MolNFT v1 · #191174 · protein
TRIM7 pryspry in complex with a MNV1-NS6 peptide lealefq
8A5M · E3 ubiquitin-protein ligase TRIM7: “TRIM7 pryspry in complex with a MNV1-NS6 peptide lealefq”. X-ray diffraction, 1 ligand (PO4), 4 pockets (best druggability 0.54). MolNFT v1 #191174 on GenesisL1: 3D structure, binding sites and…
- PDB
- 8A5M
- Type
- protein
- Length
- 352 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase TRIM7; MNV1-NS6 peptide lealefq
- EC
- 2.3.2.27
- UniProt
- Q9C029
- Ligands
- PO4
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27) | protein | 171 | 2% helix, 43% strand | Q9C029 |
| B | E3 ubiquitin-protein ligase TRIM7 (EC 2.3.2.27) | protein | 168 | 2% helix, 42% strand | Q9C029 |
| C | MNV1-NS6 peptide lealefq | protein | 6 | 67% helix, 0% strand | — |
| E | MNV1-NS6 peptide lealefq | protein | 7 | 57% helix, 0% strand | — |
Ligands and binding sites
- PO4 · Phosphate ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 105 | 0.54 | 0.83 | 22 | empty |
| 2 | 184 | 0.46 | 0.75 | 25 | PO4 |
| 3 | 110 | 0.37 | 0.74 | 22 | empty |
| 4 | 50 | 0.29 | 0.76 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–C · 402 Ų buried · 7 hydrogen bonds · protein-protein
- B–E · 386 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 348 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 8A5M · TRIM7 PRYSPRY in complex with a MNV1-NS6 peptide LEALEFQ · the same entry in another collection · chain A against A, TM-score 1.00
- Q9C029 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase TRIM7 (Q9C029) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9C029
- Elsewhere: RCSB PDB 8A5M · PDBe 8A5M · UniProt Q9C029
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