MolNFT v1 · #113551 · protein
A complex of of RNF4-ring domain, UBEV2, UBC13-ub (isopeptide crosslink)
5AIT · E3 ubiquitin-protein ligase RNF4: “A complex of of RNF4-ring domain, UBEV2, UBC13-ub (isopeptide crosslink)”. X-ray diffraction, 1 ligand (ZN), 14 pockets (best druggability 0.72). MolNFT v1 #113551 on GenesisL1: 3D structure…
- PDB
- 5AIT
- Type
- protein
- Length
- 851 residues
- Chains
- 7
- 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, P0CH28, Q15819
- Ligands
- ZN
- Pockets
- 14 · best druggability 0.72
Structure
x-ray diffraction · 5 distinct chains · 27% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF4 (EC 6.3.2.-) | protein | 129 | 26% helix, 27% strand | O88846 |
| B, E | Ubiquitin-conjugating enzyme E2 N (EC 6.3.2.19) | protein | 147 | 36% helix, 18% strand | P61088 |
| C, F | Polyubiquitin-C | protein | 75 | 20% helix, 31% strand | P0CH28 |
| D | Ubiquitin-conjugating enzyme E2 variant 2 | protein | 140 | 25% helix, 20% strand | Q15819 |
| G | Ubiquitin-conjugating enzyme E2 variant 2 | protein | 138 | 25% helix, 20% strand | Q15819 |
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
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 179 | 0.72 | 0.89 | 31 | empty |
| 2 | 215 | 0.52 | 0.77 | 21 | empty |
| 3 | 194 | 0.52 | 0.77 | 28 | empty |
| 4 | 80 | 0.46 | 0.81 | 19 | empty |
| 5 | 167 | 0.46 | 0.76 | 27 | empty |
Interfaces
7 interfaces between chains.
- B–C · 938 Ų buried · 9 hydrogen bonds · protein-protein
- E–G · 738 Ų buried · 4 hydrogen bonds · protein-protein
- B–D · 709 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 549 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 506 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 5AIT · A complex of of RNF4-RING domain, UbeV2, Ubc13-Ub (isopeptide crosslink) · the same entry in another collection · chain G against G, 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
- Q15819 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 variant 2 (Q15819) · a predicted model of the same protein · chain D against A, TM-score 0.98
- P0CH28 · AlphaFold monomer V2.0 prediction for polyubiquitin-C (P0CH28) · a predicted model of the same protein · chain C against A, TM-score 0.90
- 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 P0CH28
- Every structure of UniProt Q15819
- Elsewhere: RCSB PDB 5AIT · PDBe 5AIT · UniProt O88846 · UniProt P61088 · UniProt P0CH28 · UniProt Q15819
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