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Crystal structure of the PDZ tandem of human syntenin in complex with tnefaf peptide

Analyse Crystal structure of the PDZ tandem of human syntenin in complex with tnefaf… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1W9Q
Type: protein
Length: 331 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Syntenin 1; Tnefaf peptide
UniProt: O00560
Ligands: BEZ
Pockets: 1 · best druggability 0.30

Structure

x-ray diffraction · 2 distinct chains · 17% helix, 39% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Syntenin 1	protein	163	17% helix, 39% strand	O00560
S	Tnefaf peptide	protein	5	0% helix, 40% strand	—

Ligands and binding sites

BEZ · Benzoic acid · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	62	0.30	0.74	13	empty

Interfaces

2 interfaces between chains.

A–B · 1060 Å² buried · 14 hydrogen bonds · protein-protein
B–S · 431 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

1W9Q · Crystal structure of the PDZ tandem of human syntenin in complex with TNEFAF peptide · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt O00560
Elsewhere: RCSB PDB 1W9Q · PDBe 1W9Q · UniProt O00560

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