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Crystal structure of xiap-BIR2 domain complexed with ligand bound

Analyse Crystal structure of xiap-BIR2 domain complexed with ligand bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
4WVU
Type
protein
Length
83 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
E3 ubiquitin-protein ligase xiap; 3,11-difluoro-6,8,13-trimethyl-8H-QUINO[4,3,2-KL]ACRIDIN…
EC
6.3.2.-
UniProt
P98170
Ligands
3V8, ZN, SO4

Structure

x-ray diffraction · 2 distinct chains · 31% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AE3 ubiquitin-protein ligase xiap (EC 6.3.2.-)protein7933% helix, 15% strandP98170
B3,11-difluoro-6,8,13-trimethyl-8H-QUINO[4,3,2-KL]ACRIDIN- 13-iumprotein40% helix, 0% strand—

Ligands and binding sites

  • 3V8 · (4S)-4-[4-(2-carboxyethyl)-1H-1,2,3-triazol-1-yl]-L-proline · ligand · chains A, B
  • ZN · Zinc ion · metal · chains A
  • SO4 · Sulfate ion · ion · chains A
  • GOL · Glycerol · additive · chains A

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

Interfaces

1 interface between chains.

  • A–B · 400 Ų buried · 10 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 3 covalent, 2 modified (covalent ligand, nonstandard).

Compared structures

  • 4WVU · Crystal structure of xiap-BIR2 domain complexed with ligand bound · the same entry in another collection · chain A against A, TM-score 1.00

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