MolNFT v1 · #169903 · protein
Structure of HIV-1 vpr in complex with the human nucleotide excision repair protein HHR23A
6XQI · Protein vpr: “Structure of HIV-1 vpr in complex with the human nucleotide excision repair protein HHR23A”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.61). MolNFT v1 #169903 on GenesisL1: 3D structure, binding…
- PDB
- 6XQI
- Type
- protein
- Length
- 343 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein vpr; UV excision repair protein RAD23 homolog a; Asn-pro-leu-glu-phe-leu
- UniProt
- P12520, P54725
- Ligands
- ZN
- Pockets
- 5 · best druggability 0.61
Structure
x-ray diffraction · 5 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Protein vpr | protein | 62 | 84% helix, 0% strand | P12520 |
| C | Protein vpr | protein | 63 | 79% helix, 0% strand | P12520 |
| D | Protein vpr | protein | 64 | 81% helix, 0% strand | P12520 |
| F, G | UV excision repair protein RAD23 homolog a | protein | 40 | 70% helix, 0% strand | P54725 |
| H, I | Asn-pro-leu-glu-phe-leu | protein | 6 | 0% helix, 0% strand | — |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 169 | 0.61 | 0.84 | 19 | empty |
| 2 | 56 | 0.52 | 0.87 | 18 | empty |
| 3 | 61 | 0.31 | 0.75 | 16 | empty |
| 4 | 56 | 0.31 | 0.76 | 11 | empty |
| 5 | 59 | 0.31 | 0.75 | 15 | empty |
Interfaces
10 interfaces between chains.
- A–B · 923 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 913 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 859 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 700 Ų buried · 8 hydrogen bonds · protein-protein
- D–G · 694 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 6XQI · Structure of HIV-1 Vpr in complex with the human nucleotide excision repair protein hHR23A · the same entry in another collection · chain I against I, TM-score 1.00
- P54725 · AlphaFold monomer V2.0 prediction for UV excision repair protein RAD23 homolog a (P54725) · a predicted model of the same protein · chain F against A, TM-score 0.90
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 P12520
- Every structure of UniProt P54725
- Elsewhere: RCSB PDB 6XQI · PDBe 6XQI · UniProt P12520 · UniProt P54725
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