MolNFT v1 · #72549 · protein
Crystal structure of the pki nes-CRM1-rangtp nuclear export complex
3NBY · Snurportin-1: “Crystal structure of the pki nes-CRM1-rangtp nuclear export complex”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.86). MolNFT v1 #72549 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3NBY
- Type
- protein
- Length
- 2,973 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Snurportin-1; GTP-binding nuclear protein ran; Exportin-1
- UniProt
- O95149, P62826, Q6P5F9
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 50% helix, 11% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Snurportin-1 | protein | 272 | 19% helix, 26% strand | O95149 |
| C, F | GTP-binding nuclear protein ran | protein | 171 | 27% helix, 26% strand | P62826 |
| A, D | Exportin-1 | protein | 1041 | 71% helix, 1% strand | Q6P5F9 |
| E | Snurportin-1 | protein | 277 | 18% helix, 27% 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1099 | 0.86 | 0.87 | 112 | MG, GTP |
| 2 | 1172 | 0.86 | 0.87 | 113 | GTP, MG |
| 3 | 995 | 0.81 | 0.82 | 93 | empty |
| 4 | 804 | 0.80 | 0.83 | 78 | empty |
| 5 | 866 | 0.80 | 0.82 | 96 | empty |
Interfaces
6 interfaces between chains.
- E–D · 2466 Ų buried · 29 hydrogen bonds · protein-protein
- B–A · 2421 Ų buried · 29 hydrogen bonds · protein-protein
- F–D · 2361 Ų buried · 29 hydrogen bonds · protein-protein
- C–A · 2330 Ų buried · 25 hydrogen bonds · protein-protein
- A–D · 552 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3NBY · Crystal structure of the PKI NES-CRM1-RanGTP nuclear export complex · the same entry in another collection · chain D against D, 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 0.93
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 O95149
- Every structure of UniProt P62826
- Every structure of UniProt Q6P5F9
- Elsewhere: RCSB PDB 3NBY · PDBe 3NBY · UniProt O95149 · UniProt P62826 · UniProt Q6P5F9
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