Research workbench
Crystal structure of kpt-330 bound to CRM1 (E582K, 537-dltvk-541 to glceq)
Analyse Crystal structure of kpt-330 bound to CRM1 (E582K, 537-dltvk-541 to glceq) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XJS
- Type
- protein
- Length
- 1,342 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein ran; Ran-specific GTPase-activating protein 1; Exportin-1
- UniProt
- P62826, P41920, P30822
- Ligands
- GNP, V6A, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 208 | 30% helix, 22% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 123 | 15% helix, 50% strand | P41920 |
| C | Exportin-1 | protein | 1011 | 78% helix, 1% strand | P30822 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- V6A · selinexor, bound form · ligand · chains C
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 829 | 0.85 | 0.88 | 122 | empty |
| 2 | 635 | 0.75 | 0.81 | 75 | empty |
| 3 | 681 | 0.65 | 0.75 | 54 | empty |
| 4 | 128 | 0.64 | 0.87 | 29 | GNP, MG |
| 5 | 123 | 0.57 | 0.84 | 19 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2095 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2077 Ų buried · 34 hydrogen bonds · protein-protein
- B–C · 190 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XJS · Crystal Structure of KPT-330 bound to CRM1 (E582K, 537-DLTVK-541 to GLCEQ) · the same entry in another collection · chain A against A, TM-score 1.00
- P41920 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 1 (P41920) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P62826
- Every structure of UniProt P41920
- Every structure of UniProt P30822
- Elsewhere: RCSB PDB 6XJS · PDBe 6XJS · UniProt P62826 · UniProt P41920 · UniProt P30822
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