Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	M	Y	F	K	R	M	K	D	E	W	T	G	L	V	E	Q	A	D	P	P	I	R	A	K	A	A	E	I	A	V	A	H	A	H	Y	L	S	I	E	F	Y	R	I	V	R	I	D	P	H	A	E	E	F	L	S	N	E	Q
Secondary structure
SS confidence
Disorder		?	?																																																					?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		V	E	R	Q	L	K	S	A	M	E	R	W	I	I	N	V	L	S	A	Q	V	D	D	V	E	R	L	I	Q	I	Q	H	T	V	A	E	V	H	A	R	I	G	I	P	V	E	I	V	E	M	G	F	R	V	L	K	K	I	L	Y
Secondary structure
SS confidence
Disorder																																						?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		P	V	I	F	S	S	D	Y	S	A	A	E	K	L	Q	V	Y	H	F	S	I	N	S	I	D	I	A	M	E	V	M	T	R	A	F	T	F	S	D	S	S	A	S	K	E	D	E	N	Y	R	I	F	S	L	L	E	N	A	E	E
Secondary structure
SS confidence
Disorder							?		?																																			?															?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	K	E	R	Q	I	A	S	I	L	S	W	E	I	D	I	I	Y	K	I	L	L	D	S	D	L	G	S	S	L	P	L	S	Q	A	D	F	G	L	W	F	N	H	K	G	R	H	Y	F	S	G	I	A	E	V	G	H	I	S	R
Secondary structure
SS confidence
Disorder																						?		?	?	?	?	?	?	?		?	?	?	?															?	?				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		L	I	Q	D	F	D	G	I	F	N	Q	T	M	R	N	T	R	N	L	N	N	R	S	L	R	V	K	F	L	L	Q	I	R	N	T	V	S	Q	I	I	T	L	L	R	E	L	F	E	E	V	S	R	H	E	V	G	M	D	V	L
Secondary structure
SS confidence
Disorder																?	?	?	?	?	?	?																																		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	K	L	L	N	R	R	F	L	P	T	I	F	K	R	E	I	A	H	A	N	R	T	G	T	P	L	S	V	L	I	I	D	V	D	K	F	K	E	I	N	D	T	W	G	H	N	T	G	D	E	I	L	R	K	V	S	Q	A	F
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		Y	D	N	V	R	S	S	D	Y	V	F	R	Y	G	G	D	E	F	I	I	V	L	T	E	A	S	E	N	E	T	L	R	T	A	E	R	I	R	S	R	V	E	K	T	K	L	K	A	A	N	G	E	D	I	A	L	S	L	S	I
Secondary structure
SS confidence
Disorder																																																?		?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.	.	.	.	.	.	.	.	460
Sequence		G	A	A	M	F	N	G	H	P	D	Y	E	R	L	I	Q	I	A	D	E	A	L	Y	I	A	K	R	R	G	R	N	R	V	E	L	W	K	A	S	L
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 1w25 chain B Region: 264 - 458 Aligned: 195 Modelled: 195 Confidence: 100.0% Identity: 35% PDB header:signaling protein Chain: B: PDB Molecule:stalked-cell differentiation controlling protein; PDBTitle: response regulator pled in complex with c-digmp Phyre2 PDB 3ezu chain A Region: 280 - 455 Aligned: 166 Modelled: 176 Confidence: 100.0% Identity: 30% PDB header:signaling protein Chain: A: PDB Molecule:ggdef domain protein; PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution Phyre2 PDB 3bre chain A Region: 251 - 458 Aligned: 208 Modelled: 208 Confidence: 100.0% Identity: 34% PDB header:signaling protein Chain: A: PDB Molecule:probable two-component response regulator; PDBTitle: crystal structure of p.aeruginosa pa3702 Phyre2 PDB 3i5a chain A Region: 251 - 454 Aligned: 204 Modelled: 204 Confidence: 100.0% Identity: 32% PDB header:signaling protein Chain: A: PDB Molecule:response regulator/ggdef domain protein; PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae Phyre2 PDB 3i5c chain A Region: 269 - 455 Aligned: 187 Modelled: 187 Confidence: 100.0% Identity: 37% PDB header:signaling protein Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa Phyre2 PDB 3hva chain A Region: 294 - 454 Aligned: 160 Modelled: 161 Confidence: 100.0% Identity: 18% PDB header:transferase Chain: A: PDB Molecule:protein fimx; PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa Phyre2 PDB 3i5b chain A Region: 294 - 456 Aligned: 163 Modelled: 163 Confidence: 100.0% Identity: 40% PDB header:signaling protein Chain: A: PDB Molecule:wspr response regulator; PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa Phyre2 PDB 3ign chain A Region: 293 - 455 Aligned: 162 Modelled: 159 Confidence: 100.0% Identity: 39% PDB header:transferase Chain: A: PDB Molecule:diguanylate cyclase; PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a Phyre2 PDB 3icl chain A Region: 297 - 458 Aligned: 161 Modelled: 161 Confidence: 100.0% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:eal/ggdef domain protein; PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c Phyre2 PDB 3qyy chain B Region: 291 - 455 Aligned: 154 Modelled: 154 Confidence: 100.0% Identity: 31% PDB header:signaling protein/inhibitor Chain: B: PDB Molecule:response regulator; PDBTitle: a novel interaction mode between a microbial ggdef domain and the bis-2 (3, 5 )-cyclic di-gmp Phyre2 PDB 1w25 chain A domain 3 Region: 300 - 458 Aligned: 159 Modelled: 159 Confidence: 100.0% Identity: 41% Fold: Ferredoxin-like Superfamily: Nucleotide cyclase Family: GGDEF domain Phyre2 PDB 3mtk chain A Region: 290 - 460 Aligned: 161 Modelled: 171 Confidence: 100.0% Identity: 24% PDB header:transferase Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase; PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c Phyre2 PDB 3pjw chain A Region: 287 - 460 Aligned: 171 Modelled: 174 Confidence: 99.9% Identity: 23% PDB header:lyase Chain: A: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23 Phyre2 PDB 3hvw chain A Region: 304 - 460 Aligned: 152 Modelled: 157 Confidence: 99.9% Identity: 13% PDB header:lyase Chain: A: PDB Molecule:diguanylate-cyclase (dgc); PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c Phyre2 PDB 3gfz chain B Region: 294 - 460 Aligned: 136 Modelled: 138 Confidence: 99.6% Identity: 10% PDB header:hydrolase, signaling protein Chain: B: PDB Molecule:klebsiella pneumoniae blrp1; PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex Phyre2 PDB 3p7n chain B Region: 280 - 352 Aligned: 73 Modelled: 73 Confidence: 98.6% Identity: 11% PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis Phyre2 PDB 1or4 chain A Region: 16 - 151 Aligned: 134 Modelled: 136 Confidence: 98.3% Identity: 15% Fold: Globin-like Superfamily: Globin-like Family: Globins Phyre2 PDB 2w31 chain A Region: 16 - 156 Aligned: 139 Modelled: 141 Confidence: 98.0% Identity: 20% PDB header:oxygen transport Chain: A: PDB Molecule:globin; PDBTitle: globin domain of geobacter sulfurreducens globin-coupled2 sensor Phyre2 PDB 2vee chain C Region: 16 - 155 Aligned: 138 Modelled: 140 Confidence: 97.8% Identity: 14% PDB header:transport protein Chain: C: PDB Molecule:protoglobin; PDBTitle: structure of protoglobin from methanosarcina acetivorans2 c2a Phyre2 PDB 2qv6 chain D Region: 323 - 460 Aligned: 122 Modelled: 138 Confidence: 97.7% Identity: 20% PDB header:hydrolase Chain: D: PDB Molecule:gtp cyclohydrolase iii; PDBTitle: gtp cyclohydrolase iii from m. jannaschii (mj0145)2 complexed with gtp and metal ions Phyre2 1 c1w25B_ 2 c3ezuA_ 3 c3breA_ 4 c3i5aA_ 5 c3i5cA_ 6 c3hvaA_ 7 c3i5bA_ 8 c3ignA_ 9 c3iclA_ 10 c3qyyB_ 11 d1w25a3 12 c3mtkA_ 13 c3pjwA_ 14 c3hvwA_ 15 c3gfzB_ 16 c3p7nB_ 17 d1or4a_ 18 c2w31A_ 19 c2veeC_ 20 c2qv6D_ 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

Detailed template information

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

1 c1w25B_ 100.0 35 PDB header:signaling protein Chain: B: PDB Molecule:stalked-cell differentiation controlling protein; PDBTitle: response regulator pled in complex with c-digmp 2 c3ezuA_ 100.0 30 PDB header:signaling protein Chain: A: PDB Molecule:ggdef domain protein; PDBTitle: crystal structure of multidomain protein of unknown function with2 ggdef-domain (np_951600.1) from geobacter sulfurreducens at 1.95 a3 resolution 3 c3breA_ 100.0 34 PDB header:signaling protein Chain: A: PDB Molecule:probable two-component response regulator; PDBTitle: crystal structure of p.aeruginosa pa3702 4 c3i5aA_ 100.0 32 PDB header:signaling protein Chain: A: PDB Molecule:response regulator/ggdef domain protein; PDBTitle: crystal structure of full-length wpsr from pseudomonas syringae 5 c3i5cA_ 100.0 37 PDB header:signaling protein Chain: A: PDB Molecule:fusion of general control protein gcn4 and wspr response PDBTitle: crystal structure of a fusion protein containing the leucine zipper of2 gcn4 and the ggdef domain of wspr from pseudomonas aeruginosa 6 c3hvaA_ 100.0 18 PDB header:transferase Chain: A: PDB Molecule:protein fimx; PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa 7 c3i5bA_ 100.0 40 PDB header:signaling protein Chain: A: PDB Molecule:wspr response regulator; PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa 8 c3ignA_ 100.0 39 PDB header:transferase Chain: A: PDB Molecule:diguanylate cyclase; PDBTitle: crystal structure of the ggdef domain from marinobacter2 aquaeolei diguanylate cyclase complexed with c-di-gmp -3 northeast structural genomics consortium target mqr89a 9 c3iclA_ 100.0 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:eal/ggdef domain protein; PDBTitle: x-ray structure of protein (eal/ggdef domain protein) from2 m.capsulatus, northeast structural genomics consortium3 target mcr174c 10 c3qyyB_ 100.0 31 PDB header:signaling protein/inhibitor Chain: B: PDB Molecule:response regulator; PDBTitle: a novel interaction mode between a microbial ggdef domain and the bis-2 (3, 5 )-cyclic di-gmp 11 d1w25a3 100.0 41 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:GGDEF domain 12 c3mtkA_ 100.0 24 PDB header:transferase Chain: A: PDB Molecule:diguanylate cyclase/phosphodiesterase; PDBTitle: x-ray structure of diguanylate cyclase/phosphodiesterase from2 caldicellulosiruptor saccharolyticus, northeast structural genomics3 consortium target clr27c 13 c3pjwA_ 99.9 23 PDB header:lyase Chain: A: PDB Molecule:cyclic dimeric gmp binding protein; PDBTitle: structure of pseudomonas fluorescence lapd ggdef-eal dual domain, i23 14 c3hvwA_ 99.9 13 PDB header:lyase Chain: A: PDB Molecule:diguanylate-cyclase (dgc); PDBTitle: crystal structure of the ggdef domain of the pa2567 protein2 from pseudomonas aeruginosa, northeast structural genomics3 consortium target par365c 15 c3gfzB_ 99.6 10 PDB header:hydrolase, signaling protein Chain: B: PDB Molecule:klebsiella pneumoniae blrp1; PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex 16 c3p7nB_ 98.6 11 PDB header:dna binding protein Chain: B: PDB Molecule:sensor histidine kinase; PDBTitle: crystal structure of light activated transcription factor el222 from2 erythrobacter litoralis 17 d1or4a_ 98.3 15 Fold:Globin-like Superfamily:Globin-like Family:Globins 18 c2w31A_ 98.0 20 PDB header:oxygen transport Chain: A: PDB Molecule:globin; PDBTitle: globin domain of geobacter sulfurreducens globin-coupled2 sensor 19 c2veeC_ 97.8 14 PDB header:transport protein Chain: C: PDB Molecule:protoglobin; PDBTitle: structure of protoglobin from methanosarcina acetivorans2 c2a 20 c2qv6D_ 97.7 20 PDB header:hydrolase Chain: D: PDB Molecule:gtp cyclohydrolase iii; PDBTitle: gtp cyclohydrolase iii from m. jannaschii (mj0145)2 complexed with gtp and metal ions 21 c1cjkA_ not modelled 95.3 10 PDB header:lyase/lyase/signaling protein Chain: A: PDB Molecule:adenylate cyclase, type v; PDBTitle: complex of gs-alpha with the catalytic domains of mammalian adenylyl2 cyclase: complex with adenosine 5'-(alpha thio)-triphosphate (rp),3 mg, and mn 22 d1fx2a_ not modelled 95.3 18 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 23 d1azsa_ not modelled 93.5 10 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 24 c3uvjC_ not modelled 91.5 13 PDB header:lyase Chain: C: PDB Molecule:guanylate cyclase soluble subunit alpha-3; PDBTitle: crystal structure of the catalytic domain of the heterodimeric human2 soluble guanylate cyclase 1. 25 c3mr7B_ not modelled 91.4 10 PDB header:hydrolase Chain: B: PDB Molecule:adenylate/guanylate cyclase/hydrolase, alpha/beta fold PDBTitle: crystal structure of adenylate/guanylate cyclase/hydrolase from2 silicibacter pomeroyi 26 d1fx4a_ not modelled 91.0 18 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 27 c2aq4A_ not modelled 88.3 27 PDB header:transferase Chain: A: PDB Molecule:dna repair protein rev1; PDBTitle: ternary complex of the catalytic core of rev1 with dna and dctp. 28 c1wc6B_ not modelled 86.8 15 PDB header:lyase Chain: B: PDB Molecule:adenylate cyclase; PDBTitle: soluble adenylyl cyclase cyac from s. platensis in complex2 with rp-atpalphas in presence of bicarbonate 29 c1y10C_ not modelled 86.6 16 PDB header:lyase Chain: C: PDB Molecule:hypothetical protein rv1264/mt1302; PDBTitle: mycobacterial adenylyl cyclase rv1264, holoenzyme, inhibited state 30 c1yk9A_ not modelled 86.1 17 PDB header:lyase Chain: A: PDB Molecule:adenylate cyclase; PDBTitle: crystal structure of a mutant form of the mycobacterial2 adenylyl cyclase rv1625c 31 c2w01C_ not modelled 83.0 10 PDB header:lyase Chain: C: PDB Molecule:adenylate cyclase; PDBTitle: crystal structure of the guanylyl cyclase cya2 32 c3r5gB_ not modelled 83.0 13 PDB header:lyase Chain: B: PDB Molecule:cyab; PDBTitle: crystal structure of the adenylyl cyclase cyab from p. aeruginosa 33 d1azsb_ not modelled 81.5 13 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 34 c3gqcB_ not modelled 78.5 22 PDB header:transferase/dna Chain: B: PDB Molecule:dna repair protein rev1; PDBTitle: structure of human rev1-dna-dntp ternary complex 35 d1wc1a_ not modelled 77.3 17 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 36 c1s97D_ not modelled 77.1 15 PDB header:transferase/dna Chain: D: PDB Molecule:dna polymerase iv; PDBTitle: dpo4 with gt mismatch 37 c1k1qA_ not modelled 73.4 20 PDB header:transcription Chain: A: PDB Molecule:dbh protein; PDBTitle: crystal structure of a dinb family error prone dna2 polymerase from sulfolobus solfataricus 38 d1k1sa2 not modelled 70.2 18 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 39 c3onqB_ not modelled 65.8 10 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:regulator of polyketide synthase expression; PDBTitle: crystal structure of regulator of polyketide synthase expression2 bad_0249 from bifidobacterium adolescentis 40 c3et6A_ not modelled 63.6 12 PDB header:lyase Chain: A: PDB Molecule:soluble guanylyl cyclase beta; PDBTitle: the crystal structure of the catalytic domain of a eukaryotic2 guanylate cyclase 41 c1ybuA_ not modelled 63.2 15 PDB header:hydrolase Chain: A: PDB Molecule:lipj; PDBTitle: mycobacterium tuberculosis adenylyl cyclase rv1900c chd, in complex2 with a substrate analog. 42 d1im4a_ not modelled 62.8 18 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 43 c3mr2A_ not modelled 59.0 20 PDB header:transferase/dna Chain: A: PDB Molecule:dna polymerase eta; PDBTitle: human dna polymerase eta in complex with normal dna and incoming2 nucleotide (nrm) 44 d1jx4a2 not modelled 57.1 11 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 45 c2oh2B_ not modelled 54.9 23 PDB header:transferase/dna Chain: B: PDB Molecule:dna polymerase kappa; PDBTitle: ternary complex of human dna polymerase 46 c2r8kB_ not modelled 50.2 33 PDB header:replication, transferase/dna Chain: B: PDB Molecule:dna polymerase eta; PDBTitle: structure of the eukaryotic dna polymerase eta in complex with 1,2-2 d(gpg)-cisplatin containing dna 47 c1jihA_ not modelled 48.7 33 PDB header:translation Chain: A: PDB Molecule:dna polymerase eta; PDBTitle: yeast dna polymerase eta 48 c3l7xA_ not modelled 46.5 27 PDB header:cell cycle Chain: A: PDB Molecule:putative hit-like protein involved in cell-cycle PDBTitle: the crystal structure of smu.412c from streptococcus mutans ua159 49 d1jiha2 not modelled 38.8 33 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 50 d1s69a_ not modelled 38.2 10 Fold:Globin-like Superfamily:Globin-like Family:Truncated hemoglobin 51 c2ig3A_ not modelled 37.0 18 PDB header:oxygen storage/transport Chain: A: PDB Molecule:group iii truncated haemoglobin; PDBTitle: crystal structure of group iii truncated hemoglobin from campylobacter2 jejuni 52 d1dlya_ not modelled 36.3 17 Fold:Globin-like Superfamily:Globin-like Family:Truncated hemoglobin 53 c1dlyA_ not modelled 36.3 17 PDB header:oxygen storage/transport Chain: A: PDB Molecule:hemoglobin; PDBTitle: x-ray crystal structure of hemoglobin from the green2 unicellular alga chlamydomonas eugametos 54 c3rbuA_ not modelled 36.1 14 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:glutamate carboxypeptidase 2; PDBTitle: n-terminally avitev-tagged human glutamate carboxypeptidase ii in2 complex with 2-pmpa 55 d1ux8a_ not modelled 35.6 11 Fold:Globin-like Superfamily:Globin-like Family:Truncated hemoglobin 56 c1t3nB_ not modelled 35.3 30 PDB header:replication/dna Chain: B: PDB Molecule:polymerase (dna directed) iota; PDBTitle: structure of the catalytic core of dna polymerase iota in2 complex with dna and dttp 57 c2bmmA_ not modelled 34.1 11 PDB header:oxygen storage/transport Chain: A: PDB Molecule:thermostable hemoglobin from thermobifida fusca; PDBTitle: x-ray structure of a novel thermostable hemoglobin from the2 actinobacterium thermobifida fusca 58 c2wz1B_ not modelled 33.4 10 PDB header:lyase Chain: B: PDB Molecule:guanylate cyclase soluble subunit beta-1; PDBTitle: structure of the catalytic domain of human soluble2 guanylate cyclase 1 beta 3. 59 c2kscA_ not modelled 32.9 17 PDB header:unknown function Chain: A: PDB Molecule:cyanoglobin; PDBTitle: solution structure of synechococcus sp. pcc 7002 hemoglobin 60 c1cx8F_ not modelled 32.9 26 PDB header:metal transport Chain: F: PDB Molecule:transferrin receptor protein; PDBTitle: crytal structure of the ectodomain of human transferrin receptor 61 c3i24B_ not modelled 32.7 16 PDB header:hydrolase Chain: B: PDB Molecule:hit family hydrolase; PDBTitle: crystal structure of a hit family hydrolase protein from2 vibrio fischeri. northeast structural genomics consortium3 target id vfr176 62 c3mpbA_ not modelled 32.2 35 PDB header:isomerase Chain: A: PDB Molecule:sugar isomerase; PDBTitle: z5688 from e. coli o157:h7 bound to fructose 63 c2fllA_ not modelled 29.8 30 PDB header:replication/dna Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: ternary complex of human dna polymerase iota with dna and dttp 64 c2xykB_ not modelled 29.2 12 PDB header:oxygen storage/transport Chain: B: PDB Molecule:2-on-2 hemoglobin; PDBTitle: group ii 2-on-2 hemoglobin from the plant pathogen2 agrobacterium tumefaciens 65 c2ootA_ not modelled 28.2 16 PDB header:hydrolase Chain: A: PDB Molecule:glutamate carboxypeptidase 2; PDBTitle: a high resolution structure of ligand-free human glutamate2 carboxypeptidase ii 66 c3p0tB_ not modelled 27.6 11 PDB header:unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an hit-like protein from mycobacterium2 paratuberculosis 67 d1w55a2 not modelled 26.7 20 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 68 c3imiB_ not modelled 25.6 13 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hit family protein; PDBTitle: 2.01 angstrom resolution crystal structure of a hit family protein2 from bacillus anthracis str. 'ames ancestor' 69 d1y23a_ not modelled 23.9 18 Fold:HIT-like Superfamily:HIT-like Family:HIT (HINT, histidine triad) family of protein kinase-interacting proteins 70 d1t0aa_ not modelled 23.9 28 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 71 c3f0gA_ not modelled 23.7 24 PDB header:lyase Chain: A: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase; PDBTitle: co-crystal structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate2 synthase with cmp 72 d1gx1a_ not modelled 23.7 24 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 73 c3oheA_ not modelled 23.5 16 PDB header:hydrolase Chain: A: PDB Molecule:histidine triad (hit) protein; PDBTitle: crystal structure of a histidine triad protein (maqu_1709) from2 marinobacter aquaeolei vt8 at 1.20 a resolution 74 c2ylaA_ not modelled 23.4 14 PDB header:hydrolase Chain: A: PDB Molecule:beta-n-acetylhexosaminidase; PDBTitle: inhibition of the pneumococcal virulence factor strh and2 molecular insights into n-glycan recognition and3 hydrolysis 75 c3anoA_ not modelled 22.9 20 PDB header:transferase Chain: A: PDB Molecule:ap-4-a phosphorylase; PDBTitle: crystal structure of a novel diadenosine 5',5'''-p1,p4-tetraphosphate2 phosphorylase from mycobacterium tuberculosis h37rv 76 d1iv3a_ not modelled 22.9 20 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 77 d1vh8a_ not modelled 22.8 24 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 78 d2o5aa1 not modelled 22.8 15 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Iojap/YbeB-like 79 d1yhta1 not modelled 21.8 23 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain 80 c1xaxA_ not modelled 21.8 17 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical upf0054 protein hi0004; PDBTitle: nmr structure of hi0004, a putative essential gene product2 from haemophilus influenzae 81 d1vr6a1 not modelled 21.6 18 Fold:TIM beta/alpha-barrel Superfamily:Aldolase Family:Class I DAHP synthetase 82 d1oz9a_ not modelled 21.3 20 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Predicted metal-dependent hydrolase 83 c2kloA_ not modelled 21.0 7 PDB header:cell cycle Chain: A: PDB Molecule:dna replication factor cdt1; PDBTitle: structure of the cdt1 c-terminal domain 84 c1w57A_ not modelled 20.7 20 PDB header:transferase Chain: A: PDB Molecule:ispd/ispf bifunctional enzyme; PDBTitle: structure of the bifunctional ispdf from campylobacter2 jejuni containing zn 85 c2yl8A_ not modelled 20.7 11 PDB header:hydrolase Chain: A: PDB Molecule:beta-n-acetylhexosaminidase; PDBTitle: inhibition of the pneumococcal virulence factor strh and2 molecular insights into n-glycan recognition and3 hydrolysis 86 c2pmpA_ not modelled 20.7 28 PDB header:lyase Chain: A: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate synthase; PDBTitle: structure of 2c-methyl-d-erythritol 2,4-cyclodiphosphate synthase from2 the isoprenoid biosynthetic pathway of arabidopsis thaliana 87 c1qbaA_ not modelled 20.4 21 PDB header:glycosyl hydrolase Chain: A: PDB Molecule:chitobiase; PDBTitle: bacterial chitobiase, glycosyl hydrolase family 20 88 c3rpmA_ not modelled 19.3 14 PDB header:hydrolase Chain: A: PDB Molecule:beta-n-acetyl-hexosaminidase; PDBTitle: crystal structure of the first gh20 domain of a novel beta-n-acetyl-2 hexosaminidase strh from streptococcus pneumoniae r6 89 c3aq8A_ not modelled 19.0 11 PDB header:oxygen binding Chain: A: PDB Molecule:group 1 truncated hemoglobin; PDBTitle: crystal structure of truncated hemoglobin from tetrahymena pyriformis,2 q46e mutant, fe(iii) form 90 d1xm5a_ not modelled 19.0 14 Fold:Zincin-like Superfamily:Metalloproteases ("zincins"), catalytic domain Family:Predicted metal-dependent hydrolase 91 c2byvE_ not modelled 18.9 25 PDB header:regulation Chain: E: PDB Molecule:rap guanine nucleotide exchange factor 4; PDBTitle: structure of the camp responsive exchange factor epac2 in2 its auto-inhibited state 92 c1m04A_ not modelled 18.1 17 PDB header:hydrolase Chain: A: PDB Molecule:beta-n-acetylhexosaminidase; PDBTitle: mutant streptomyces plicatus beta-hexosaminidase (d313n) in complex2 with product (glcnac) 93 d1n8pa_ not modelled 17.7 19 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:Cystathionine synthase-like 94 d1qbaa3 not modelled 17.6 21 Fold:TIM beta/alpha-barrel Superfamily:(Trans)glycosidases Family:beta-N-acetylhexosaminidase catalytic domain 95 d1idra_ not modelled 17.3 15 Fold:Globin-like Superfamily:Globin-like Family:Truncated hemoglobin 96 c2jroA_ not modelled 17.3 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: solution nmr structure of so0334 from shewanella oneidensis. northeast2 structural genomics target sor75 97 d1dlwa_ not modelled 17.0 12 Fold:Globin-like Superfamily:Globin-like Family:Truncated hemoglobin 98 c3ugsB_ not modelled 16.9 17 PDB header:transferase Chain: B: PDB Molecule:undecaprenyl pyrophosphate synthase; PDBTitle: crystal structure of a probable undecaprenyl diphosphate synthase2 (upps) from campylobacter jejuni 99 d1cgme_ not modelled 16.7 15 Fold:Four-helical up-and-down bundle Superfamily:TMV-like viral coat proteins Family:TMV-like viral coat proteins

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