MolNFT v1 · #98778 · protein
Crystal structure of the catalytic core of E3 ligase hoip
4LJQ · E3 ubiquitin-protein ligase RNF31: “Crystal structure of the catalytic core of E3 ligase hoip”. X-ray diffraction, 1 ligand (ZN), 10 pockets (best druggability 0.83). MolNFT v1 #98778 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4LJQ
- Type
- protein
- Length
- 764 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31
- EC
- 6.3.2.-
- UniProt
- Q96EP0
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 4 distinct chains · 33% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 192 | 30% helix, 9% strand | Q96EP0 |
| A | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 190 | 35% helix, 9% strand | Q96EP0 |
| C | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 192 | 34% helix, 9% strand | Q96EP0 |
| D | E3 ubiquitin-protein ligase RNF31 (EC 6.3.2.-) | protein | 190 | 34% helix, 9% strand | Q96EP0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 18 copies · chains B, C, A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1087 | 0.83 | 0.83 | 98 | empty |
| 2 | 728 | 0.72 | 0.78 | 69 | empty |
| 3 | 431 | 0.68 | 0.80 | 47 | empty |
| 4 | 437 | 0.67 | 0.79 | 32 | empty |
| 5 | 368 | 0.58 | 0.75 | 30 | empty |
Interfaces
3 interfaces between chains.
- B–C · 954 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 444 Ų buried · 7 hydrogen bonds · protein-protein
- B–A · 441 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 1 disulfide (engineered, disulfide).
Compared structures
- 4LJQ · Crystal structure of the catalytic core of E3 ligase HOIP · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.95
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
- Elsewhere: RCSB PDB 4LJQ · PDBe 4LJQ · UniProt Q96EP0
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