Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	S	I	T	L	S	D	S	A	A	A	R	V	N	T	F	L	A	N	R	G	K	G	F	G	L	R	L	G	V	R	T	S	G	C	S	G	M	A	Y	V	L	E	F	V	D	E	P	T	P	E	D	I	V	F	E	D	K	G	V
Secondary structure
SS confidence
Disorder		?	?																		?	?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.
Sequence		K	V	V	V	D	G	K	S	L	Q	F	L	D	G	T	Q	L	D	F	V	K	E	G	L	N	E	G	F	K	F	T	N	P	N	V	K	D	E	C	G	C	G	E	S	F	H	V
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 2d2a chain A Region: 1 - 107 Aligned: 107 Modelled: 107 Confidence: 100.0% Identity: 47% PDB header:metal transport Chain: A: PDB Molecule:sufa protein; PDBTitle: crystal structure of escherichia coli sufa involved in2 biosynthesis of iron-sulfur clusters Phyre2 PDB 2apn chain A Region: 1 - 107 Aligned: 107 Modelled: 107 Confidence: 100.0% Identity: 33% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein hi1723; PDBTitle: hi1723 solution structure Phyre2 PDB 1x0g chain A Region: 3 - 107 Aligned: 98 Modelled: 105 Confidence: 100.0% Identity: 31% PDB header:metal binding protein Chain: A: PDB Molecule:isca; PDBTitle: crystal structure of isca with the [2fe-2s] cluster Phyre2 PDB 1s98 chain A Region: 2 - 97 Aligned: 96 Modelled: 96 Confidence: 100.0% Identity: 99% Fold: HesB-like domain Superfamily: HesB-like domain Family: HesB-like domain Phyre2 PDB 2k4z chain A Region: 1 - 95 Aligned: 94 Modelled: 95 Confidence: 100.0% Identity: 31% PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dsrr; PDBTitle: solution nmr structure of allochromatium vinosum dsrr:2 northeast structural genomics consortium target op5 Phyre2 PDB 1nwb chain A Region: 1 - 93 Aligned: 93 Modelled: 93 Confidence: 100.0% Identity: 33% Fold: HesB-like domain Superfamily: HesB-like domain Family: HesB-like domain Phyre2 PDB 2p2e chain A domain 1 Region: 1 - 95 Aligned: 93 Modelled: 95 Confidence: 98.9% Identity: 19% Fold: HesB-like domain Superfamily: HesB-like domain Family: HesB-like domain Phyre2 PDB 2qgo chain A Region: 1 - 95 Aligned: 89 Modelled: 95 Confidence: 98.7% Identity: 15% PDB header:biosynthetic protein Chain: A: PDB Molecule:putative fe-s biosynthesis protein; PDBTitle: crystal structure of a putative fe-s biosynthesis protein from2 lactobacillus acidophilus Phyre2 PDB 2a6s chain A domain 1 Region: 1 - 20 Aligned: 20 Modelled: 20 Confidence: 19.1% Identity: 10% Fold: RelE-like Superfamily: RelE-like Family: YoeB/Txe-like Phyre2 PDB 1sp2 chain A Region: 98 - 106 Aligned: 9 Modelled: 9 Confidence: 12.6% Identity: 44% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 1zfd chain A Region: 100 - 106 Aligned: 7 Modelled: 7 Confidence: 10.6% Identity: 43% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 3kxe chain D Region: 1 - 18 Aligned: 18 Modelled: 18 Confidence: 10.5% Identity: 28% PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex Phyre2 PDB 3g5o chain C Region: 1 - 16 Aligned: 16 Modelled: 16 Confidence: 10.0% Identity: 13% PDB header:toxin/antitoxin Chain: C: PDB Molecule:uncharacterized protein rv2866; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis Phyre2 PDB 2yuj chain A Region: 58 - 102 Aligned: 40 Modelled: 45 Confidence: 9.9% Identity: 33% PDB header:protein binding Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like; PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1 Phyre2 PDB 2kdx chain A Region: 85 - 107 Aligned: 23 Modelled: 23 Confidence: 9.5% Identity: 22% PDB header:metal-binding protein Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein PDBTitle: solution structure of hypa protein Phyre2 PDB 1a1i chain A domain 1 Region: 100 - 106 Aligned: 7 Modelled: 7 Confidence: 9.4% Identity: 29% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 1aay chain A domain 1 Region: 100 - 106 Aligned: 7 Modelled: 7 Confidence: 9.0% Identity: 29% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 1ubd chain C domain 3 Region: 100 - 106 Aligned: 7 Modelled: 7 Confidence: 8.8% Identity: 57% Fold: beta-beta-alpha zinc fingers Superfamily: beta-beta-alpha zinc fingers Family: Classic zinc finger, C2H2 Phyre2 PDB 1zc1 chain A Region: 59 - 102 Aligned: 39 Modelled: 44 Confidence: 8.7% Identity: 23% PDB header:protein turnover Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1; PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites Phyre2 PDB 3c3j chain A Region: 99 - 106 Aligned: 8 Modelled: 8 Confidence: 8.7% Identity: 38% PDB header:isomerase Chain: A: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase; PDBTitle: crystal structure of tagatose-6-phosphate ketose/aldose isomerase from2 escherichia coli Phyre2 1 c2d2aA_ 2 c2apnA_ 3 c1x0gA_ 4 d1s98a_ 5 c2k4zA_ 6 d1nwba_ 7 d2p2ea1 8 c2qgoA_ 9 d2a6sa1 10 d1sp2a_ 11 d1zfda_ 12 c3kxeD_ 13 c3g5oC_ 14 c2yujA_ 15 c2kdxA_ 16 d1a1ia1 17 d1aaya1 18 d1ubdc3 19 c1zc1A_ 20 c3c3jA_ 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

Detailed template information

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

1 c2d2aA_ 100.0 47 PDB header:metal transport Chain: A: PDB Molecule:sufa protein; PDBTitle: crystal structure of escherichia coli sufa involved in2 biosynthesis of iron-sulfur clusters 2 c2apnA_ 100.0 33 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:protein hi1723; PDBTitle: hi1723 solution structure 3 c1x0gA_ 100.0 31 PDB header:metal binding protein Chain: A: PDB Molecule:isca; PDBTitle: crystal structure of isca with the [2fe-2s] cluster 4 d1s98a_ 100.0 99 Fold:HesB-like domain Superfamily:HesB-like domain Family:HesB-like domain 5 c2k4zA_ 100.0 31 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:dsrr; PDBTitle: solution nmr structure of allochromatium vinosum dsrr:2 northeast structural genomics consortium target op5 6 d1nwba_ 100.0 33 Fold:HesB-like domain Superfamily:HesB-like domain Family:HesB-like domain 7 d2p2ea1 98.9 19 Fold:HesB-like domain Superfamily:HesB-like domain Family:HesB-like domain 8 c2qgoA_ 98.7 15 PDB header:biosynthetic protein Chain: A: PDB Molecule:putative fe-s biosynthesis protein; PDBTitle: crystal structure of a putative fe-s biosynthesis protein from2 lactobacillus acidophilus 9 d2a6sa1 19.1 10 Fold:RelE-like Superfamily:RelE-like Family:YoeB/Txe-like 10 d1sp2a_ 12.6 44 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 11 d1zfda_ 10.6 43 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 12 c3kxeD_ 10.5 28 PDB header:protein binding Chain: D: PDB Molecule:antitoxin protein pard-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex 13 c3g5oC_ 10.0 13 PDB header:toxin/antitoxin Chain: C: PDB Molecule:uncharacterized protein rv2866; PDBTitle: the crystal structure of the toxin-antitoxin complex relbe2 (rv2865-2 2866) from mycobacterium tuberculosis 14 c2yujA_ 9.9 33 PDB header:protein binding Chain: A: PDB Molecule:ubiquitin fusion degradation 1-like; PDBTitle: solution structure of human ubiquitin fusion degradation2 protein 1 homolog ufd1 15 c2kdxA_ 9.5 22 PDB header:metal-binding protein Chain: A: PDB Molecule:hydrogenase/urease nickel incorporation protein PDBTitle: solution structure of hypa protein 16 d1a1ia1 9.4 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 17 d1aaya1 9.0 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 18 d1ubdc3 8.8 57 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 19 c1zc1A_ 8.7 23 PDB header:protein turnover Chain: A: PDB Molecule:ubiquitin fusion degradation protein 1; PDBTitle: ufd1 exhibits the aaa-atpase fold with two distinct2 ubiquitin interaction sites 20 c3c3jA_ 8.7 38 PDB header:isomerase Chain: A: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase; PDBTitle: crystal structure of tagatose-6-phosphate ketose/aldose isomerase from2 escherichia coli 21 d1a1ha1 not modelled 8.6 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 22 d1lk5a2 not modelled 8.2 24 Fold:Ferredoxin-like Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain Family:D-ribose-5-phosphate isomerase (RpiA), lid domain 23 d1a1ga1 not modelled 8.2 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 24 d1f2ig1 not modelled 8.1 38 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 25 d1tf3a2 not modelled 7.8 43 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 26 d1u86a1 not modelled 7.8 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 27 d1wgea1 not modelled 7.7 40 Fold:Rubredoxin-like Superfamily:CSL zinc finger Family:CSL zinc finger 28 c3odpA_ not modelled 7.5 38 PDB header:isomerase Chain: A: PDB Molecule:putative tagatose-6-phosphate ketose/aldose isomerase; PDBTitle: crystal structure of a putative tagatose-6-phosphate ketose/aldose2 isomerase (nt01cx_0292) from clostridium novyi nt at 2.35 a3 resolution 29 c3a44D_ not modelled 7.5 12 PDB header:metal binding protein Chain: D: PDB Molecule:hydrogenase nickel incorporation protein hypa; PDBTitle: crystal structure of hypa in the dimeric form 30 c2kvfA_ not modelled 7.3 38 PDB header:transcription Chain: A: PDB Molecule:zinc finger and btb domain-containing protein 32; PDBTitle: structure of the three-cys2his2 domain of mouse testis zinc2 finger protein 31 d1adta2 not modelled 6.7 27 Fold:Zn-binding domains of ADDBP Superfamily:Zn-binding domains of ADDBP Family:Zn-binding domains of ADDBP 32 c2wh44_ not modelled 6.6 80 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: insights into translational termination from the structure2 of rf2 bound to the ribosome 33 c1gxsC_ not modelled 6.6 14 PDB header:lyase Chain: C: PDB Molecule:p-(s)-hydroxymandelonitrile lyase chain a; PDBTitle: crystal structure of hydroxynitrile lyase from sorghum2 bicolor in complex with inhibitor benzoic acid: a novel3 cyanogenic enzyme 34 d1wmia1 not modelled 6.4 0 Fold:RelE-like Superfamily:RelE-like Family:RelE-like 35 c2ab3A_ not modelled 6.2 67 PDB header:rna binding protein Chain: A: PDB Molecule:znf29; PDBTitle: solution structures and characterization of hiv rre iib rna2 targeting zinc finger proteins 36 c3f1f4_ not modelled 6.0 80 PDB header:ribosome Chain: 4: PDB Molecule:50s ribosomal protein l31; PDBTitle: crystal structure of a translation termination complex2 formed with release factor rf2. this file contains the 50s3 subunit of one 70s ribosome. the entire crystal structure4 contains two 70s ribosomes as described in remark 400. 37 d1m0sa2 not modelled 6.0 22 Fold:Ferredoxin-like Superfamily:D-ribose-5-phosphate isomerase (RpiA), lid domain Family:D-ribose-5-phosphate isomerase (RpiA), lid domain 38 d2h85a2 not modelled 5.8 29 Fold:EndoU-like Superfamily:EndoU-like Family:Nsp15 C-terminal domain-like 39 d1ncsa_ not modelled 5.7 43 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 40 d1u8sa1 not modelled 5.6 32 Fold:Ferredoxin-like Superfamily:ACT-like Family:Glycine cleavage system transcriptional repressor 41 d1qabe_ not modelled 5.5 24 Fold:Lipocalins Superfamily:Lipocalins Family:Retinol binding protein-like 42 d1ywsa1 not modelled 5.5 44 Fold:Rubredoxin-like Superfamily:CSL zinc finger Family:CSL zinc finger 43 d2ayua1 not modelled 5.4 27 Fold:NAP-like Superfamily:NAP-like Family:NAP-like 44 c2ayuA_ not modelled 5.4 27 PDB header:chaperone Chain: A: PDB Molecule:nucleosome assembly protein; PDBTitle: the structure of nucleosome assembly protein suggests a mechanism for2 histone binding and shuttling 45 c1bcrA_ not modelled 5.3 20 PDB header:hydrolase/hydrolase inhibitor Chain: A: PDB Molecule:serine carboxypeptidase ii; PDBTitle: complex of the wheat serine carboxypeptidase, cpdw-ii, with the2 microbial peptide aldehyde inhibitor, antipain, and arginine at room3 temperature 46 d2yt9a1 not modelled 5.3 43 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 47 c3q3wB_ not modelled 5.3 60 PDB header:transferase Chain: B: PDB Molecule:3-isopropylmalate dehydratase small subunit; PDBTitle: isopropylmalate isomerase small subunit from campylobacter jejuni. 48 c2hcuA_ not modelled 5.3 60 PDB header:lyase Chain: A: PDB Molecule:3-isopropylmalate dehydratase small subunit; PDBTitle: crystal structure of smu.1381 (or leud) from streptococcus2 mutans 49 d1x6ea2 not modelled 5.2 50 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 50 d2dlka2 not modelled 5.2 57 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 51 d2glia3 not modelled 5.1 29 Fold:beta-beta-alpha zinc fingers Superfamily:beta-beta-alpha zinc fingers Family:Classic zinc finger, C2H2 52 c3kxeB_ not modelled 5.1 24 PDB header:protein binding Chain: B: PDB Molecule:toxin protein pare-1; PDBTitle: a conserved mode of protein recognition and binding in a2 pard-pare toxin-antitoxin complex

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

---

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