Research workbench
Xiap-BIR3 in complex with a potent divalent smac mimetic
Analyse Xiap-BIR3 in complex with a potent divalent smac mimetic in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4EC4
- Type
- protein
- Length
- 1,067 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Baculoviral iap repeat-containing protein 4
- EC
- 6.3.2.-
- UniProt
- P98170
- Ligands
- 0O6, ZN
- Pockets
- 8 · best druggability 0.67
Structure
x-ray diffraction · 7 distinct chains · 43% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 109 | 43% helix, 7% strand | P98170 |
| B | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 106 | 49% helix, 8% strand | P98170 |
| C, D | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 105 | 40% helix, 8% strand | P98170 |
| E, J | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 108 | 45% helix, 7% strand | P98170 |
| F | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 105 | 45% helix, 8% strand | P98170 |
| G, L | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 107 | 37% helix, 7% strand | P98170 |
| K | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 107 | 40% helix, 7% strand | P98170 |
Ligands and binding sites
- 0O6 · (3S,6S,7S,9aS,3'S,6'S,7'S,9a'S)-N,N'-(benzene-1,4-diylbis{butane-4,1-diyl-1H-1,2,3-triazole-1,4-diyl[(S)-phenylmethanediyl]})bis[7-(hydroxymethyl)-6-{[(2S)-2-(methylamino)butanoyl]amino}-5-oxooctahydro-1H-pyrrolo[1,2-a]azepine-3-carboxamide] · ligand · 5 copies · chains A, F, B, G, D, K, E, L, C, J
- ZN · Zinc ion · metal · 10 copies · chains A, B, C, D, E, J, F, G, K, L
- P33 · 3,6,9,12,15,18-hexaoxaicosane-1,20-diol · additive · 3 copies · chains A, F, D, K, C, J
- 2PE · Nonaethylene glycol · additive · 2 copies · chains E, L, B, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 576 | 0.67 | 0.77 | 55 | 0O6, P33 |
| 2 | 588 | 0.66 | 0.76 | 54 | P33 |
| 3 | 611 | 0.66 | 0.76 | 55 | 0O6, P33 |
| 4 | 615 | 0.65 | 0.76 | 68 | 2PE |
| 5 | 577 | 0.65 | 0.76 | 62 | 0O6, 2PE |
Interfaces
16 interfaces between chains.
- E–L · 810 Ų buried · 10 hydrogen bonds · protein-protein
- A–F · 754 Ų buried · 8 hydrogen bonds · protein-protein
- B–G · 704 Ų buried · 8 hydrogen bonds · protein-protein
- D–K · 679 Ų buried · 11 hydrogen bonds · protein-protein
- C–J · 639 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 4EC4 · XIAP-BIR3 in complex with a potent divalent Smac mimetic · the same entry in another collection · chain L against L, 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 F against A, TM-score 0.94
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 4EC4 · PDBe 4EC4 · UniProt P98170
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