Research workbench
Structure of xiap-BIR1 V86E mutant
Analyse Structure of xiap-BIR1 V86E mutant in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QCI
- Type
- protein
- Length
- 300 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap
- EC
- 2.3.2.27
- UniProt
- P98170
- Ligands
- ZN, NA
- Pockets
- 4 · best druggability 0.48
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 78 | 24% helix, 10% strand | P98170 |
| B | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 77 | 29% helix, 10% strand | P98170 |
| C | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 73 | 36% helix, 11% strand | P98170 |
| D | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 72 | 26% helix, 11% strand | P98170 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
- NA · Sodium ion · metal · 2 copies · chains A, B, C, D
- PEG · Di(hydroxyethyl)ether · additive · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.48 | 0.82 | 28 | empty |
| 2 | 104 | 0.39 | 0.76 | 23 | PEG |
| 3 | 98 | 0.32 | 0.72 | 28 | empty |
| 4 | 56 | 0.30 | 0.76 | 14 | empty |
Interfaces
5 interfaces between chains.
- A–B · 595 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 539 Ų buried · 15 hydrogen bonds · protein-protein
- A–C · 321 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 115 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 63 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6QCI · Structure of XIAP-BIR1 V86E mutant · the same entry in another collection · chain D against D, 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 6QCI · PDBe 6QCI · UniProt P98170
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