MolNFT v1 · #114198 · protein
Crystal structure of HIV-1 vpr C-terminal domain and dibb-M-importin- ALPHA2 complex
5B56 · Importin subunit alpha-1: “Crystal structure of HIV-1 vpr C-terminal domain and dibb-M-importin- ALPHA2 complex”. X-ray diffraction, 5 pockets (best druggability 0.56). MolNFT v1 #114198 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5B56
- Type
- protein
- Length
- 909 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Importin subunit alpha-1; Protein vpr
- UniProt
- P52293, Q73369
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 72% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Importin subunit alpha-1 | protein | 429 | 74% helix, 0% strand | P52293 |
| B | Importin subunit alpha-1 | protein | 432 | 72% helix, 0% strand | P52293 |
| C, D, E, F | Protein vpr | protein | 12 | 0% helix, 0% strand | Q73369 |
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 | 225 | 0.56 | 0.79 | 27 | empty |
| 2 | 69 | 0.52 | 0.85 | 13 | empty |
| 3 | 75 | 0.47 | 0.82 | 13 | empty |
| 4 | 104 | 0.38 | 0.75 | 19 | empty |
| 5 | 51 | 0.28 | 0.75 | 14 | empty |
Interfaces
7 interfaces between chains.
- A–E · 772 Ų buried · 20 hydrogen bonds · protein-protein
- B–F · 722 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 710 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 684 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 112 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 5B56 · Crystal structure of HIV-1 VPR C-Terminal domain and DIBB-M-Importin-Alpha2 complex · the same entry in another collection · chain A against A, TM-score 1.00
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 P52293
- Every structure of UniProt Q73369
- Elsewhere: RCSB PDB 5B56 · PDBe 5B56 · UniProt P52293 · UniProt Q73369
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