MolNFT v1 · #169673 · protein
Crystal structure of kpt-8602 bound to CRM1 (537-dltvk-541 to glceq)
6XJT · GTP-binding nuclear protein ran: “Crystal structure of kpt-8602 bound to CRM1 (537-dltvk-541 to glceq)”. X-ray diffraction, 3 ligands (GNP, 6L8, MG), 14 pockets (best druggability 0.79). MolNFT v1 #169673 on GenesisL1: 3D structure…
- PDB
- 6XJT
- 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, 6L8, MG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 9% 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, 54% strand | P41920 |
| C | Exportin-1 | protein | 1011 | 78% helix, 1% strand | P30822 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- 6L8 · (2R)-3-{3-[3,5-bis(trifluoromethyl)phenyl]-1H-1,2,4-triazol-1-yl}-2-(pyrimidin-5-yl)propanamide · ligand · chains C
- MG · Magnesium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 415 | 0.79 | 0.88 | 51 | empty |
| 2 | 305 | 0.76 | 0.88 | 52 | empty |
| 3 | 1103 | 0.74 | 0.77 | 97 | empty |
| 4 | 675 | 0.65 | 0.75 | 55 | empty |
| 5 | 131 | 0.63 | 0.86 | 28 | GNP, MG |
Interfaces
3 interfaces between chains.
- A–B · 2097 Ų buried · 32 hydrogen bonds · protein-protein
- A–C · 2086 Ų buried · 27 hydrogen bonds · protein-protein
- B–C · 203 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 6XJT · Crystal Structure of KPT-8602 bound to CRM1 (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 6XJT · PDBe 6XJT · UniProt P62826 · UniProt P41920 · UniProt P30822
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.