MolNFT v1 · #189275 · protein
Crystal structure of UBE2L3 bound to hoip RING1 domain.
7V8F · E3 ubiquitin-protein ligase RNF31: “Crystal structure of UBE2L3 bound to hoip RING1 domain.”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.39). MolNFT v1 #189275 on GenesisL1: 3D structure, binding sites and…
- PDB
- 7V8F
- Type
- protein
- Length
- 255 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF31; Ubiquitin-conjugating enzyme E2 L3
- EC
- 2.3.2.31, 2.3.2.23
- UniProt
- Q96EP0, P68036
- Ligands
- ZN
- Pockets
- 1 · best druggability 0.39
Structure
x-ray diffraction · 2 distinct chains · 42% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | E3 ubiquitin-protein ligase RNF31 (EC 2.3.2.31) | protein | 101 | 50% helix, 10% strand | Q96EP0 |
| A | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 154 | 36% helix, 18% strand | P68036 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains B, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.39 | 0.74 | 28 | empty |
Interfaces
1 interface between chains.
- B–A · 589 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 7V8F · Crystal structure of UBE2L3 bound to HOIP RING1 domain. · the same entry in another collection · chain B against B, TM-score 1.00
- P68036 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 L3 (P68036) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q96EP0 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF31 (Q96EP0) · a predicted model of the same protein · chain B 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 P68036
- Elsewhere: RCSB PDB 7V8F · PDBe 7V8F · UniProt Q96EP0 · UniProt P68036
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