Research workbench
Crystal structure of xiap BIR3 with T3256336
Analyse Crystal structure of xiap BIR3 with T3256336 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HY0
- Type
- protein
- Length
- 773 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase xiap
- EC
- 6.3.2.-
- UniProt
- P98170
- Ligands
- 1AQ, ZN
- Pockets
- 6 · best druggability 0.75
Structure
x-ray diffraction · 3 distinct chains · 45% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, E, F, H | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 96 | 45% helix, 8% strand | P98170 |
| C | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 97 | 42% helix, 8% strand | P98170 |
| D, G | E3 ubiquitin-protein ligase xiap (EC 6.3.2.-) | protein | 98 | 49% helix, 8% strand | P98170 |
Ligands and binding sites
- 1AQ · (3S,7R,8aR)-2-{(2S)-2-(4,4-difluorocyclohexyl)-2-[(N-methyl-L-alanyl)amino]acetyl}-N-[(4R)-3,4-dihydro-2H-chromen-4-yl]-7-ethoxyoctahydropyrrolo[1,2-a]pyrazine-3-carboxamide · ligand · 8 copies · chains A, B, D, G, C, H, E, F
- ZN · Zinc ion · metal · 14 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
6 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 662 | 0.75 | 0.81 | 84 | 1AQ |
| 2 | 816 | 0.74 | 0.78 | 79 | 1AQ |
| 3 | 622 | 0.74 | 0.81 | 70 | 1AQ |
| 4 | 333 | 0.62 | 0.78 | 42 | 1AQ |
| 5 | 196 | 0.57 | 0.80 | 31 | empty |
Interfaces
13 interfaces between chains.
- A–B · 952 Ų buried · 19 hydrogen bonds · protein-protein
- D–E · 938 Ų buried · 14 hydrogen bonds · protein-protein
- F–G · 936 Ų buried · 18 hydrogen bonds · protein-protein
- C–H · 897 Ų buried · 19 hydrogen bonds · protein-protein
- B–E · 449 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4HY0 · Crystal structure of XIAP BIR3 with T3256336 · 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 4HY0 · PDBe 4HY0 · UniProt P98170
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