MolNFT v1 · #141998 · protein
LFS829 in complex with CRM1-ran-RANBP1
5ZPU · GTP-binding nuclear protein ran: “LFS829 in complex with CRM1-ran-RANBP1”. X-ray diffraction, 4 ligands (GTP, D29, MG), 13 pockets (best druggability 0.86). MolNFT v1 #141998 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 5ZPU
- Type
- protein
- Length
- 1,338 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
- GTP, D29, MG, CL
- Pockets
- 13 · best druggability 0.86
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 | 203 | 30% helix, 24% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 120 | 16% helix, 56% strand | P41920 |
| C | Exportin-1,EXPORTIN-1 | protein | 1015 | 76% helix, 1% strand | P30822 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- D29 · (Z)-{[(3E)-4-{(R)-[3,5-bis(trifluoromethyl) phenyl]sulfinyl}but-3-en-1-yl]imino}methanethiol · ligand · chains C
- MG · Magnesium ion · metal · chains A
- CL · Chloride ion · ion · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.86 | 0.88 | 119 | empty |
| 2 | 1077 | 0.79 | 0.80 | 110 | empty |
| 3 | 131 | 0.63 | 0.87 | 29 | GTP, MG |
| 4 | 116 | 0.56 | 0.83 | 16 | empty |
| 5 | 163 | 0.55 | 0.80 | 24 | D29 |
Interfaces
3 interfaces between chains.
- A–C · 2307 Ų buried · 32 hydrogen bonds · protein-protein
- A–B · 1901 Ų buried · 28 hydrogen bonds · protein-protein
- B–C · 278 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 covalent (covalent ligand).
Compared structures
- 5ZPU · LFS829 in complex with CRM1-Ran-RanBP1 · 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 0.98
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 5ZPU · PDBe 5ZPU · UniProt P62826 · UniProt P41920 · UniProt P30822
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