MolNFT v1 · #33440 · protein
RING1B-BMI1 E3 catalytic domain structure
2CKL · Polycomb group ring finger protein 4: “RING1B-BMI1 E3 catalytic domain structure”. X-ray diffraction, 2 ligands (ZN, IOD), 2 pockets (best druggability 0.49). MolNFT v1 #33440 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 2CKL
- Type
- protein
- Length
- 194 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Polycomb group ring finger protein 4; Ubiquitin ligase protein RING2
- EC
- 6.3.2.-
- UniProt
- P25916, Q9CQJ4
- Ligands
- ZN, IOD
- Pockets
- 2 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Polycomb group ring finger protein 4 | protein | 98 | 45% helix, 16% strand | P25916 |
| B | Ubiquitin ligase protein RING2 (EC 6.3.2.-) | protein | 96 | 32% helix, 17% strand | Q9CQJ4 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 83 | 0.49 | 0.83 | 18 | empty |
| 2 | 52 | 0.32 | 0.77 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 2327 Ų buried · 39 hydrogen bonds · protein-protein
Compared structures
- 2CKL · Ring1b-Bmi1 E3 catalytic domain structure · the same entry in another collection · chain A against A, TM-score 1.00
- P25916 · AlphaFold monomer V2.0 prediction for polycomb complex protein bmi-1 (P25916) · a predicted model of the same protein · chain A against A, TM-score 0.99
- Q9CQJ4 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RING2 (Q9CQJ4) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 P25916
- Every structure of UniProt Q9CQJ4
- Elsewhere: RCSB PDB 2CKL · PDBe 2CKL · UniProt P25916 · UniProt Q9CQJ4
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