Research workbench
Crystal structure of CRM1 inhibitor ratjadone a in complex with CRM1(K579A)-ran-RANBP1
Analyse Crystal structure of CRM1 inhibitor ratjadone a in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HAX
- Type
- protein
- Length
- 1,348 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exportin-1; GTP-binding nuclear protein ran; Ran-specific GTPase-activating protein 1
- UniProt
- P30822, P62826, P41920
- Ligands
- RJA, GNP, MG, CL
- Pockets
- 15 · best druggability 0.86
Structure
x-ray diffraction · 3 distinct chains · 65% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Exportin-1 | protein | 1017 | 78% helix, 1% strand | P30822 |
| A | GTP-binding nuclear protein ran | protein | 200 | 31% helix, 24% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 131 | 15% helix, 47% strand | P41920 |
Ligands and binding sites
- RJA · Ratjadone A, bound form · ligand · chains C
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 3 copies · chains C, A
- GOL · Glycerol · additive · 3 copies · chains C, A
- EDO · 1,2-ethanediol · additive · 3 copies · chains C, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 816 | 0.86 | 0.88 | 110 | GOL, EDO |
| 2 | 632 | 0.73 | 0.80 | 63 | empty |
| 3 | 256 | 0.68 | 0.84 | 41 | empty |
| 4 | 122 | 0.65 | 0.88 | 29 | GNP, MG |
| 5 | 409 | 0.58 | 0.75 | 36 | empty |
Interfaces
3 interfaces between chains.
- C–A · 2240 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2005 Ų buried · 33 hydrogen bonds · protein-protein
- C–B · 265 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4HAX · Crystal structure of CRM1 inhibitor Ratjadone A in complex with CRM1(K579A)-Ran-RanBP1 · the same entry in another collection · chain C against C, TM-score 1.00
- P30822 · AlphaFold monomer V2.0 prediction for exportin-1 (P30822) · a predicted model of the same protein · chain C against A, TM-score 0.99
- 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 0.94
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 P30822
- Every structure of UniProt P62826
- Every structure of UniProt P41920
- Elsewhere: RCSB PDB 4HAX · PDBe 4HAX · UniProt P30822 · UniProt P62826 · UniProt P41920
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