MolNFT v1 · #102818 · protein
Crystal structure of xiap BIR1 domain
4OXC · E3 ubiquitin-protein ligase xiap: “Crystal structure of xiap BIR1 domain”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.32). MolNFT v1 #102818 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4OXC
- Type
- protein
- Length
- 310 residues
- Chains
- 4
- 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
- ZN
- Pockets
- 1 · best druggability 0.32
Structure
x-ray diffraction · 2 distinct chains · 26% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 78 | 24% helix, 10% strand | P98170 |
| B, D | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 77 | 27% helix, 10% strand | P98170 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
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 | 71 | 0.32 | 0.75 | 20 | empty |
Interfaces
5 interfaces between chains.
- B–D · 556 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 515 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 345 Ų buried · 1 hydrogen bond · protein-protein
- A–B · 109 Ų buried · 0 hydrogen bonds · protein-protein
- C–D · 62 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 4OXC · Crystal structure of XIAP BIR1 domain · 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 4OXC · PDBe 4OXC · UniProt P98170
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