MolNFT v1 · #106588 · protein
PCGF5-RING1B-UBCH5C complex
4S3O · Ubiquitin-conjugating enzyme E2 D3: “PCGF5-RING1B-UBCH5C complex”. X-ray diffraction, 1 ligand (ZN), 9 pockets (best druggability 0.64). MolNFT v1 #106588 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4S3O
- Type
- protein
- Length
- 690 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D3; E3 ubiquitin-protein ligase RING2; Polycomb group…
- EC
- 6.3.2.19, 6.3.2.-
- UniProt
- P61077, Q99496, Q86SE9
- Ligands
- ZN
- Pockets
- 9 · best druggability 0.64
Structure
x-ray diffraction · 5 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin-conjugating enzyme E2 D3 (EC 6.3.2.19) | protein | 148 | 37% helix, 18% strand | P61077 |
| B | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 105 | 35% helix, 14% strand | Q99496 |
| E | E3 ubiquitin-protein ligase RING2 (EC 6.3.2.-) | protein | 99 | 36% helix, 14% strand | Q99496 |
| C | Polycomb group ring finger protein 5 | protein | 95 | 44% helix, 17% strand | Q86SE9 |
| F | Polycomb group ring finger protein 5 | protein | 95 | 47% helix, 16% strand | Q86SE9 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains B, E, C, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 402 | 0.64 | 0.78 | 56 | empty |
| 2 | 91 | 0.60 | 0.88 | 17 | empty |
| 3 | 212 | 0.50 | 0.76 | 30 | empty |
| 4 | 192 | 0.50 | 0.76 | 25 | empty |
| 5 | 68 | 0.44 | 0.82 | 22 | empty |
Interfaces
5 interfaces between chains.
- B–C · 2283 Ų buried · 26 hydrogen bonds · protein-protein
- E–F · 1952 Ų buried · 21 hydrogen bonds · protein-protein
- D–E · 580 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 568 Ų buried · 8 hydrogen bonds · protein-protein
- A–D · 390 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 4S3O · PCGF5-RING1B-UbcH5c complex · the same entry in another collection · chain F against F, TM-score 1.00
- Q99496 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RING2 (Q99496) · 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 0.99
- Q86SE9 · AlphaFold monomer V2.0 prediction for polycomb group ring finger protein 5 (Q86SE9) · 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 P61077
- Every structure of UniProt Q99496
- Every structure of UniProt Q86SE9
- Elsewhere: RCSB PDB 4S3O · PDBe 4S3O · UniProt P61077 · UniProt Q99496 · UniProt Q86SE9
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