MolNFT v1 · #77789 · protein
BMI1/RING1B-UBCH5C complex structure
3RPG · Ubiquitin-conjugating enzyme E2 D3: “BMI1/RING1B-UBCH5C complex structure”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.58). MolNFT v1 #77789 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3RPG
- Type
- protein
- Length
- 349 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D3; Polycomb complex protein bmi-1; E3 ubiquitin-protein…
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P61077, P35226, Q99496
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 36% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) | protein | 149 | 37% helix, 18% strand | P61077 |
| B | Polycomb complex protein bmi-1 | protein | 99 | 43% helix, 16% strand | P35226 |
| C | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 101 | 26% helix, 18% strand | Q99496 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 300 | 0.58 | 0.77 | 40 | empty |
| 2 | 101 | 0.55 | 0.84 | 21 | empty |
| 3 | 60 | 0.33 | 0.76 | 20 | empty |
Interfaces
2 interfaces between chains.
- B–C · 2345 Ų buried · 31 hydrogen bonds · protein-protein
- A–C · 653 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 3RPG · Bmi1/Ring1b-UbcH5c complex 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 0.99
- P61077 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D3 (P61077) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q99496 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RING2 (Q99496) · a predicted model of the same protein · chain C against A, TM-score 0.93
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 P61077
- Every structure of UniProt P35226
- Every structure of UniProt Q99496
- Elsewhere: RCSB PDB 3RPG · PDBe 3RPG · UniProt P61077 · UniProt P35226 · UniProt Q99496
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