MolNFT v1 · #82411 · protein
Crystal structure of the human APOBEC3C having HIV-1 vif-binding interface
3VM8 · Probable DNA dc->du-editing enzyme apobec-3C: “Crystal structure of the human APOBEC3C having HIV-1 vif-binding interface”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.68). MolNFT v1 #82411 on GenesisL1: 3D…
- PDB
- 3VM8
- Type
- protein
- Length
- 374 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Probable DNA dc->du-editing enzyme apobec-3C
- EC
- 3.5.4.-
- UniProt
- Q9NRW3
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.68
Structure
x-ray diffraction · 1 distinct chain · 38% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Probable DNA dc->du-editing enzyme apobec-3C (EC 3.5.4.-) | protein | 187 | 38% helix, 22% strand | Q9NRW3 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.68 | 0.80 | 40 | empty |
| 2 | 115 | 0.53 | 0.82 | 24 | empty |
| 3 | 83 | 0.47 | 0.82 | 22 | empty |
| 4 | 53 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 898 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3VM8 · Crystal structure of the human APOBEC3C having HIV-1 Vif-binding interface · the same entry in another collection · chain A against A, TM-score 1.00
- Q9NRW3 · AlphaFold monomer V2.0 prediction for DNA dc->du-editing enzyme apobec-3C (Q9NRW3) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q9NRW3
- Elsewhere: RCSB PDB 3VM8 · PDBe 3VM8 · UniProt Q9NRW3
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