MolNFT v1 · #183495 · protein
Catalytic module of yeast chelator-gid SR4 E3 ubiquitin ligase
7NS4 · E3 ubiquitin-protein ligase RMD5: “Catalytic module of yeast chelator-gid SR4 E3 ubiquitin ligase”. Electron microscopy, 1 ligand (ZN), 10 pockets (best druggability 0.75). MolNFT v1 #183495 on GenesisL1: 3D structure, binding sites…
- PDB
- 7NS4
- Type
- protein
- Length
- 698 residues
- Chains
- 2
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase RMD5; Protein FYV10
- EC
- 2.3.2.27
- UniProt
- Q12508, P40492
- Ligands
- ZN
- Pockets
- 10 · best druggability 0.75
Structure
electron microscopy · 2 distinct chains · 57% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| b | E3 ubiquitin-protein ligase RMD5 (EC 2.3.2.27) | protein | 340 | 54% helix, 4% strand | Q12508 |
| i | Protein FYV10 (EC 2.3.2.27) | protein | 358 | 59% helix, 3% strand | P40492 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains b, i
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.75 | 0.97 | 25 | empty |
| 2 | 900 | 0.72 | 0.76 | 105 | empty |
| 3 | 58 | 0.65 | 0.93 | 15 | empty |
| 4 | 109 | 0.55 | 0.83 | 21 | empty |
| 5 | 198 | 0.47 | 0.75 | 34 | empty |
Interfaces
1 interface between chains.
- b–i · 6592 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 7NS4 · Catalytic module of yeast Chelator-GID SR4 E3 ubiquitin ligase · the same entry in another collection · chain b against b, TM-score 1.00
- P40492 · AlphaFold monomer V2.0 prediction for protein FYV10 (P40492) · a predicted model of the same protein · chain i against A, TM-score 0.86
- Q12508 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase RMD5 (Q12508) · a predicted model of the same protein · chain b against A, TM-score 0.56
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 Q12508
- Every structure of UniProt P40492
- Elsewhere: RCSB PDB 7NS4 · PDBe 7NS4 · UniProt Q12508 · UniProt P40492
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