MolNFT v1 · #93723 · protein
Crystal structure of CRM1 inhibitor leptomycin B in complex with CRM1(537DLTVK541/GLCEQ)-ran-RANBP1
4HB4 · GTP-binding nuclear protein ran: “Crystal structure of CRM1 inhibitor leptomycin B in complex with CRM1(537DLTVK541/GLCEQ)-ran-RANBP1”. X-ray diffraction, 4 ligands (GNP, LMB, MG), 15 pockets (best druggability 0.87). MolNFT v1…
- PDB
- 4HB4
- Type
- protein
- Length
- 1,347 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, LMB, MG, CL
- Pockets
- 15 · best druggability 0.87
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 | 209 | 31% helix, 22% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 121 | 16% helix, 50% strand | P41920 |
| C | Exportin-1 | protein | 1017 | 78% helix, 1% strand | P30822 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- LMB · Leptomycin B, bound form · ligand · chains C
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · 4 copies · chains C
- EDO · 1,2-ethanediol · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · chains C
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 | 966 | 0.87 | 0.88 | 121 | EDO |
| 2 | 518 | 0.70 | 0.80 | 55 | empty |
| 3 | 209 | 0.69 | 0.86 | 41 | empty |
| 4 | 137 | 0.63 | 0.86 | 29 | GNP, MG |
| 5 | 420 | 0.59 | 0.75 | 38 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2242 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2064 Ų buried · 30 hydrogen bonds · protein-protein
- B–C · 239 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 4HB4 · Crystal structure of CRM1 inhibitor Leptomycin B in complex with… · 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
- 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
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 4HB4 · PDBe 4HB4 · UniProt P62826 · UniProt P41920 · UniProt P30822
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