3DLigandSite

Structural Bioinformatics Group

Division of Molecular Biosciences
Faculty of Natural Sciences

3DLigandSite -Ligand binding site prediction Server

3DLigandSite Results

Submission Successful - Job-id: example4 Current Status: STATUS:finished

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You can bookmark this page: http://www.sbg.bio.imperial.ac.uk/3dligandsite/3dligand_report.cgi?jobid=example4

Please cite: Wass, M.N. and Sternberg, M.J. (2009) Prediction of ligand binding sites using homologous structures and conservation at CASP8, Proteins, 77 Suppl 9:147-51. PubMed

Submission Details
Email:	mw3@ic.ac.uk
Unique Job identifier:	example4
Description:	T0483 example
Date:	Sun Feb 7 12:07:06 GMT 2010
Submission Type:	structure
Query Seq:	GLAACEGEYSQKYSTMSPLGSGAFGFVWTAVDKEKNKEVVVKFIKKEKVL EDCWIEDPKLGKVTLEIAILSRVEHANIIKVLDIFENQGFFQLVMEKHSG LDLFAFIDRHPRLDEPLASYIFRQLVSAVGYLRLKDIIHRDIKDENIVIA EDFTIKLIDFGSAAYLERGKLFYTFCGTIEYCAPEVLMGNPYRGPELEMW SLGVTLYTLVFEENPFCELEETVEAAIHPPYLVSKELMSLVSGLLQPVPE RRTTLEKLVTDPWVTQPVNLADYTWEEVFRVNKPESGVLSAASLEMGNRS LSDVAQAQELCGGE

Structural Model
User provided file:	T0483example.pdb
Structural Search confidence data from search of structural library with Mammoth
Average lnE:	26.6587
Maximum LnE:	28.43
Min LnE:	26.22

Ligand Clusters Identified Note prediction based on first cluster Click on other clusters to view the potential sites associated with them
			MAMMOTH Scores
Cluster	Ligands	Structures	Av	min	max
1	33	23	26.7	26.2	28.4
2	2	2	26.4	26.3	26.5
3	1	1	26.2	26.2	26.2
4	1	1	26.5	26.5	26.5
5	1	1	26.9	26.9	26.9

Predicted Binding Site
Residue	Amino acid	contact	av distance	JS divergence
59	LYS	14	0.00	0.75
61	LYS	13	0.37	0.38
92	ILE	14	0.00	0.54
108	MET	9	0.60	0.60
109	GLU	14	0.00	0.82
110	LYS	14	0.00	0.65
111	HIS	14	0.00	0.53
113	SER	12	0.40	0.48
116	ASP	14	0.23	0.76
159	GLU	30	0.10	0.83
160	ASN	9	0.66	0.87
162	VAL	10	0.49	0.65
172	ILE	19	0.12	0.49
173	ASP	27	0.16	0.85
181	GLU	23	0.20	0.24
182	ARG	28	0.17	0.21
183	GLY	9	0.00	0.35

Heterogens present in Predicted Binding Site
Heterogen	Count	source structures
STU	4	3d7t_B,1snu_B,1sm2_B,3d7t_A
ADP	4	1ol7_A,1mq4_A,3dls_F,1ol5_A
MG	19	2w5b_A,1ol7_A,1mq4_A,1x8b_A,2v7a_B, 2vwy_A,3dls_F,2vwz_A,2gs7_A,2g1t_B, 3is5_A,1ol5_A,2r5t_A
AMP	1	1yxu_C
ATP	5	2biy_A,1h1w_A,1ql6_A,1ol6_A,1phk_A

Structural View of Prediction

Display Modification

Whole protein

Predicted residues

Heterogens

View

Prediction colour legend: Other residues Predicted Binding Site

Conservation Score Colour legend: 0-0.15 0.16-0.30 0.31-0.40 0.41-0.50
0.51-0.60 0.61-0.70 0.71-0.80 0.81-1.00

Mark Wass