Research workbench
Crystal structure of the nuclear export complex CRM1-SNURPORTIN1- rangtp
Analyse Crystal structure of the nuclear export complex CRM1-SNURPORTIN1- rangtp in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GJX
- Type
- protein
- Length
- 2,977 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, NA, MG, CL
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 54% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Snurportin-1 | protein | 274 | 23% helix, 27% strand | O95149 |
| C, F | GTP-binding nuclear protein ran | protein | 171 | 29% helix, 27% strand | P62826 |
| A, D | Exportin-1 | protein | 1041 | 74% helix, 1% strand | Q6P5F9 |
| E | Snurportin-1 | protein | 279 | 23% helix, 27% strand | O95149 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, F
- NA · Sodium ion · metal · 2 copies · chains B, E
- MG · Magnesium ion · metal · 2 copies · chains C, F
- CL · Chloride ion · ion · chains E, 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, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1174 | 0.86 | 0.87 | 154 | GTP |
| 2 | 571 | 0.83 | 0.89 | 102 | GTP, MG |
| 3 | 465 | 0.82 | 0.89 | 53 | empty |
| 4 | 1179 | 0.81 | 0.82 | 101 | empty |
| 5 | 782 | 0.80 | 0.84 | 76 | empty |
Interfaces
6 interfaces between chains.
- E–D · 2477 Ų buried · 28 hydrogen bonds · protein-protein
- B–A · 2386 Ų buried · 20 hydrogen bonds · protein-protein
- F–D · 2348 Ų buried · 23 hydrogen bonds · protein-protein
- C–A · 2301 Ų buried · 23 hydrogen bonds · protein-protein
- A–D · 544 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 3GJX · Crystal Structure of the Nuclear Export Complex CRM1-Snurportin1-RanGTP · 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 B against A, TM-score 0.94
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 3GJX · PDBe 3GJX · UniProt O95149 · UniProt P62826 · UniProt Q6P5F9
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