Research workbench
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
- 4WVT
- Type
- protein
- Length
- 168 residues
- Chains
- 4
- 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
- 3V7, ZN
- Pockets
- 1 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 32% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 79 | 34% helix, 11% strand | P98170 |
| C, D | 3,11-difluoro-6,8,13-trimethyl-8H-QUINO[4,3,2-KL]ACRIDIN- 13-ium | protein | 5 | 0% helix, 60% strand | — |
Ligands and binding sites
- 3V7 · 3-[4-(hydroxymethyl)-1H-1,2,3-triazol-1-yl]propan-1-ol · ligand · 2 copies · chains C, A, D
- 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, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 215 | 0.49 | 0.75 | 26 | 3V7 |
Interfaces
4 interfaces between chains.
- B–D · 393 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 389 Ų buried · 9 hydrogen bonds · protein-protein
- A–D · 107 Ų buried · 0 hydrogen bonds · protein-protein
- A–B · 82 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 covalent, 2 modified (covalent ligand, nonstandard).
Compared structures
- 4WVT · Crystal structure of XIAP-BIR2 domain complexed with ligand bound · 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 4WVT · PDBe 4WVT · UniProt P98170
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