Secondary structure and disorder prediction

		1	.	.	.	.	.	.	.	.	10	.	.	.	.	.	.	.	.	.	20	.	.	.	.	.	.	.	.	.	30	.	.	.	.	.	.	.	.	.	40	.	.	.	.	.	.	.	.	.	50	.	.	.	.	.	.	.	.	.	60
Sequence		M	A	I	E	R	T	F	S	I	I	K	P	N	A	V	A	K	N	V	I	G	N	I	F	A	R	F	E	A	A	G	F	K	I	V	G	T	K	M	L	H	L	T	V	E	Q	A	R	G	F	Y	A	E	H	D	G	K	P	F	F
Secondary structure
SS confidence
Disorder		?	?	?	?	?																									?																									?	?
Disorder confidence
		.	.	.	.	.	.	.	.	.	70	.	.	.	.	.	.	.	.	.	80	.	.	.	.	.	.	.	.	.	90	.	.	.	.	.	.	.	.	.	100	.	.	.	.	.	.	.	.	.	110	.	.	.	.	.	.	.	.	.	120
Sequence		D	G	L	V	E	F	M	T	S	G	P	I	V	V	S	V	L	E	G	E	N	A	V	Q	R	H	R	D	L	L	G	A	T	N	P	A	N	A	L	A	G	T	L	R	A	D	Y	A	D	S	L	T	E	N	G	T	H	G	S	D
Secondary structure
SS confidence
Disorder
Disorder confidence
		.	.	.	.	.	.	.	.	.	130	.	.	.	.	.	.	.	.	.	140	.	.	.
Sequence		S	V	E	S	A	A	R	E	I	A	Y	F	F	G	E	G	E	V	C	P	R	T	R
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 2hur chain F Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 100% PDB header:signaling protein,transferase Chain: F: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: escherichia coli nucleoside diphosphate kinase Phyre2 PDB 1s57 chain A Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 40% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1ehw chain A Region: 1 - 141 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 39% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1w7w chain A Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 42% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 3js9 chain A Region: 3 - 143 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 38% PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase family protein; PDBTitle: crystal structure of nucleoside diphosphate kinase family protein from2 babesia bovis Phyre2 PDB 2vu5 chain A Region: 3 - 143 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 46% PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of pndk from bacillus anthracis Phyre2 PDB 1w7w chain F Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 42% PDB header:transferase Chain: F: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: structure and mutational analysis of a plant mitochondrial2 nucleoside diphosphate kinase: identification of residues3 involved in serine phosphorylation and oligomerization. Phyre2 PDB 3bbb chain A domain 1 Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 42% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1xiq chain A Region: 3 - 143 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 39% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1nhk chain L Region: 2 - 142 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 57% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 3q89 chain H Region: 3 - 143 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 45% PDB header:transferase Chain: H: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of staphylococcus aureus nucleoside diphosphate2 kinase complexed with cdp Phyre2 PDB 1nb2 chain A Region: 4 - 143 Aligned: 140 Modelled: 140 Confidence: 100.0% Identity: 47% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1ucn chain A Region: 3 - 143 Aligned: 141 Modelled: 141 Confidence: 100.0% Identity: 42% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 3mpd chain A Region: 3 - 143 Aligned: 140 Modelled: 141 Confidence: 100.0% Identity: 39% PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of nucleoside diphosphate kinase from2 encephalitozoon cuniculi, cubic form, apo Phyre2 PDB 2dya chain A domain 1 Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 47% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1be4 chain A Region: 4 - 143 Aligned: 140 Modelled: 140 Confidence: 100.0% Identity: 43% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1u8w chain A Region: 3 - 142 Aligned: 140 Modelled: 140 Confidence: 100.0% Identity: 43% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 1hlw chain A Region: 1 - 143 Aligned: 143 Modelled: 143 Confidence: 100.0% Identity: 45% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 PDB 3ngt chain J Region: 4 - 143 Aligned: 140 Modelled: 140 Confidence: 100.0% Identity: 51% PDB header:transferase Chain: J: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: structure of leishmania ndkb complexed with amp. Phyre2 PDB 1zs6 chain A domain 1 Region: 2 - 143 Aligned: 142 Modelled: 142 Confidence: 100.0% Identity: 45% Fold: Ferredoxin-like Superfamily: Nucleoside diphosphate kinase, NDK Family: Nucleoside diphosphate kinase, NDK Phyre2 1 c2hurF_ 2 d1s57a_ 3 d1ehwa_ 4 d1w7wa_ 5 c3js9A_ 6 c2vu5A_ 7 c1w7wF_ 8 d3bbba1 9 d1xiqa_ 10 d1nhkl_ 11 c3q89H_ 12 d1nb2a_ 13 d1ucna_ 14 c3mpdA_ 15 d2dyaa1 16 d1be4a_ 17 d1u8wa_ 18 d1hlwa_ 19 c3ngtJ_ 20 d1zs6a1 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

Detailed template information

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

1 c2hurF_ 100.0 100 PDB header:signaling protein,transferase Chain: F: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: escherichia coli nucleoside diphosphate kinase 2 d1s57a_ 100.0 40 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 3 d1ehwa_ 100.0 39 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 4 d1w7wa_ 100.0 42 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 5 c3js9A_ 100.0 38 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase family protein; PDBTitle: crystal structure of nucleoside diphosphate kinase family protein from2 babesia bovis 6 c2vu5A_ 100.0 46 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of pndk from bacillus anthracis 7 c1w7wF_ 100.0 42 PDB header:transferase Chain: F: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: structure and mutational analysis of a plant mitochondrial2 nucleoside diphosphate kinase: identification of residues3 involved in serine phosphorylation and oligomerization. 8 d3bbba1 100.0 42 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 9 d1xiqa_ 100.0 39 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 10 d1nhkl_ 100.0 57 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 11 c3q89H_ 100.0 45 PDB header:transferase Chain: H: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of staphylococcus aureus nucleoside diphosphate2 kinase complexed with cdp 12 d1nb2a_ 100.0 47 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 13 d1ucna_ 100.0 42 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 14 c3mpdA_ 100.0 39 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of nucleoside diphosphate kinase from2 encephalitozoon cuniculi, cubic form, apo 15 d2dyaa1 100.0 47 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 16 d1be4a_ 100.0 43 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 17 d1u8wa_ 100.0 43 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 18 d1hlwa_ 100.0 45 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 19 c3ngtJ_ 100.0 51 PDB header:transferase Chain: J: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: structure of leishmania ndkb complexed with amp. 20 d1zs6a1 100.0 45 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 21 d1wkja1 not modelled 100.0 50 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 22 d1pkua1 not modelled 100.0 42 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 23 d2az3a1 not modelled 100.0 47 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 24 d1xqia1 not modelled 100.0 44 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 25 d1nsqa_ not modelled 100.0 46 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 26 d1k44a_ not modelled 100.0 46 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 27 c2az1B_ not modelled 100.0 45 PDB header:transferase Chain: B: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: structure of a halophilic nucleoside diphosphate kinase2 from halobacterium salinarum 28 c3b54A_ not modelled 100.0 41 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: saccharomyces cerevisiae nucleoside diphosphate kinase 29 d2b8qa1 not modelled 100.0 37 Fold:Ferredoxin-like Superfamily:Nucleoside diphosphate kinase, NDK Family:Nucleoside diphosphate kinase, NDK 30 c3b6bF_ not modelled 100.0 37 PDB header:transferase Chain: F: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of acanthamoeba polyphaga mimivirus2 nucleoside diphosphate kinase complexed with dgdp 31 c3r9lA_ not modelled 100.0 46 PDB header:transferase Chain: A: PDB Molecule:nucleoside diphosphate kinase; PDBTitle: crystal structure of nucleoside diphosphate kinase from giardia2 lamblia featuring a disordered dinucleotide binding site 32 c2bx6A_ not modelled 98.4 18 PDB header:transduction protein Chain: A: PDB Molecule:xrp2 protein; PDBTitle: crystal structure of the human retinitis pigmentosa2 protein 2 (rp2) 33 c3bqsB_ not modelled 36.9 16 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:uncharacterized protein; PDBTitle: crystal structure of an uncharacterized protein from2 listeria monocytogenes, trigonal form 34 c3p04A_ not modelled 35.3 18 PDB header:structural genomics, unknown function Chain: A: PDB Molecule:uncharacterized bcr; PDBTitle: crystal structure of the bcr protein from corynebacterium glutamicum.2 northeast structural genomics consortium target cgr8 35 c1y7pB_ not modelled 22.5 19 PDB header:structural genomics, unknown function Chain: B: PDB Molecule:hypothetical protein af1403; PDBTitle: 1.9 a crystal structure of a protein of unknown function2 af1403 from archaeoglobus fulgidus, probable metabolic3 regulator 36 d2fi0a1 not modelled 17.5 29 Fold:SP0561-like Superfamily:SP0561-like Family:SP0561-like 37 c2qgqF_ not modelled 15.0 19 PDB header:structural genomics, unknown function Chain: F: PDB Molecule:protein tm_1862; PDBTitle: crystal structure of tm_1862 from thermotoga maritima.2 northeast structural genomics consortium target vr77 38 d1ywxa1 not modelled 11.4 12 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:Ribosomal protein S24e 39 d2g7oa1 not modelled 11.3 27 Fold:TraM-like Superfamily:TraM-like Family:TraM-like 40 c3odnA_ not modelled 10.0 19 PDB header:membrane protein Chain: A: PDB Molecule:dally-like protein; PDBTitle: the crystal structure of drosophila dally-like protein core domain 41 d1xn9a_ not modelled 9.8 6 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:Ribosomal protein S24e 42 c3iz6U_ not modelled 9.7 8 PDB header:ribosome Chain: U: PDB Molecule:40s ribosomal protein s24 (s24e); PDBTitle: localization of the small subunit ribosomal proteins into a 5.5 a2 cryo-em map of triticum aestivum translating 80s ribosome 43 d1wdcc_ not modelled 9.2 22 Fold:EF Hand-like Superfamily:EF-hand Family:Calmodulin-like 44 c1kxfA_ not modelled 9.1 43 PDB header:viral protein Chain: A: PDB Molecule:sindbis virus capsid protein; PDBTitle: sindbis virus capsid, (wild-type) residues 1-264,2 tetragonal crystal form (form ii) 45 d1ep5a_ not modelled 9.0 43 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 46 d1kvka2 not modelled 9.0 16 Fold:Ferredoxin-like Superfamily:GHMP Kinase, C-terminal domain Family:Mevalonate kinase 47 c3ceuA_ not modelled 7.8 8 PDB header:transferase Chain: A: PDB Molecule:thiamine phosphate pyrophosphorylase; PDBTitle: crystal structure of thiamine phosphate pyrophosphorylase2 (bt_0647) from bacteroides thetaiotaomicron. northeast3 structural genomics consortium target btr268 48 d1wyka_ not modelled 7.8 43 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 49 d1vcpa_ not modelled 7.7 48 Fold:Trypsin-like serine proteases Superfamily:Trypsin-like serine proteases Family:Viral proteases 50 d2f06a1 not modelled 7.5 10 Fold:Ferredoxin-like Superfamily:ACT-like Family:BT0572-like 51 c3zvrA_ not modelled 6.9 27 PDB header:hydrolase Chain: A: PDB Molecule:dynamin-1; PDBTitle: crystal structure of dynamin 52 d1ufza_ not modelled 6.9 14 Fold:RuvA C-terminal domain-like Superfamily:HBS1-like domain Family:HBS1-like domain 53 c3grzA_ not modelled 6.1 10 PDB header:transferase Chain: A: PDB Molecule:ribosomal protein l11 methyltransferase; PDBTitle: crystal structure of ribosomal protein l11 methylase from2 lactobacillus delbrueckii subsp. bulgaricus 54 d2g1da1 not modelled 6.0 12 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:Ribosomal protein S24e 55 d1whza_ not modelled 5.9 18 Fold:dsRBD-like Superfamily:YcfA/nrd intein domain Family:YcfA-like 56 d1ul7a_ not modelled 5.7 21 Fold:TBP-like Superfamily:KA1-like Family:Kinase associated domain 1, KA1 57 c2vldA_ not modelled 5.5 50 PDB header:hydrolase Chain: A: PDB Molecule:upf0286 protein pyrab01260; PDBTitle: crystal structure of a repair endonuclease from pyrococcus2 abyssi 58 c3ebhA_ not modelled 5.4 15 PDB header:hydrolase inhibitor Chain: A: PDB Molecule:m1 family aminopeptidase; PDBTitle: structure of the m1 alanylaminopeptidase from malaria complexed with2 bestatin 59 d2v94a1 not modelled 5.3 8 Fold:Ribosomal proteins S24e, L23 and L15e Superfamily:Ribosomal proteins S24e, L23 and L15e Family:Ribosomal protein S24e 60 c2o01J_ not modelled 5.3 36 PDB header:photosynthesis Chain: J: PDB Molecule:photosystem i reaction center subunit ix; PDBTitle: the structure of a plant photosystem i supercomplex at 3.42 angstrom resolution 61 d1d02a_ not modelled 5.2 30 Fold:Restriction endonuclease-like Superfamily:Restriction endonuclease-like Family:Restriction endonuclease MunI

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