MolNFT v1 · #72550 · protein
Crystal structure of the HIV-1 rev nes-CRM1-rangtp nuclear export complex (crystal I)
3NBZ · Exportin-1: “Crystal structure of the HIV-1 rev nes-CRM1-rangtp nuclear export complex (crystal I)”. X-ray diffraction, 3 ligands (GTP, MG, NA), 20 pockets (best druggability 0.85). MolNFT v1 #72550 on GenesisL1: 3D structure…
- PDB
- 3NBZ
- Type
- protein
- Length
- 3,006 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exportin-1; Snurportin-1; GTP-binding nuclear protein ran
- UniProt
- Q6P5F9, O95149, P62826
- Ligands
- GTP, MG, NA
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 51% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Exportin-1 | protein | 1038 | 73% helix, 1% strand | Q6P5F9 |
| B | Snurportin-1 | protein | 291 | 17% helix, 26% strand | O95149 |
| C, F | GTP-binding nuclear protein ran | protein | 173 | 25% helix, 27% strand | P62826 |
| E | Snurportin-1 | protein | 293 | 19% helix, 25% strand | O95149 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, F
- MG · Magnesium ion · metal · 2 copies · chains C, F
- NA · Sodium ion · metal · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1089 | 0.85 | 0.85 | 103 | GTP, MG |
| 2 | 972 | 0.84 | 0.85 | 94 | empty |
| 3 | 996 | 0.83 | 0.84 | 112 | empty |
| 4 | 820 | 0.82 | 0.85 | 78 | empty |
| 5 | 679 | 0.81 | 0.86 | 71 | empty |
Interfaces
6 interfaces between chains.
- D–E · 2460 Ų buried · 24 hydrogen bonds · protein-protein
- D–F · 2371 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 2312 Ų buried · 17 hydrogen bonds · protein-protein
- A–C · 2237 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 570 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 3NBZ · Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal I) · the same entry in another collection · chain F against F, TM-score 1.00
- Q6P5F9 · AlphaFold monomer V2.0 prediction for exportin-1 (Q6P5F9) · a predicted model of the same protein · chain A against A, TM-score 0.94
- O95149 · AlphaFold monomer V2.0 prediction for snurportin-1 (O95149) · a predicted model of the same protein · chain E against A, TM-score 0.92
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 Q6P5F9
- Every structure of UniProt O95149
- Every structure of UniProt P62826
- Elsewhere: RCSB PDB 3NBZ · PDBe 3NBZ · UniProt Q6P5F9 · UniProt O95149 · UniProt P62826
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