MolNFT v1 · #184227 · protein
Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized
7OIK · E3 ubiquitin-protein ligase RNF213: “Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized”. Electron microscopy, 3 ligands (ATP, ZN, MG), 20 pockets (best druggability 0.83). MolNFT v1 #184227 on GenesisL1: 3D…
- PDB
- 7OIK
- Type
- protein
- Length
- 4,579 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RNF213; Ubiquitin-conjugating enzyme E2 L3
- EC
- 2.3.2.27, 3.6.4.-, 2.3.2.23
- UniProt
- E9Q555, P68036
- Ligands
- ATP, ZN, MG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 2 distinct chains · 52% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase RNF213 (EC 2.3.2.27, 3.6.4.-) | protein | 4426 | 52% helix, 6% strand | E9Q555 |
| B | Ubiquitin-conjugating enzyme E2 L3 (EC 2.3.2.23) | protein | 153 | 37% helix, 17% strand | P68036 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · chains A
- ZN · Zinc ion · metal · 2 copies · chains A
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1057 | 0.83 | 0.84 | 95 | empty |
| 2 | 788 | 0.81 | 0.84 | 83 | empty |
| 3 | 1024 | 0.80 | 0.81 | 134 | empty |
| 4 | 1051 | 0.80 | 0.81 | 98 | empty |
| 5 | 879 | 0.79 | 0.82 | 93 | empty |
Interfaces
1 interface between chains.
- A–B · 738 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7OIK · Mouse RNF213:UBE2L3 transthiolation intermediate, chemically stabilized · 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 B against A, TM-score 0.98
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 E9Q555
- Every structure of UniProt P68036
- Elsewhere: RCSB PDB 7OIK · PDBe 7OIK · UniProt E9Q555 · UniProt P68036
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