Research workbench
Crystal structure of xiap-BIR3 in complex with a bivalent compound
Analyse Crystal structure of xiap-BIR3 in complex with a bivalent compound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3G76
- Type
- protein
- Length
- 802 residues
- Chains
- 8
- 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
- CZ3, ZN
- Pockets
- 7 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 97 | 41% helix, 9% strand | P98170 |
| B, D, H | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 105 | 47% helix, 9% strand | P98170 |
| C | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 96 | 41% helix, 9% strand | P98170 |
| E, G | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 95 | 41% helix, 8% strand | P98170 |
| F | Baculoviral iap repeat-containing protein 4 (EC 6.3.2.-) | protein | 104 | 45% helix, 9% strand | P98170 |
Ligands and binding sites
- CZ3 · 1,1'-{hexa-2,4-diyne-1,6-diylbis[oxy{(2S,3R)-2-[(N-methyl-L-alanyl)amino]-1-oxobutane-3,1-diyl}(2S)pyrrolidine-1,2-diylmethanediyl]}bis[5-(phenylsulfanyl)-1H-tetrazole] · ligand · 8 copies · chains A, D, B, C, E, H, F, G
- 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
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 501 | 0.64 | 0.76 | 59 | empty |
| 2 | 447 | 0.61 | 0.76 | 48 | empty |
| 3 | 193 | 0.48 | 0.76 | 29 | empty |
| 4 | 177 | 0.48 | 0.76 | 23 | empty |
| 5 | 167 | 0.46 | 0.76 | 23 | empty |
Interfaces
12 interfaces between chains.
- A–E · 472 Ų buried · 3 hydrogen bonds · protein-protein
- C–G · 445 Ų buried · 3 hydrogen bonds · protein-protein
- G–H · 289 Ų buried · 6 hydrogen bonds · protein-protein
- E–F · 285 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 280 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3G76 · Crystal structure of XIAP-BIR3 in complex with a bivalent compound · 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 C 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 3G76 · PDBe 3G76 · UniProt P98170
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