MolNFT v1 · #97696 · protein

Structure of xiap-BIR3 and inhibitor

4KMP · E3 ubiquitin-protein ligase xiap: “Structure of xiap-BIR3 and inhibitor”. X-ray diffraction, 2 ligands (GT6, ZN), 1 pocket (best druggability 0.61). MolNFT v1 #97696 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4KMP
Type: protein
Length: 196 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: E3 ubiquitin-protein ligase xiap
EC: 6.3.2.-
UniProt: P98170
Ligands: GT6, ZN
Pockets: 1 · best druggability 0.61

Structure

x-ray diffraction · 1 distinct chain · 43% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	E3 ubiquitin-protein ligase xiap (EC 6.3.2.-)	protein	98	43% helix, 8% strand	P98170

Ligands and binding sites

GT6 · (2S,2'S)-N,N'-[(6,6'-difluoro-1H,1'H-2,2'-biindole-3,3'-diyl)bis{methanediyl[(2R,4S)-4-hydroxypyrrolidine-2,1-diyl][(2S)-1-oxobutane-1,2-diyl]}]bis[2-(methylamino)propanamide] · ligand · chains A, B
ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	419	0.61	0.76	41	GT6

Interfaces

1 interface between chains.

A–B · 224 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

4KMP · Structure of XIAP-BIR3 and inhibitor · 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 P98170
Elsewhere: RCSB PDB 4KMP · PDBe 4KMP · UniProt P98170

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