Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	E	K	D	Y	L	R	I	S	S	T	V	L	V	S	L	L	F	G	L	A	L	V	L	V	N	S	W	F	N	Q	P	G	V	E	E	V	V	P	R	S	T	Y	L	M	V	M	I	A	L	F	F	I	D	T	V	A	F	I	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?	?	?																									?		?							?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		M	Q	L	Y	F	I	Y	D	R	R	Q	F	S	N	C	V	L	S	L	A	F	L	S	C	L	I	Y	F	V	I	T	V	I	I	I	Q	Q	I	I	E	E	R	L	T	S	S	V	V	Q	N	D	I	A	I	Y	Y	L	F	R	Q
Secondary structure
SS confidence
Disorder								?																																		?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		M	S	L	C	I	L	I	F	L	A	L	V	N	K	V	S	E	N	T	K	Q	R	N	L	F	S	K	K	M	T	L	C	I	S	L	F	F	V	F	G	G	P	I	V	A	H	I	L	S	S	H	Y	E	S	Y	N	L	H	I	A
Secondary structure
SS confidence
Disorder															?	?	?	?	?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		E	L	T	N	E	N	G	Q	V	V	W	K	A	S	Y	V	T	I	M	I	F	M	W	L	T	L	L	S	V	N	L	Y	F	N	G	L	R	Y	D	I	W	N	G	V	T	V	I	A	F	C	A	V	L	Y	N	I	S	L	L	F
Secondary structure
SS confidence
Disorder																																			?
Disorder confidence
		.	.	.	.	.	.	.	.	.	250	.	.	.	.	.	.	.	.	.	260	.	.	.	.	.	.	.	.	.	270	.	.	.	.	.	.	.	.	.	280	.	.	.	.	.	.	.	.	.	290	.	.	.	.	.	.	.	.	.	300
Sequence		M	S	R	Y	S	V	S	T	W	Y	I	S	R	T	I	E	V	V	S	K	L	T	V	M	V	I	F	M	C	H	I	F	S	A	L	R	V	T	K	N	I	A	H	R	D	P	L	T	N	I	F	N	R	N	Y	F	F	N	E	L
Secondary structure
SS confidence
Disorder			?	?	?	?	?																																				?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	310	.	.	.	.	.	.	.	.	.	320	.	.	.	.	.	.	.	.	.	330	.	.	.	.	.	.	.	.	.	340	.	.	.	.	.	.	.	.	.	350	.	.	.	.	.	.	.	.	.	360
Sequence		T	V	Q	S	A	S	A	Q	K	T	P	Y	C	V	M	I	M	D	I	D	H	F	K	K	V	N	D	T	W	G	H	P	V	G	D	Q	V	I	K	T	V	V	N	I	I	G	K	S	I	R	P	D	D	L	L	A	R	V	G	G
Secondary structure
SS confidence
Disorder									?
Disorder confidence
		.	.	.	.	.	.	.	.	.	370	.	.	.	.	.	.	.	.	.	380	.	.	.	.	.	.	.	.	.	390	.	.	.	.	.	.	.	.	.	400	.	.	.	.	.	.	.	.	.	410	.	.	.	.	.	.	.	.	.	420
Sequence		E	E	F	G	V	L	L	T	D	I	D	T	E	R	A	K	A	L	A	E	R	I	R	E	N	V	E	R	L	T	G	D	N	P	E	Y	A	I	P	Q	K	V	T	I	S	I	G	A	V	V	T	Q	E	N	A	L	N	P	N	E
Secondary structure
SS confidence
Disorder																																	?	?	?	?	?		?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	430	.	.	.	.	.	.	.	.	.	440	.	.	.	.	.	.	.	.	.	450	.	.
Sequence		I	Y	R	L	A	D	N	A	L	Y	E	A	K	E	T	G	R	N	K	V	V	V	R	D	V	V	N	F	C	E	S	P
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: 251 - 443 Aligned: 193 Modelled: 193 Confidence: 100.0% Identity: 32% 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: 257 - 442 Aligned: 175 Modelled: 186 Confidence: 100.0% Identity: 31% 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: 239 - 444 Aligned: 206 Modelled: 206 Confidence: 100.0% Identity: 27% 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: 241 - 441 Aligned: 201 Modelled: 201 Confidence: 100.0% Identity: 27% 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: 256 - 442 Aligned: 187 Modelled: 187 Confidence: 100.0% Identity: 30% 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 3i5b chain A Region: 281 - 444 Aligned: 164 Modelled: 164 Confidence: 100.0% Identity: 34% 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: 280 - 442 Aligned: 161 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 1w25 chain A domain 3 Region: 287 - 444 Aligned: 158 Modelled: 158 Confidence: 100.0% Identity: 36% Fold: Ferredoxin-like Superfamily: Nucleotide cyclase Family: GGDEF domain Phyre2 PDB 3hva chain A Region: 281 - 441 Aligned: 159 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 3icl chain A Region: 284 - 444 Aligned: 158 Modelled: 160 Confidence: 100.0% Identity: 30% 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: 277 - 442 Aligned: 153 Modelled: 166 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 3mtk chain A Region: 277 - 444 Aligned: 158 Modelled: 168 Confidence: 100.0% Identity: 22% 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: 267 - 448 Aligned: 178 Modelled: 182 Confidence: 99.9% Identity: 21% 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: 291 - 447 Aligned: 153 Modelled: 157 Confidence: 99.9% Identity: 17% 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: 278 - 444 Aligned: 135 Modelled: 137 Confidence: 99.4% Identity: 8% 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: 267 - 337 Aligned: 71 Modelled: 71 Confidence: 98.2% Identity: 10% 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 2qv6 chain D Region: 308 - 444 Aligned: 117 Modelled: 129 Confidence: 97.2% Identity: 21% 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 PDB 1cjk chain A Region: 311 - 411 Aligned: 100 Modelled: 101 Confidence: 95.6% Identity: 11% 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 Phyre2 PDB 1fx2 chain A Region: 308 - 417 Aligned: 107 Modelled: 110 Confidence: 95.4% Identity: 15% Fold: Ferredoxin-like Superfamily: Nucleotide cyclase Family: Adenylyl and guanylyl cyclase catalytic domain Phyre2 PDB 1wc1 chain A Region: 306 - 442 Aligned: 137 Modelled: 137 Confidence: 95.0% Identity: 15% Fold: Ferredoxin-like Superfamily: Nucleotide cyclase Family: Adenylyl and guanylyl cyclase catalytic domain Phyre2 1 c1w25B_ 2 c3ezuA_ 3 c3breA_ 4 c3i5aA_ 5 c3i5cA_ 6 c3i5bA_ 7 c3ignA_ 8 d1w25a3 9 c3hvaA_ 10 c3iclA_ 11 c3qyyB_ 12 c3mtkA_ 13 c3pjwA_ 14 c3hvwA_ 15 c3gfzB_ 16 c3p7nB_ 17 c2qv6D_ 18 c1cjkA_ 19 d1fx2a_ 20 d1wc1a_ 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 32 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 31 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 27 PDB header:signaling protein Chain: A: PDB Molecule:probable two-component response regulator; PDBTitle: crystal structure of p.aeruginosa pa3702 4 c3i5aA_ 100.0 27 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 30 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 c3i5bA_ 100.0 34 PDB header:signaling protein Chain: A: PDB Molecule:wspr response regulator; PDBTitle: crystal structure of the isolated ggdef domain of wpsr from2 pseudomonas aeruginosa 7 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 8 d1w25a3 100.0 36 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:GGDEF domain 9 c3hvaA_ 100.0 18 PDB header:transferase Chain: A: PDB Molecule:protein fimx; PDBTitle: crystal structure of fimx ggdef domain from pseudomonas2 aeruginosa 10 c3iclA_ 100.0 30 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 11 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 12 c3mtkA_ 100.0 22 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 21 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 17 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_ 99.4 8 PDB header:hydrolase, signaling protein Chain: B: PDB Molecule:klebsiella pneumoniae blrp1; PDBTitle: klebsiella pneumoniae blrp1 ph 6 manganese/cy-digmp complex 16 c3p7nB_ 98.2 10 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 c2qv6D_ 97.2 21 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 18 c1cjkA_ 95.6 11 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 19 d1fx2a_ 95.4 15 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 20 d1wc1a_ 95.0 15 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 21 c3mr7B_ not modelled 94.7 15 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 22 c1wc6B_ not modelled 94.5 14 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 23 d1azsa_ not modelled 94.4 11 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 24 c2w01C_ not modelled 94.0 13 PDB header:lyase Chain: C: PDB Molecule:adenylate cyclase; PDBTitle: crystal structure of the guanylyl cyclase cya2 25 c1ybuA_ not modelled 93.6 17 PDB header:hydrolase Chain: A: PDB Molecule:lipj; PDBTitle: mycobacterium tuberculosis adenylyl cyclase rv1900c chd, in complex2 with a substrate analog. 26 d1fx4a_ not modelled 93.3 22 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 27 c3uvjC_ not modelled 92.1 11 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. 28 c2aq4A_ not modelled 92.0 25 PDB header:transferase Chain: A: PDB Molecule:dna repair protein rev1; PDBTitle: ternary complex of the catalytic core of rev1 with dna and dctp. 29 c1yk9A_ not modelled 91.5 14 PDB header:lyase Chain: A: PDB Molecule:adenylate cyclase; PDBTitle: crystal structure of a mutant form of the mycobacterial2 adenylyl cyclase rv1625c 30 c1y10C_ not modelled 89.8 13 PDB header:lyase Chain: C: PDB Molecule:hypothetical protein rv1264/mt1302; PDBTitle: mycobacterial adenylyl cyclase rv1264, holoenzyme, inhibited state 31 c3gqcB_ not modelled 85.9 27 PDB header:transferase/dna Chain: B: PDB Molecule:dna repair protein rev1; PDBTitle: structure of human rev1-dna-dntp ternary complex 32 c3et6A_ not modelled 84.1 8 PDB header:lyase Chain: A: PDB Molecule:soluble guanylyl cyclase beta; PDBTitle: the crystal structure of the catalytic domain of a eukaryotic2 guanylate cyclase 33 d1azsb_ not modelled 82.4 15 Fold:Ferredoxin-like Superfamily:Nucleotide cyclase Family:Adenylyl and guanylyl cyclase catalytic domain 34 d1im4a_ not modelled 80.9 21 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 35 c1s97D_ not modelled 79.1 19 PDB header:transferase/dna Chain: D: PDB Molecule:dna polymerase iv; PDBTitle: dpo4 with gt mismatch 36 c1k1qA_ not modelled 76.8 20 PDB header:transcription Chain: A: PDB Molecule:dbh protein; PDBTitle: crystal structure of a dinb family error prone dna2 polymerase from sulfolobus solfataricus 37 c3mr2A_ not modelled 75.1 26 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) 38 c2r8kB_ not modelled 75.0 25 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 39 d1k1sa2 not modelled 74.1 20 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 40 c3onqB_ not modelled 73.8 7 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 41 c3l7xA_ not modelled 71.0 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 42 c1jihA_ not modelled 70.5 25 PDB header:translation Chain: A: PDB Molecule:dna polymerase eta; PDBTitle: yeast dna polymerase eta 43 c2oh2B_ not modelled 68.7 23 PDB header:transferase/dna Chain: B: PDB Molecule:dna polymerase kappa; PDBTitle: ternary complex of human dna polymerase 44 c3i24B_ not modelled 67.7 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 45 c3l5aA_ not modelled 64.4 19 PDB header:oxidoreductase Chain: A: PDB Molecule:nadh/flavin oxidoreductase/nadh oxidase; PDBTitle: crystal structure of a probable nadh-dependent flavin oxidoreductase2 from staphylococcus aureus 46 d1jx4a2 not modelled 62.9 20 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 47 d1jiha2 not modelled 62.0 25 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 48 c3p0tB_ not modelled 58.6 13 PDB header:unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an hit-like protein from mycobacterium2 paratuberculosis 49 c2wz1B_ not modelled 54.8 12 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. 50 c3l0oB_ not modelled 53.3 24 PDB header:hydrolase Chain: B: PDB Molecule:transcription termination factor rho; PDBTitle: structure of rna-free rho transcription termination factor from2 thermotoga maritima 51 c1t3nB_ not modelled 50.2 25 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 52 d2o5aa1 not modelled 49.8 10 Fold:Nucleotidyltransferase Superfamily:Nucleotidyltransferase Family:Iojap/YbeB-like 53 c3nrdB_ not modelled 49.0 22 PDB header:nucleotide binding protein Chain: B: PDB Molecule:histidine triad (hit) protein; PDBTitle: crystal structure of a histidine triad (hit) protein (smc02904) from2 sinorhizobium meliloti 1021 at 2.06 a resolution 54 d1gx1a_ not modelled 47.9 14 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 55 c3oheA_ not modelled 47.4 13 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 56 c3hf3A_ not modelled 47.3 21 PDB header:oxidoreductase Chain: A: PDB Molecule:chromate reductase; PDBTitle: old yellow enzyme from thermus scotoductus sa-01 57 c1qgeE_ not modelled 46.8 29 PDB header:hydrolase Chain: E: PDB Molecule:protein (triacylglycerol hydrolase); PDBTitle: new crystal form of pseudomonas glumae (formerly chromobacterium2 viscosum atcc 6918) lipase 58 d1xxaa_ not modelled 45.8 16 Fold:DCoH-like Superfamily:C-terminal domain of arginine repressor Family:C-terminal domain of arginine repressor 59 c3imiB_ not modelled 44.0 16 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' 60 c2fllA_ not modelled 42.6 23 PDB header:replication/dna Chain: A: PDB Molecule:dna polymerase iota; PDBTitle: ternary complex of human dna polymerase iota with dna and dttp 61 c2pmpA_ not modelled 42.4 14 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 62 d1t94a2 not modelled 41.9 30 Fold:DNA/RNA polymerases Superfamily:DNA/RNA polymerases Family:Lesion bypass DNA polymerase (Y-family), catalytic domain 63 d1t0aa_ not modelled 40.4 17 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 64 c1t94B_ not modelled 40.1 26 PDB header:replication Chain: B: PDB Molecule:polymerase (dna directed) kappa; PDBTitle: crystal structure of the catalytic core of human dna2 polymerase kappa 65 c3f0gA_ not modelled 39.4 17 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 66 d1w55a2 not modelled 39.2 15 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 67 d1gwja_ not modelled 38.8 21 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 68 d1iv3a_ not modelled 36.4 14 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 69 c2jroA_ not modelled 33.3 17 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 70 c3k30B_ not modelled 32.1 13 PDB header:oxidoreductase Chain: B: PDB Molecule:histamine dehydrogenase; PDBTitle: histamine dehydrogenase from nocardiodes simplex 71 d1y23a_ not modelled 31.4 15 Fold:HIT-like Superfamily:HIT-like Family:HIT (HINT, histidine triad) family of protein kinase-interacting proteins 72 c3af5A_ not modelled 29.2 15 PDB header:hydrolase Chain: A: PDB Molecule:putative uncharacterized protein ph1404; PDBTitle: the crystal structure of an archaeal cpsf subunit, ph1404 from2 pyrococcus horikoshii 73 d1ps9a1 not modelled 29.0 17 Fold:TIM beta/alpha-barrel Superfamily:FMN-linked oxidoreductases Family:FMN-linked oxidoreductases 74 c3atyA_ not modelled 28.1 21 PDB header:oxidoreductase Chain: A: PDB Molecule:prostaglandin f2a synthase; PDBTitle: crystal structure of tcoye 75 c3ksvA_ not modelled 27.2 11 PDB header:unknown function Chain: A: PDB Molecule:uncharacterized protein; PDBTitle: hypothetical protein from leishmania major 76 d2ox6a1 not modelled 25.8 14 Fold:lambda repressor-like DNA-binding domains Superfamily:lambda repressor-like DNA-binding domains Family:YdiL-like 77 c2zztA_ not modelled 25.2 20 PDB header:transport protein Chain: A: PDB Molecule:putative uncharacterized protein; PDBTitle: crystal structure of the cytosolic domain of the cation2 diffusion facilitator family protein 78 c3nx3A_ not modelled 24.9 21 PDB header:transferase Chain: A: PDB Molecule:acetylornithine aminotransferase; PDBTitle: crystal structure of acetylornithine aminotransferase (argd) from2 campylobacter jejuni 79 c1ps9A_ not modelled 24.9 17 PDB header:oxidoreductase Chain: A: PDB Molecule:2,4-dienoyl-coa reductase; PDBTitle: the crystal structure and reaction mechanism of e. coli 2,4-2 dienoyl coa reductase 80 c3i4sB_ not modelled 24.7 18 PDB header:hydrolase Chain: B: PDB Molecule:histidine triad protein; PDBTitle: crystal structure of histidine triad protein blr8122 from2 bradyrhizobium japonicum 81 d1vh8a_ not modelled 24.5 20 Fold:Bacillus chorismate mutase-like Superfamily:IpsF-like Family:IpsF-like 82 c1xaxA_ not modelled 24.1 15 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 83 c3iyuY_ not modelled 23.4 17 PDB header:virus Chain: Y: PDB Molecule:outer capsid protein vp4; PDBTitle: atomic model of an infectious rotavirus particle 84 c3b6nA_ not modelled 22.4 16 PDB header:lyase Chain: A: PDB Molecule:2-c-methyl-d-erythritol 2,4-cyclodiphosphate PDBTitle: crystal structure of 2c-methyl-d-erythritol 2,4-2 cyclodiphosphate synthase pv003920 from plasmodium vivax 85 c2eh6A_ not modelled 21.9 16 PDB header:transferase Chain: A: PDB Molecule:acetylornithine aminotransferase; PDBTitle: crystal structure of acetylornithine aminotransferase from aquifex2 aeolicus vf5 86 d1cm3a_ not modelled 21.5 14 Fold:HPr-like Superfamily:HPr-like Family:HPr-like 87 c3nuiA_ not modelled 20.9 10 PDB header:transferase Chain: A: PDB Molecule:pyruvate transaminase; PDBTitle: crystal structure of omega-transferase from vibrio fluvialis js17 88 d1z7da1 not modelled 19.9 20 Fold:PLP-dependent transferase-like Superfamily:PLP-dependent transferases Family:GABA-aminotransferase-like 89 d1iwga2 not modelled 19.6 17 Fold:Ferredoxin-like Superfamily:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains Family:Multidrug efflux transporter AcrB pore domain; PN1, PN2, PC1 and PC2 subdomains 90 c1w57A_ not modelled 19.5 20 PDB header:transferase Chain: A: PDB Molecule:ispd/ispf bifunctional enzyme; PDBTitle: structure of the bifunctional ispdf from campylobacter2 jejuni containing zn 91 c3upsA_ not modelled 19.4 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:iojap-like protein; PDBTitle: crystal structure of iojap-like protein from zymomonas mobilis 92 d1kdga2 not modelled 19.1 46 Fold:FAD-linked reductases, C-terminal domain Superfamily:FAD-linked reductases, C-terminal domain Family:GMC oxidoreductases 93 d1xpua3 not modelled 18.5 20 Fold:P-loop containing nucleoside triphosphate hydrolases Superfamily:P-loop containing nucleoside triphosphate hydrolases Family:RecA protein-like (ATPase-domain) 94 c1z5wA_ not modelled 18.3 15 PDB header:structural protein Chain: A: PDB Molecule:tubulin gamma-1 chain; PDBTitle: crystal structure of gamma-tubulin bound to gtp 95 c2hl2A_ not modelled 18.2 19 PDB header:ligase Chain: A: PDB Molecule:threonyl-trna synthetase; PDBTitle: crystal structure of the editing domain of threonyl-trna2 synthetase from pyrococcus abyssi in complex with an3 analog of seryladenylate 96 d1b4ba_ not modelled 18.0 9 Fold:DCoH-like Superfamily:C-terminal domain of arginine repressor Family:C-terminal domain of arginine repressor 97 c2ordA_ not modelled 17.6 10 PDB header:transferase Chain: A: PDB Molecule:acetylornithine aminotransferase; PDBTitle: crystal structure of acetylornithine aminotransferase (ec 2.6.1.11)2 (acoat) (tm1785) from thermotoga maritima at 1.40 a resolution 98 c2uzhB_ not modelled 17.6 14 PDB header:lyase Chain: B: PDB Molecule:2c-methyl-d-erythritol 2,4-cyclodiphosphate PDBTitle: mycobacterium smegmatis 2c-methyl-d-erythritol-2,4-2 cyclodiphosphate synthase (ispf) 99 c3anoA_ not modelled 17.6 21 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

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