Research workbench
Inhibitor compound-induced confrontational change in RING1B-BMI1 domain structure
Analyse Inhibitor compound-induced confrontational change in RING1B-BMI1 domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6WI8
- Type
- protein
- Length
- 399 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RING2,POLYCOMB complex protein bmi-1 chimera
- EC
- 5.-.-.-
- UniProt
- X6RFN3, P35226
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 31% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RING2,POLYCOMB complex protein bmi-1 chimera (EC 5.-.-.-) | protein | 200 | 32% helix, 19% strand | X6RFN3, P35226 |
| B | E3 ubiquitin-protein ligase RING2,POLYCOMB complex protein bmi-1 chimera (EC 5.-.-.-) | protein | 199 | 30% helix, 19% strand | X6RFN3, P35226 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 461 | 0.73 | 0.83 | 34 | empty |
| 2 | 106 | 0.58 | 0.85 | 19 | empty |
| 3 | 97 | 0.53 | 0.83 | 20 | empty |
| 4 | 70 | 0.43 | 0.81 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 330 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6WI8 · Inhibitor compound-induced confrontational change in Ring1b-Bmi1 domain structure · the same entry in another collection · chain A against A, TM-score 1.00
- P35226 · AlphaFold monomer V2.0 prediction for polycomb complex protein bmi-1 (P35226) · a predicted model of the same protein · chain B against A, TM-score 0.50
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 X6RFN3
- Every structure of UniProt P35226
- Elsewhere: RCSB PDB 6WI8 · PDBe 6WI8 · UniProt X6RFN3 · UniProt P35226
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