MolNFT v1 · #85856 · protein
RNF4 - UBCH5A - ubiquitin heterotrimeric complex
4AP4 · E3 ubiquitin ligase RNF4: “RNF4 - UBCH5A - ubiquitin heterotrimeric complex”. X-ray diffraction, 1 ligand (ZN), 7 pockets (best druggability 0.75). MolNFT v1 #85856 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4AP4
- Type
- protein
- Length
- 580 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin ligase RNF4; Ubiquitin-conjugating enzyme E2 D1; Ubiquitin C
- EC
- 6.3.2.-, 6.3.2.19
- UniProt
- O88846, P51668, F5H7Y5
- Ligands
- ZN
- Pockets
- 7 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 31% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin ligase RNF4 (EC 6.3.2.-) | protein | 129 | 26% helix, 24% strand | O88846 |
| B | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 151 | 36% helix, 18% strand | P51668 |
| C | Ubiquitin C | protein | 76 | 24% helix, 34% strand | F5H7Y5 |
| E | Ubiquitin-conjugating enzyme E2 D1 (EC 6.3.2.19) | protein | 147 | 36% helix, 18% strand | P51668 |
| F | Ubiquitin C | protein | 77 | 23% helix, 36% strand | F5H7Y5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 417 | 0.75 | 0.85 | 66 | empty |
| 2 | 476 | 0.74 | 0.83 | 64 | empty |
| 3 | 56 | 0.40 | 0.81 | 17 | empty |
| 4 | 77 | 0.36 | 0.77 | 19 | empty |
| 5 | 91 | 0.35 | 0.75 | 17 | empty |
Interfaces
6 interfaces between chains.
- E–F · 947 Ų buried · 19 hydrogen bonds · protein-protein
- B–C · 931 Ų buried · 18 hydrogen bonds · protein-protein
- A–B · 610 Ų buried · 6 hydrogen bonds · protein-protein
- A–F · 513 Ų buried · 6 hydrogen bonds · protein-protein
- A–E · 501 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 4AP4 · Rnf4 - ubch5a - ubiquitin heterotrimeric complex · the same entry in another collection · chain C against C, TM-score 1.00
- P51668 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D1 (P51668) · a predicted model of the same protein · chain E against A, TM-score 0.97
- O88846 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF4 (O88846) · a predicted model of the same protein · chain A against A, TM-score 0.49
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 O88846
- Every structure of UniProt P51668
- Every structure of UniProt F5H7Y5
- Elsewhere: RCSB PDB 4AP4 · PDBe 4AP4 · UniProt O88846 · UniProt P51668 · UniProt F5H7Y5
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