MolNFT v1 · #113552 · protein
A complex of RNF4-ring domain, UBC13-ub (isopeptide crosslink)
5AIU · E3 ubiquitin-protein ligase RNF4: “A complex of RNF4-ring domain, UBC13-ub (isopeptide crosslink)”. X-ray diffraction, 1 ligand (ZN), 8 pockets (best druggability 0.73). MolNFT v1 #113552 on GenesisL1: 3D structure, binding sites…
- PDB
- 5AIU
- Type
- protein
- Length
- 575 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF4; Ubiquitin-conjugating enzyme E2 N; Polyubiquitin-C
- EC
- 6.3.2.-, 6.3.2.19
- UniProt
- O88846, P61088, P0CG48
- Ligands
- ZN
- Pockets
- 8 · best druggability 0.73
Structure
x-ray diffraction · 3 distinct chains · 29% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF4 (EC 6.3.2.-) | protein | 123 | 26% helix, 21% strand | O88846 |
| B, E | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 150 | 35% helix, 21% strand | P61088 |
| C, F | Polyubiquitin-C | protein | 76 | 20% helix, 34% strand | P0CG48 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A
- EDO · 1,2-ethanediol · additive · 6 copies · chains A, B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.73 | 0.91 | 27 | EDO |
| 2 | 239 | 0.68 | 0.85 | 37 | empty |
| 3 | 63 | 0.41 | 0.81 | 16 | empty |
| 4 | 67 | 0.38 | 0.78 | 17 | empty |
| 5 | 84 | 0.34 | 0.75 | 15 | empty |
Interfaces
6 interfaces between chains.
- B–C · 967 Ų buried · 19 hydrogen bonds · protein-protein
- E–F · 923 Ų buried · 18 hydrogen bonds · protein-protein
- A–E · 549 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 512 Ų buried · 3 hydrogen bonds · protein-protein
- A–C · 465 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 5AIU · A complex of RNF4-RING domain, Ubc13-Ub (isopeptide crosslink) · the same entry in another collection · chain B against B, TM-score 1.00
- P61088 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 N (P61088) · a predicted model of the same protein · chain B against A, TM-score 0.99
- 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 P61088
- Every structure of UniProt P0CG48
- Elsewhere: RCSB PDB 5AIU · PDBe 5AIU · UniProt O88846 · UniProt P61088 · UniProt P0CG48
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