MolNFT v1 · #108327 · protein
RNF38-UBCH5B-ub complex
4V3K · Ubiquitin-conjugating enzyme E2 D2: “RNF38-UBCH5B-ub complex”. X-ray diffraction, 2 ligands (ZN, CL), 7 pockets (best druggability 0.66). MolNFT v1 #108327 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4V3K
- Type
- protein
- Length
- 591 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ubiquitin-conjugating enzyme E2 D2; Polyubiquitin-C; E3 ubiquitin-protein ligase RNF38
- EC
- 6.3.2.19
- UniProt
- P62837, P0CG48, Q9H0F5
- Ligands
- ZN, CL
- Pockets
- 7 · best druggability 0.66
Structure
x-ray diffraction · 4 distinct chains · 27% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Ubiquitin-conjugating enzyme E2 D2 (EC 6.3.2.19) | protein | 146 | 36% helix, 18% strand | P62837 |
| B, E | Polyubiquitin-C | protein | 77 | 23% helix, 36% strand | P0CG48 |
| C | E3 ubiquitin-protein ligase RNF38 (EC 6.3.2.19) | protein | 75 | 20% helix, 21% strand | Q9H0F5 |
| F | E3 ubiquitin-protein ligase RNF38 (EC 6.3.2.19) | protein | 70 | 21% helix, 23% strand | Q9H0F5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains C, F
- CL · Chloride ion · ion · 6 copies · chains A, D, C
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 610 | 0.66 | 0.76 | 67 | CL |
| 2 | 168 | 0.59 | 0.83 | 28 | empty |
| 3 | 135 | 0.52 | 0.80 | 21 | empty |
| 4 | 126 | 0.40 | 0.75 | 24 | empty |
| 5 | 111 | 0.39 | 0.75 | 14 | empty |
Interfaces
8 interfaces between chains.
- D–E · 945 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 871 Ų buried · 20 hydrogen bonds · protein-protein
- A–C · 548 Ų buried · 5 hydrogen bonds · protein-protein
- D–F · 538 Ų buried · 5 hydrogen bonds · protein-protein
- B–C · 437 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 isopeptide (isopeptide).
Compared structures
- 4V3K · RNF38-UbcH5B-UB complex · the same entry in another collection · chain F against F, TM-score 1.00
- P62837 · AlphaFold monomer V2.0 prediction for ubiquitin-conjugating enzyme E2 D2 (P62837) · a predicted model of the same protein · chain A against A, TM-score 0.98
- Q9H0F5 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RNF38 (Q9H0F5) · a predicted model of the same protein · chain F against A, TM-score 0.97
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 P62837
- Every structure of UniProt P0CG48
- Every structure of UniProt Q9H0F5
- Elsewhere: RCSB PDB 4V3K · PDBe 4V3K · UniProt P62837 · UniProt P0CG48 · UniProt Q9H0F5
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