MolNFT v1 · #98777 · protein
Structure of an active ligase (hoip-H889A)/UBIQUITIN transfer complex
4LJP · E3 ubiquitin-protein ligase RNF31: “Structure of an active ligase (hoip-H889A)/UBIQUITIN transfer complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.76). MolNFT v1 #98777 on GenesisL1: 3D structure, binding…
- PDB
- 4LJP
- Type
- protein
- Length
- 291 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Polyubiquitin-C
- EC
- 6.3.2.-
- UniProt
- Q96EP0, E1B9K1
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 29% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 215 | 31% helix, 13% strand | Q96EP0 |
| B | Polyubiquitin-C | protein | 76 | 24% helix, 33% strand | E1B9K1 |
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
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 657 | 0.76 | 0.82 | 54 | empty |
| 2 | 217 | 0.67 | 0.85 | 45 | empty |
| 3 | 128 | 0.59 | 0.84 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 845 Ų buried · 14 hydrogen bonds · protein-protein
Compared structures
- 4LJP · Structure of an active ligase (HOIP-H889A)/ubiquitin transfer complex · the same entry in another collection · chain A against A, TM-score 1.00
- Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 Q96EP0
- Every structure of UniProt E1B9K1
- Elsewhere: RCSB PDB 4LJP · PDBe 4LJP · UniProt Q96EP0 · UniProt E1B9K1
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