Research workbench
Crystal structure of the HIV-1 rev nes-CRM1-rangtp nuclear export complex (crystal II)
Analyse Crystal structure of the HIV-1 rev nes-CRM1-rangtp nuclear export complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3NC0
- Type
- protein
- Length
- 3,012 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, IPH, MG
- Pockets
- 20 · best druggability 0.87
Structure
x-ray diffraction · 5 distinct chains · 57% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exportin-1 | protein | 1038 | 71% helix, 1% strand | Q6P5F9 |
| B | Snurportin-1 | protein | 293 | 16% helix, 25% strand | O95149 |
| C, F | GTP-binding nuclear protein ran | protein | 173 | 25% helix, 28% strand | P62826 |
| D | Exportin-1 | protein | 1041 | 72% helix, 1% strand | Q6P5F9 |
| E | Snurportin-1 | protein | 294 | 17% helix, 25% strand | O95149 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, F
- IPH · Phenol · ligand · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains C, F
- PEG · Di(hydroxyethyl)ether · additive · 12 copies · chains A, B, C, D, F
- GOL · Glycerol · additive · 10 copies · chains A, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 972 | 0.87 | 0.88 | 136 | empty |
| 2 | 1101 | 0.86 | 0.87 | 137 | GTP, MG, PEG |
| 3 | 1071 | 0.84 | 0.85 | 98 | empty |
| 4 | 1079 | 0.83 | 0.84 | 120 | PEG |
| 5 | 733 | 0.83 | 0.86 | 65 | GOL |
Interfaces
7 interfaces between chains.
- D–E · 2480 Ų buried · 21 hydrogen bonds · protein-protein
- D–F · 2361 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2336 Ų buried · 16 hydrogen bonds · protein-protein
- A–C · 2285 Ų buried · 24 hydrogen bonds · protein-protein
- A–D · 537 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3NC0 · Crystal structure of the HIV-1 Rev NES-CRM1-RanGTP nuclear export complex (crystal II) · 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 0.95
- 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 3NC0 · PDBe 3NC0 · UniProt Q6P5F9 · UniProt O95149 · UniProt P62826
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