Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	K	S	V	L	K	V	S	L	A	A	L	T	L	A	F	A	V	S	S	H	A	A	D	K	K	L	V	V	A	T	D	T	A	F	V	P	F	E	F	K	Q	G	D	K	Y	V	G	F	D	V	D	L	W	A	A	I	A	K	E
Secondary structure
SS confidence
Disorder		?	?															?	?	?	?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		L	K	L	D	Y	E	L	K	P	M	D	F	S	G	I	I	P	A	L	Q	T	K	N	V	D	L	A	L	A	G	I	T	I	T	D	E	R	K	K	A	I	D	F	S	D	G	Y	Y	K	S	G	L	L	V	M	V	K	A	N	N
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.	.	.	.	.	.	.	150	.	.	.	.	.	.	.	.	.	160	.	.	.	.	.	.	.	.	.	170	.	.	.	.	.	.	.	.	.	180
Sequence		N	D	V	K	S	V	K	D	L	D	G	K	V	V	A	V	K	S	G	T	G	S	V	D	Y	A	K	A	N	I	K	T	K	D	L	R	Q	F	P	N	I	D	N	A	Y	M	E	L	G	T	N	R	A	D	A	V	L	H	D	T
Secondary structure
SS confidence
Disorder				?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	190	.	.	.	.	.	.	.	.	.	200	.	.	.	.	.	.	.	.	.	210	.	.	.	.	.	.	.	.	.	220	.	.	.	.	.	.	.	.	.	230	.	.	.	.	.	.	.	.	.	240
Sequence		P	N	I	L	Y	F	I	K	T	A	G	N	G	Q	F	K	A	V	G	D	S	L	E	A	Q	Q	Y	G	I	A	F	P	K	G	S	D	E	L	R	D	K	V	N	G	A	L	K	T	L	R	E	N	G	T	Y	N	E	I	Y	K
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.
Sequence		K	W	F	G	T	E	P	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 1wdn chain A Region: 26 - 248 Aligned: 223 Modelled: 223 Confidence: 100.0% Identity: 100% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Phosphate binding protein-like Phyre2 PDB 2q2a chain D Region: 15 - 248 Aligned: 234 Modelled: 234 Confidence: 100.0% Identity: 37% PDB header:transport protein Chain: D: PDB Molecule:artj; PDBTitle: crystal structures of the arginine-, lysine-, histidine-2 binding protein artj from the thermophilic bacterium3 geobacillus stearothermophilus Phyre2 PDB 3g41 chain A Region: 23 - 246 Aligned: 224 Modelled: 224 Confidence: 100.0% Identity: 21% PDB header:transport protein Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae Phyre2 PDB 2iee chain B Region: 23 - 247 Aligned: 225 Modelled: 225 Confidence: 100.0% Identity: 21% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable abc transporter extracellular-binding PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574. Phyre2 PDB 3k4u chain A Region: 24 - 247 Aligned: 224 Modelled: 211 Confidence: 100.0% Identity: 28% PDB header:transport protein Chain: A: PDB Molecule:binding component of abc transporter; PDBTitle: crystal structure of putative binding component of abc transporter2 from wolinella succinogenes dsm 1740 complexed with lysine Phyre2 PDB 2yln chain A Region: 17 - 246 Aligned: 228 Modelled: 230 Confidence: 100.0% Identity: 22% PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation Phyre2 PDB 1hsl chain A Region: 22 - 247 Aligned: 226 Modelled: 226 Confidence: 100.0% Identity: 28% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Phosphate binding protein-like Phyre2 PDB 3i6v chain A Region: 26 - 247 Aligned: 214 Modelled: 222 Confidence: 100.0% Identity: 27% PDB header:transport protein Chain: A: PDB Molecule:periplasmic his/glu/gln/arg/opine family-binding protein; PDBTitle: crystal structure of a periplasmic his/glu/gln/arg/opine family-2 binding protein from silicibacter pomeroyi in complex with lysine Phyre2 PDB 3h7m chain A Region: 23 - 247 Aligned: 224 Modelled: 225 Confidence: 100.0% Identity: 27% PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of a histidine kinase sensor domain with2 similarity to periplasmic binding proteins Phyre2 PDB 3del chain C Region: 25 - 248 Aligned: 223 Modelled: 224 Confidence: 100.0% Identity: 22% PDB header:protein binding, transport protein Chain: C: PDB Molecule:arginine binding protein; PDBTitle: the structure of ct381, the arginine binding protein from the2 periplasm chlamydia trachomatis Phyre2 PDB 3hv1 chain A Region: 19 - 246 Aligned: 227 Modelled: 228 Confidence: 100.0% Identity: 27% PDB header:transport protein Chain: A: PDB Molecule:polar amino acid abc uptake transporter substrate PDBTitle: crystal structure of a polar amino acid abc uptake2 transporter substrate binding protein from streptococcus3 thermophilus Phyre2 PDB 1lst chain A Region: 22 - 247 Aligned: 226 Modelled: 226 Confidence: 100.0% Identity: 29% Fold: Periplasmic binding protein-like II Superfamily: Periplasmic binding protein-like II Family: Phosphate binding protein-like Phyre2 PDB 2o1m chain B Region: 23 - 244 Aligned: 221 Modelled: 222 Confidence: 100.0% Identity: 23% PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable amino-acid abc transporter PDBTitle: crystal structure of the probable amino-acid abc2 transporter extracellular-binding protein ytmk from3 bacillus subtilis. northeast structural genomics4 consortium target sr572 Phyre2 PDB 3kzg chain B Region: 26 - 243 Aligned: 217 Modelled: 218 Confidence: 100.0% Identity: 26% PDB header:transport protein Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila Phyre2 PDB 2y7i chain B Region: 24 - 244 Aligned: 220 Modelled: 221 Confidence: 100.0% Identity: 28% PDB header:arginine-binding protein Chain: B: PDB Molecule:stm4351; PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351. Phyre2 PDB 3r39 chain A Region: 20 - 245 Aligned: 223 Modelled: 226 Confidence: 100.0% Identity: 24% PDB header:transport protein Chain: A: PDB Molecule:putative periplasmic binding protein; PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica Phyre2 PDB 3mpl chain A Region: 22 - 242 Aligned: 219 Modelled: 221 Confidence: 100.0% Identity: 19% PDB header:signaling protein Chain: A: PDB Molecule:virulence sensor protein bvgs; PDBTitle: crystal structure of bordetella pertussis bvgs vft2 domain (double2 mutant f375e/q461e) Phyre2 PDB 3kbr chain A Region: 17 - 243 Aligned: 225 Modelled: 227 Confidence: 100.0% Identity: 19% PDB header:lyase Chain: A: PDB Molecule:cyclohexadienyl dehydratase; PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01 Phyre2 PDB 2q89 chain A Region: 17 - 247 Aligned: 230 Modelled: 231 Confidence: 100.0% Identity: 21% PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter amino acid-binding protein; PDBTitle: crystal structure of ehub in complex with hydroxyectoine Phyre2 PDB 2vha chain B Region: 17 - 246 Aligned: 230 Modelled: 230 Confidence: 100.0% Identity: 22% PDB header:transport protein Chain: B: PDB Molecule:periplasmic binding transport protein; PDBTitle: debp Phyre2 1 d1wdna_ 2 c2q2aD_ 3 c3g41A_ 4 c2ieeB_ 5 c3k4uA_ 6 c2ylnA_ 7 d1hsla_ 8 c3i6vA_ 9 c3h7mA_ 10 c3delC_ 11 c3hv1A_ 12 d1lsta_ 13 c2o1mB_ 14 c3kzgB_ 15 c2y7iB_ 16 c3r39A_ 17 c3mplA_ 18 c3kbrA_ 19 c2q89A_ 20 c2vhaB_ 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

Detailed template information

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

1 d1wdna_ 100.0 100 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 2 c2q2aD_ 100.0 37 PDB header:transport protein Chain: D: PDB Molecule:artj; PDBTitle: crystal structures of the arginine-, lysine-, histidine-2 binding protein artj from the thermophilic bacterium3 geobacillus stearothermophilus 3 c3g41A_ 100.0 21 PDB header:transport protein Chain: A: PDB Molecule:amino acid abc transporter, periplasmic amino acid-binding PDBTitle: the structure of cpn0482, the arginine binding protein from the2 periplasm of chlamydia pneumoniae 4 c2ieeB_ 100.0 21 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable abc transporter extracellular-binding PDBTitle: crystal structure of yckb_bacsu from bacillus subtilis.2 northeast structural genomics consortium target sr574. 5 c3k4uA_ 100.0 28 PDB header:transport protein Chain: A: PDB Molecule:binding component of abc transporter; PDBTitle: crystal structure of putative binding component of abc transporter2 from wolinella succinogenes dsm 1740 complexed with lysine 6 c2ylnA_ 100.0 22 PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the l-cystine solute receptor of2 neisseria gonorrhoeae in the closed conformation 7 d1hsla_ 100.0 28 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 8 c3i6vA_ 100.0 27 PDB header:transport protein Chain: A: PDB Molecule:periplasmic his/glu/gln/arg/opine family-binding protein; PDBTitle: crystal structure of a periplasmic his/glu/gln/arg/opine family-2 binding protein from silicibacter pomeroyi in complex with lysine 9 c3h7mA_ 100.0 27 PDB header:transferase Chain: A: PDB Molecule:sensor protein; PDBTitle: crystal structure of a histidine kinase sensor domain with2 similarity to periplasmic binding proteins 10 c3delC_ 100.0 22 PDB header:protein binding, transport protein Chain: C: PDB Molecule:arginine binding protein; PDBTitle: the structure of ct381, the arginine binding protein from the2 periplasm chlamydia trachomatis 11 c3hv1A_ 100.0 27 PDB header:transport protein Chain: A: PDB Molecule:polar amino acid abc uptake transporter substrate PDBTitle: crystal structure of a polar amino acid abc uptake2 transporter substrate binding protein from streptococcus3 thermophilus 12 d1lsta_ 100.0 29 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 13 c2o1mB_ 100.0 23 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:probable amino-acid abc transporter PDBTitle: crystal structure of the probable amino-acid abc2 transporter extracellular-binding protein ytmk from3 bacillus subtilis. northeast structural genomics4 consortium target sr572 14 c3kzgB_ 100.0 26 PDB header:transport protein Chain: B: PDB Molecule:arginine 3rd transport system periplasmic binding PDBTitle: crystal structure of an arginine 3rd transport system2 periplasmic binding protein from legionella pneumophila 15 c2y7iB_ 100.0 28 PDB header:arginine-binding protein Chain: B: PDB Molecule:stm4351; PDBTitle: structural basis for high arginine specificity in salmonella2 typhimurium periplasmic binding protein stm4351. 16 c3r39A_ 100.0 24 PDB header:transport protein Chain: A: PDB Molecule:putative periplasmic binding protein; PDBTitle: crystal structure of periplasmic d-alanine abc transporter from2 salmonella enterica 17 c3mplA_ 100.0 19 PDB header:signaling protein Chain: A: PDB Molecule:virulence sensor protein bvgs; PDBTitle: crystal structure of bordetella pertussis bvgs vft2 domain (double2 mutant f375e/q461e) 18 c3kbrA_ 100.0 19 PDB header:lyase Chain: A: PDB Molecule:cyclohexadienyl dehydratase; PDBTitle: the crystal structure of cyclohexadienyl dehydratase precursor from2 pseudomonas aeruginosa pa01 19 c2q89A_ 100.0 21 PDB header:transport protein Chain: A: PDB Molecule:putative abc transporter amino acid-binding protein; PDBTitle: crystal structure of ehub in complex with hydroxyectoine 20 c2vhaB_ 100.0 22 PDB header:transport protein Chain: B: PDB Molecule:periplasmic binding transport protein; PDBTitle: debp 21 d1ii5a_ not modelled 100.0 19 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 22 c2xx7B_ not modelled 100.0 26 PDB header:transport protein Chain: B: PDB Molecule:glutamate receptor 2; PDBTitle: crystal structure of 1-(4-(1-pyrrolidinylcarbonyl)phenyl)-3-2 (trifluoromethyl)-4,5,6,7-tetrahydro-1h-indazole in complex with3 the ligand binding domain of the rat glua2 receptor and glutamate4 at 2.2a resolution. 23 d1mqia_ not modelled 100.0 26 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 24 c2yjpB_ not modelled 100.0 25 PDB header:transport protein Chain: B: PDB Molecule:putative abc transporter, periplasmic binding protein, PDBTitle: crystal structure of the solute receptors for l-cysteine of2 neisseria gonorrhoeae 25 c1xt8B_ not modelled 100.0 22 PDB header:transport protein Chain: B: PDB Molecule:putative amino-acid transporter periplasmic solute-binding PDBTitle: crystal structure of cysteine-binding protein from campylobacter2 jejuni at 2.0 a resolution 26 d2a5sa1 not modelled 100.0 20 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 27 c2v25B_ not modelled 100.0 24 PDB header:receptor Chain: B: PDB Molecule:major cell-binding factor; PDBTitle: structure of the campylobacter jejuni antigen peb1a, an2 aspartate and glutamate receptor with bound aspartate 28 d1xt8a1 not modelled 100.0 22 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 29 c2pyyB_ not modelled 100.0 31 PDB header:transport protein Chain: B: PDB Molecule:ionotropic glutamate receptor bacterial homologue; PDBTitle: crystal structure of the glur0 ligand-binding core from nostoc2 punctiforme in complex with (l)-glutamate 30 d1pb7a_ not modelled 100.0 20 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 31 c2rc9A_ not modelled 100.0 21 PDB header:membrane protein Chain: A: PDB Molecule:glutamate [nmda] receptor subunit 3a; PDBTitle: crystal structure of the nr3a ligand binding core complex with acpc at2 1.96 angstrom resolution 32 d1s50a1 not modelled 100.0 21 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 33 c2v3tA_ not modelled 99.9 18 PDB header:receptor Chain: A: PDB Molecule:glutamate receptor delta-2 subunit synonym PDBTitle: structure of the ligand-binding core of the ionotropic2 glutamate receptor-like glurdelta2 in the apo form 34 d2f34a1 not modelled 99.9 22 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 35 c1yaeB_ not modelled 99.9 25 PDB header:membrane protein Chain: B: PDB Molecule:glutamate receptor, ionotropic kainate 2; PDBTitle: structure of the kainate receptor subunit glur6 agonist binding domain2 complexed with domoic acid 36 c3kg2A_ not modelled 99.8 26 PDB header:membrane protein, transport protein Chain: A: PDB Molecule:glutamate receptor 2; PDBTitle: ampa subtype ionotropic glutamate receptor in complex with competitive2 antagonist zk 200775 37 c3n5lA_ not modelled 98.6 13 PDB header:transport protein Chain: A: PDB Molecule:binding protein component of abc phosphonate transporter; PDBTitle: crystal structure of a binding protein component of abc phosphonate2 transporter (pa3383) from pseudomonas aeruginosa at 1.97 a resolution 38 c2x26A_ not modelled 98.2 16 PDB header:transport protein Chain: A: PDB Molecule:periplasmic aliphatic sulphonates-binding protein; PDBTitle: crystal structure of the periplasmic aliphatic sulphonate2 binding protein ssua from escherichia coli 39 c3l6gA_ not modelled 98.2 15 PDB header:glycine betaine-binding protein Chain: A: PDB Molecule:betaine abc transporter permease and substrate binding PDBTitle: crystal structure of lactococcal opuac in its open conformation 40 c3e4rA_ not modelled 98.1 12 PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein; PDBTitle: crystal structure of the alkanesulfonate binding protein2 (ssua) from the phytopathogenic bacteria xanthomonas3 axonopodis pv. citri bound to hepes 41 c3ix1B_ not modelled 98.0 15 PDB header:biosynthetic protein Chain: B: PDB Molecule:n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding PDBTitle: periplasmic n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding2 protein from bacillus halodurans 42 c3ix1A_ not modelled 98.0 15 PDB header:biosynthetic protein Chain: A: PDB Molecule:n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding PDBTitle: periplasmic n-formyl-4-amino-5-aminomethyl-2-methylpyrimidine binding2 protein from bacillus halodurans 43 d1xs5a_ not modelled 98.0 11 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 44 c3uifA_ not modelled 97.9 15 PDB header:transport protein Chain: A: PDB Molecule:sulfonate abc transporter, periplasmic sulfonate-binding PDBTitle: crystal structure of putative sulfonate abc transporter, periplasmic2 sulfonate-binding protein ssua from methylobacillus flagellatus kt 45 c3un6A_ not modelled 97.8 10 PDB header:unknown function Chain: A: PDB Molecule:hypothetical protein saouhsc_00137; PDBTitle: 2.0 angstrom crystal structure of ligand binding component of abc-type2 import system from staphylococcus aureus with zinc bound 46 c2x7pA_ not modelled 97.8 14 PDB header:unknown function Chain: A: PDB Molecule:possible thiamine biosynthesis enzyme; PDBTitle: the conserved candida albicans ca3427 gene product defines a new2 family of proteins exhibiting the generic periplasmic binding3 protein structural fold 47 c3k2dA_ not modelled 97.6 15 PDB header:immune system Chain: A: PDB Molecule:abc-type metal ion transport system, periplasmic component; PDBTitle: crystal structure of immunogenic lipoprotein a from vibrio vulnificus 48 c3qslA_ not modelled 97.6 14 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of cae31940 from bordetella bronchiseptica rb50 49 c3hn0A_ not modelled 97.6 10 PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein; PDBTitle: crystal structure of an abc transporter (bdi_1369) from2 parabacteroides distasonis at 1.75 a resolution 50 c3tqwA_ not modelled 97.3 15 PDB header:transport protein Chain: A: PDB Molecule:methionine-binding protein; PDBTitle: structure of a abc transporter, periplasmic substrate-binding protein2 from coxiella burnetii 51 c3tmgA_ not modelled 97.3 9 PDB header:transport protein Chain: A: PDB Molecule:glycine betaine, l-proline abc transporter, PDBTitle: crystal structure of glycine betaine, l-proline abc transporter,2 glycine/betaine/l-proline-binding protein (prox) from borrelia3 burgdorferi 52 c2g29A_ not modelled 97.1 11 PDB header:transport protein Chain: A: PDB Molecule:nitrate transport protein nrta; PDBTitle: crystal structure of the periplasmic nitrate-binding2 protein nrta from synechocystis pcc 6803 53 c3gxaA_ not modelled 96.7 13 PDB header:protein binding Chain: A: PDB Molecule:outer membrane lipoprotein gna1946; PDBTitle: crystal structure of gna1946 54 c1p99A_ not modelled 96.6 13 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:hypothetical protein pg110; PDBTitle: 1.7a crystal structure of protein pg110 from staphylococcus2 aureus 55 d1p99a_ not modelled 96.6 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 56 d1zbma1 not modelled 96.6 12 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 57 c3ir1F_ not modelled 96.4 13 PDB header:protein binding Chain: F: PDB Molecule:outer membrane lipoprotein gna1946; PDBTitle: crystal structure of lipoprotein gna1946 from neisseria2 meningitidis 58 d1atga_ not modelled 95.9 10 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 59 d2czla1 not modelled 95.6 9 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 60 c2de4B_ not modelled 95.5 11 PDB header:hydrolase Chain: B: PDB Molecule:dibenzothiophene desulfurization enzyme b; PDBTitle: crystal structure of dszb c27s mutant in complex with biphenyl-2-2 sulfinic acid 61 c2rejA_ not modelled 95.3 14 PDB header:choline-binding protein Chain: A: PDB Molecule:putative glycine betaine abc transporter protein; PDBTitle: abc-transporter choline binding protein in unliganded semi-2 closed conformation 62 c2i4cA_ not modelled 95.0 8 PDB header:transport protein Chain: A: PDB Molecule:bicarbonate transporter; PDBTitle: crystal structure of bicarbonate transport protein cmpa from2 synechocystis sp. pcc 6803 in complex with bicarbonate and calcium 63 c2dvzA_ not modelled 94.0 15 PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: structure of a periplasmic transporter 64 c3jv9B_ not modelled 93.9 12 PDB header:transcription Chain: B: PDB Molecule:transcriptional regulator, lysr family; PDBTitle: the structure of a reduced form of oxyr from n. meningitidis 65 d2nxoa1 not modelled 93.5 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 66 c3ho7A_ not modelled 93.5 11 PDB header:transcription Chain: A: PDB Molecule:oxyr; PDBTitle: crystal structure of oxyr from porphyromonas gingivalis 67 c2qpqC_ not modelled 93.4 10 PDB header:transport protein Chain: C: PDB Molecule:protein bug27; PDBTitle: structure of bug27 from bordetella pertussis 68 c2f5xC_ not modelled 93.0 18 PDB header:transport protein Chain: C: PDB Molecule:bugd; PDBTitle: structure of periplasmic binding protein bugd 69 c3fj7A_ not modelled 92.3 16 PDB header:protein binding Chain: A: PDB Molecule:major antigenic peptide peb3; PDBTitle: crystal structure of l-phospholactate bound peb3 70 c3oxnD_ not modelled 92.2 14 PDB header:transcription regulator Chain: D: PDB Molecule:putative transcriptional regulator, lysr family; PDBTitle: the crystal structure of a putative transcriptional regulator from2 vibrio parahaemolyticus 71 c2ql3G_ not modelled 90.8 12 PDB header:transcription Chain: G: PDB Molecule:probable transcriptional regulator, lysr family protein; PDBTitle: crystal structure of the c-terminal domain of a probable lysr family2 transcriptional regulator from rhodococcus sp. rha1 72 d1us5a_ not modelled 89.0 17 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 73 d1i6aa_ not modelled 89.0 11 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 74 c3r6uA_ not modelled 88.9 17 PDB header:transport protein Chain: A: PDB Molecule:choline-binding protein; PDBTitle: crystal structure of choline binding protein opubc from bacillus2 subtilis 75 c2hpgB_ not modelled 87.9 12 PDB header:ligand binding protein Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding PDBTitle: the crystal structure of a thermophilic trap periplasmic2 binding protein 76 c2uyeA_ not modelled 86.7 11 PDB header:transcription Chain: A: PDB Molecule:regulatory protein; PDBTitle: double mutant y110s,f111v dntr from burkholderia sp. strain2 dnt in complex with thiocyanate 77 d2ozza1 not modelled 86.1 9 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 78 c3lr1A_ not modelled 85.9 12 PDB header:transport protein Chain: A: PDB Molecule:tungstate abc transporter, periplasmic tungstate- PDBTitle: the crystal structure of the tungstate abc transporter from2 geobacter sulfurreducens 79 d1amfa_ not modelled 84.2 14 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 80 d1utha_ not modelled 82.4 12 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 81 c3chgB_ not modelled 79.0 13 PDB header:ligand binding protein Chain: B: PDB Molecule:glycine betaine-binding protein; PDBTitle: the compatible solute-binding protein opuac from bacillus2 subtilis in complex with dmsa 82 d2esna2 not modelled 77.6 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 83 c3fxbB_ not modelled 76.6 17 PDB header:transport protein Chain: B: PDB Molecule:trap dicarboxylate transporter, dctp subunit; PDBTitle: crystal structure of the ectoine-binding protein ueha 84 c3pppA_ not modelled 74.6 17 PDB header:transport protein Chain: A: PDB Molecule:glycine betaine/carnitine/choline-binding protein; PDBTitle: structures of the substrate-binding protein provide insights into the2 multiple compatible solutes binding specificities of bacillus3 subtilis abc transporter opuc 85 c2hxrA_ not modelled 73.4 11 PDB header:transcription Chain: A: PDB Molecule:hth-type transcriptional regulator cynr; PDBTitle: structure of the ligand binding domain of e. coli cynr, a2 transcriptional regulator controlling cyanate metabolism 86 c2vpnB_ not modelled 73.2 14 PDB header:transport Chain: B: PDB Molecule:periplasmic substrate binding protein; PDBTitle: high-resolution structure of the periplasmic ectoine-2 binding protein from teaabc trap-transporter of halomonas3 elongata 87 c2h5yC_ not modelled 71.6 11 PDB header:metal transport Chain: C: PDB Molecule:molybdate-binding periplasmic protein; PDBTitle: crystallographic structure of the molybdate-binding protein of2 xanthomonas citri at 1.7 ang resolution bound to molybdate 88 c3b50A_ not modelled 70.8 14 PDB header:transport protein Chain: A: PDB Molecule:sialic acid-binding periplasmic protein siap; PDBTitle: structure of h. influenzae sialic acid binding protein2 bound to neu5ac. 89 c3eq1A_ not modelled 69.6 15 PDB header:transferase Chain: A: PDB Molecule:porphobilinogen deaminase; PDBTitle: the crystal structure of human porphobilinogen deaminase at2 2.8a resolution 90 d1sw5a_ not modelled 67.1 12 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 91 c2vd3B_ not modelled 65.8 13 PDB header:transferase Chain: B: PDB Molecule:atp phosphoribosyltransferase; PDBTitle: the structure of histidine inhibited hisg from2 methanobacterium thermoautotrophicum 92 c2h9bB_ not modelled 63.1 13 PDB header:transcription Chain: B: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: crystal structure of the effector binding domain of a benm variant2 (benm r156h/t157s) 93 d1pdaa1 not modelled 63.0 13 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 94 c2pfzA_ not modelled 61.1 11 PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of dctp6, a bordetella pertussis2 extracytoplasmic solute receptor binding pyroglutamic acid 95 c2h9qC_ not modelled 59.6 13 PDB header:transcription Chain: C: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: crystal structure of the effector binding domain of a catm2 variant (r156h) 96 c3n6uA_ not modelled 59.5 8 PDB header:transcription regulator Chain: A: PDB Molecule:lysr type regulator of tsambcd; PDBTitle: effector binding domain of tsar in complex with its inducer p-2 toluenesulfonate 97 c3gyyC_ not modelled 59.2 14 PDB header:transport protein Chain: C: PDB Molecule:periplasmic substrate binding protein; PDBTitle: the ectoine binding protein of the teaabc trap transporter teaa in the2 apo-state 98 c2f7cA_ not modelled 55.9 13 PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator catm; PDBTitle: catm effector binding domain with its effector cis,cis-muconate 99 c3muqB_ not modelled 55.9 12 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized conserved protein; PDBTitle: the crystal structure of a conserved functionally unknown protein from2 vibrio parahaemolyticus rimd 2210633 100 c2f78A_ not modelled 54.8 13 PDB header:gene regulation Chain: A: PDB Molecule:hth-type transcriptional regulator benm; PDBTitle: benm effector binding domain with its effector benzoate 101 d1ixca2 not modelled 54.3 9 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 102 d1z7me1 not modelled 46.5 16 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 103 c2pfyA_ not modelled 46.2 13 PDB header:transport protein Chain: A: PDB Molecule:putative exported protein; PDBTitle: crystal structure of dctp7, a bordetella pertussis2 extracytoplasmic solute receptor binding pyroglutamic acid 104 c3dtfB_ not modelled 45.7 15 PDB header:transferase Chain: B: PDB Molecule:branched-chain amino acid aminotransferase; PDBTitle: structural analysis of mycobacterial branched chain aminotransferase-2 implications for inhibitor design 105 c3kn3C_ not modelled 44.9 11 PDB header:transcription Chain: C: PDB Molecule:putative periplasmic protein; PDBTitle: crystal structure of lysr substrate binding domain (25-263) of2 putative periplasmic protein from wolinella succinogenes 106 c1nh7A_ not modelled 43.7 12 PDB header:transferase Chain: A: PDB Molecule:atp phosphoribosyltransferase; PDBTitle: atp phosphoribosyltransferase (atp-prtase) from mycobacterium2 tuberculosis 107 c3fd3A_ not modelled 35.9 7 PDB header:transcription regulator Chain: A: PDB Molecule:chromosome replication initiation inhibitor protein; PDBTitle: structure of the c-terminal domains of a lysr family protein from2 agrobacterium tumefaciens str. c58. 108 c2ypnA_ not modelled 33.8 10 PDB header:transferase Chain: A: PDB Molecule:protein (hydroxymethylbilane synthase); PDBTitle: hydroxymethylbilane synthase 109 d1r9la_ not modelled 32.2 12 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 110 c2abjG_ not modelled 32.1 15 PDB header:transferase Chain: G: PDB Molecule:branched-chain-amino-acid aminotransferase, cytosolic; PDBTitle: crystal structure of human branched chain amino acid transaminase in a2 complex with an inhibitor, c16h10n2o4f3scl, and pyridoxal 5'3 phosphate. 111 d1twya_ not modelled 30.9 14 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 112 c1twyG_ not modelled 30.9 14 PDB header:structural genomics, unknown function Chain: G: PDB Molecule:abc transporter, periplasmic substrate-binding protein; PDBTitle: crystal structure of an abc-type phosphate transport receptor from2 vibrio cholerae 113 d2a1ha1 not modelled 28.9 14 Fold:D-aminoacid aminotransferase-like PLP-dependent enzymes Superfamily:D-aminoacid aminotransferase-like PLP-dependent enzymes Family:D-aminoacid aminotransferase-like PLP-dependent enzymes 114 c3pamB_ not modelled 28.5 16 PDB header:transport protein Chain: B: PDB Molecule:transmembrane protein; PDBTitle: crystal structure of a domain of transmembrane protein of abc-type2 oligopeptide transport system from bartonella henselae str. houston-1 115 d2fyia1 not modelled 28.5 12 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 116 d1al3a_ not modelled 27.9 8 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 117 c1al3A_ not modelled 27.9 8 PDB header:transcription regulation Chain: A: PDB Molecule:cys regulon transcriptional activator cysb; PDBTitle: cofactor binding fragment of cysb from klebsiella aerogenes 118 c3lvuB_ not modelled 26.3 9 PDB header:transport protein Chain: B: PDB Molecule:abc transporter, periplasmic substrate-binding protein; PDBTitle: crystal structure of abc transporter, periplasmic substrate-binding2 protein spo2066 from silicibacter pomeroyi 119 d1h3da1 not modelled 25.2 12 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-like 120 d1vr5a1 not modelled 25.2 19 Fold:Periplasmic binding protein-like II Superfamily:Periplasmic binding protein-like II Family:Phosphate binding protein-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