Research workbench
Crystal structure of xiap-BIR2 domain with amrv bound
Analyse Crystal structure of xiap-BIR2 domain with amrv bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J48
- Type
- protein
- Length
- 164 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap; Peptide (ala-met-arg-val)
- EC
- 6.3.2.-
- UniProt
- P98170
- Ligands
- ZN, SO4
- Pockets
- 1 · best druggability 0.43
Structure
x-ray diffraction · 3 distinct chains · 34% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 84 | 35% helix, 11% strand | P98170 |
| C | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 76 | 36% helix, 11% strand | P98170 |
| B | Peptide (ala-met-arg-val) | protein | 4 | 0% helix, 50% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, C
- SO4 · Sulfate ion · ion · chains A, B
- GOL · Glycerol · additive · chains A, C
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 | 113 | 0.43 | 0.77 | 17 | empty |
Interfaces
2 interfaces between chains.
- A–C · 496 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 341 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4J48 · Crystal structure of XIAP-BIR2 domain with AMRV 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 4J48 · PDBe 4J48 · UniProt P98170
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