Research workbench
Plumbagin in complex with CRM1-RANM189D-RANBP1
Analyse Plumbagin in complex with CRM1-RANM189D-RANBP1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YSU
- Type
- protein
- Length
- 1,355 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…
- UniProt
- P62826, P41920, P30822
- Ligands
- F2X, GTP, MG, NA, NO3, CL
- Pockets
- 15 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 64% 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 | 130 | 15% helix, 51% strand | P41920 |
| C | Exportin-1,EXPORTIN-1 | protein | 1017 | 78% helix, 1% strand | P30822 |
Ligands and binding sites
- F2X · (2~{R})-2-methyl-5-oxidanyl-2,3-dihydronaphthalene-1,4-dione · ligand · 2 copies · chains C
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains C
- NO3 · Nitrate ion · ion · 4 copies · chains A, C
- CL · Chloride ion · ion · 2 copies · chains A, 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, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 863 | 0.83 | 0.86 | 82 | NO3 |
| 2 | 1152 | 0.78 | 0.80 | 100 | empty |
| 3 | 686 | 0.77 | 0.82 | 69 | empty |
| 4 | 136 | 0.64 | 0.87 | 30 | GTP, MG |
| 5 | 96 | 0.54 | 0.84 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–C · 2301 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2214 Ų buried · 33 hydrogen bonds · protein-protein
- B–C · 312 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 5YSU · Plumbagin in complex with CRM1-RanM189D-RanBP1 · the same entry in another collection · chain A against A, 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 0.95
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 5YSU · PDBe 5YSU · UniProt P62826 · UniProt P41920 · UniProt P30822
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