c2js4A_ not modelled 53.0 17 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 74 c3na7A_ not modelled 52.5 24 PDB header:gene regulation, chaperone Chain: A: PDB Molecule:hp0958; PDBTitle: 2.2 angstrom structure of the hp0958 protein from helicobacter pylori2 ccug 17874 75 d1x3za1 not modelled 52.2 22 Fold:Cysteine proteinases Superfamily:Cysteine proteinases Family:Transglutaminase core 76 c2zbkB_ not modelled 52.1 18 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 77 c2jr6A_ not modelled 51.6 13 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 78 c1m2oA_ not modelled 51.3 23 PDB header:protein transport/signaling protein Chain: A: PDB Molecule:protein transport protein sec23; PDBTitle: crystal structure of the sec23-sar1 complex 79 c2riqA_ not modelled 50.7 25 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 80 d2ct7a1 not modelled 50.1 21 Fold:RING/U-box Superfamily:RING/U-box Family:IBR domain 81 d1pd0a5 not modelled 49.8 27 Fold:Rubredoxin-like Superfamily:Zn-finger domain of Sec23/24 Family:Zn-finger domain of Sec23/24 82 d2avue1 not modelled 49.1 20 Fold:FlhC-like Superfamily:FlhC-like Family:FlhC-like 83 c2jvnA_ not modelled 48.7 21 PDB header:transferase Chain: A: PDB Molecule:poly [adp-ribose] polymerase 1; PDBTitle: domain c of human parp-1 84 c3eswA_ not modelled 46.1 22 PDB header:hydrolase Chain: A: PDB Molecule:peptide-n(4)-(n-acetyl-beta-glucosaminyl)asparagine PDBTitle: complex of yeast pngase with glcnac2-iac. 85 c2avuF_ not modelled 45.0 20 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 86 d2jnya1 not modelled 44.5 13 Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like 87 c2ba1B_ not modelled 44.1 23 PDB header:rna binding protein Chain: B: PDB Molecule:archaeal exosome rna binding protein csl4; PDBTitle: archaeal exosome core 88 d1u5ka2 not modelled 43.8 21 Fold:ArfGap/RecO-like zinc finger Superfamily:ArfGap/RecO-like zinc finger Family:RecO C-terminal domain-like 89 c3kp9A_ not modelled 43.1 67 PDB header:blood coagulation,oxidoreductase Chain: A: PDB Molecule:vkorc1/thioredoxin domain protein; PDBTitle: structure of a bacterial homolog of vitamin k epoxide reductase 90 d2b9da1 not modelled 42.7 28 Fold:E7 C-terminal domain-like Superfamily:E7 C-terminal domain-like Family:E7 C-terminal domain-like 91 c1u5kA_ not modelled 41.6 23 PDB header:recombination,replication Chain: A: PDB Molecule:hypothetical protein; PDBTitle: recombinational repair protein reco 92 d2k4xa1 not modelled 41.6 32 Fold:Rubredoxin-like Superfamily:Zn-binding ribosomal proteins Family:Ribosomal protein S27a 93 d1ctla1 not modelled 41.5 33 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 94 d1ibia1 not modelled 39.3 50 Fold:Glucocorticoid receptor-like (DNA-binding domain) Superfamily:Glucocorticoid receptor-like (DNA-binding domain) Family:LIM domain 95 d1wd2a_ not modelled 39.3 27 Fold:RING/U-box Superfamily:RING/U-box Family:RING finger domain, C3HC4 96 d1dl6a_ not modelled 39.2 22 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 97 c1nypA_ not modelled 39.1 23 PDB header:cell adhesion Chain: A: PDB Molecule:pinch protein; PDBTitle: 4th lim domain of pinch protein 98 c3d00A_ not modelled 39.0 23 PDB header:metal binding protein Chain: A: PDB Molecule:tungsten formylmethanofuran dehydrogenase subunit e; PDBTitle: crystal structure of a tungsten formylmethanofuran dehydrogenase2 subunit e (fmde)-like protein (syn_00638) from syntrophus3 aciditrophicus at 1.90 a resolution 99 d2pk7a1 not modelled 38.3 13 Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like 100 d2hf1a1 not modelled 38.3 22 Fold:Trm112p-like Superfamily:Trm112p-like Family:Trm112p-like 101 d1nuia2 not modelled 37.4 30 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:DNA primase zinc finger 102 c2qkdA_ not modelled 37.1 16 PDB header:signaling protein, cell cycle Chain: A: PDB Molecule:zinc finger protein zpr1; PDBTitle: crystal structure of tandem zpr1 domains 103 c2yrcA_ not modelled 36.8 24 PDB header:protein transport Chain: A: PDB Molecule:protein transport protein sec23a; PDBTitle: solution structure of the zf-sec23_sec24 from human sec23a 104 d1lkoa2 not modelled 36.3 41 Fold:Rubredoxin-like Superfamily:Rubredoxin-like Family:Rubredoxin 105 d1vd4a_ not modelled 36.1 33 Fold:Rubredoxin-like Superfamily:Zinc beta-ribbon Family:Transcriptional factor domain 106 c2hl7A_ not modelled 35.8 67 PDB header:oxidoreductase Chain: A: PDB Molecule:cytochrome c-type biogenesis protein ccmh; PDBTitle: crystal structure of the periplasmic domain of ccmh from pseudomonas2 aeruginosa 107 c2d56A_ not modelled 34.5 26 PDB header:antibiotic Chain: A: PDB Molecule:asabf; PDBTitle: solution structure of asabf, antibacterial peptide isolated2 from a nematode, ascaris suum 108 d2qtva5 not modelled 34.3 23 Fold:Rubredoxin-like Superfamily:Zn-finger domain of Sec23/24 Family:Zn-finger domain of Sec23/24 109 c3zvzB_ not modelled 33.9 38 PDB header:ligase Chain: B: PDB Molecule:e3 ubiquitin-protein ligase uhrf1; PDBTitle: phd finger of human uhrf1 110 c3a44D_ not modelled 32.7 23 PDB header:metal binding protein Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa; PDBTitle: crystal structure of hypa in the dimeric form 111 c1pqvS_ not modelled 30.6 19 PDB header:transferase/transcription Chain: S: PDB Molecule:transcription elongation factor s-ii; PDBTitle: rna polymerase ii-tfiis complex 112 c1y1yS_ not modelled 30.6 22 PDB header:transferase/transcription/dna-rna hybrid Chain: S: PDB Molecule:transcription elongation factor s-ii; PDBTitle: rna polymerase ii-tfiis-dna/rna complex 113 c2qneA_ not modelled 30.2 18 PDB header:transferase Chain: A: PDB Molecule:putative methyltransferase; PDBTitle: crystal structure of putative methyltransferase (zp_00558420.1) from2 desulfitobacterium hafniense y51 at 2.30 a resolution 114 c2nn6I_ not modelled 30.1 23 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 115 d2ct1a1 not modelled 29.9 38 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 116 c2yg8B_ not modelled 29.3 19 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 117 c2o10A_ not modelled 29.1 24 PDB header:metal binding protein Chain: A: PDB Molecule:muscle lim protein; PDBTitle: solution structure of the n-terminal lim domain of mlp/crp3 118 c2kw0A_ not modelled 29.1 67 PDB header:oxidoreductase Chain: A: PDB Molecule:ccmh protein; PDBTitle: solution structure of n-terminal domain of ccmh from escherichia.coli 119 c2k5rA_ not modelled 28.9 12 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein xf2673; PDBTitle: solution nmr structure of xf2673 from xylella fastidiosa.2 northeast structural genomics consortium target xfr39 120 c1x6aA_ not modelled 28.7 20 PDB header:protein binding Chain: A: PDB Molecule:lim domain kinase 2; PDBTitle: solution structures of the second lim domain of human lim-2 kinase 2 (limk2)

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