MolNFT v1 · #148139 · protein
Crystal structure of xiap-BIR3 in complex with a CIAP1-selective sm
6EY2 · E3 ubiquitin-protein ligase xiap: “Crystal structure of xiap-BIR3 in complex with a CIAP1-selective sm”. X-ray diffraction, 2 ligands (C3T, ZN), 9 pockets (best druggability 0.79). MolNFT v1 #148139 on GenesisL1: 3D structure…
- PDB
- 6EY2
- Type
- protein
- Length
- 797 residues
- Chains
- 8
- 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
- C3T, ZN
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 5 distinct chains · 47% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, H | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 99 | 47% helix, 8% strand | P98170 |
| B | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 98 | 45% helix, 8% strand | P98170 |
| D, F | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 101 | 47% helix, 8% strand | P98170 |
| E | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 100 | 47% helix, 8% strand | P98170 |
| G | E3 ubiquitin-protein ligase xiap (EC 2.3.2.27) | protein | 100 | 47% helix, 8% strand | P98170 |
Ligands and binding sites
- C3T · (3~{S},6~{S},7~{S},9~{a}~{S})-~{N}-[(4-~{tert}-butylphenyl)methyl]-7-(hydroxymethyl)-6-[[(2~{S})-2-(methylamino)butanoyl]amino]-5-oxidanylidene-1,2,3,6,7,8,9,9~{a}-octahydropyrrolo[1,2-a]azepine-3-carboxamide · ligand · 8 copies · chains A, B, C, G, F, D, E, H
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1124 | 0.79 | 0.81 | 124 | C3T |
| 2 | 486 | 0.73 | 0.82 | 37 | C3T |
| 3 | 402 | 0.73 | 0.83 | 35 | C3T |
| 4 | 678 | 0.70 | 0.78 | 68 | C3T |
| 5 | 468 | 0.69 | 0.79 | 39 | C3T |
Interfaces
13 interfaces between chains.
- E–F · 1029 Ų buried · 16 hydrogen bonds · protein-protein
- C–D · 953 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 902 Ų buried · 18 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 10 hydrogen bonds · protein-protein
- A–G · 449 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6EY2 · Crystal structure of XIAP-BIR3 in complex with a cIAP1-selective SM · the same entry in another collection · chain H against H, TM-score 1.00
- P98170 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase xiap (P98170) · a predicted model of the same protein · chain D against A, TM-score 0.97
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 6EY2 · PDBe 6EY2 · UniProt P98170
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