MolNFT v1 · #116584 · protein
Crystal structure of HRIO2 nes reverse mutant peptide in complex with CRM1-ran-RANBP1
5DI9 · GTP-binding nuclear protein ran: “Crystal structure of HRIO2 nes reverse mutant peptide in complex with CRM1-ran-RANBP1”. X-ray diffraction, 4 ligands (GNP, MG, ZN), 12 pockets (best druggability 0.85). MolNFT v1 #116584 on…
- PDB
- 5DI9
- Type
- protein
- Length
- 1,347 residues
- Chains
- 4
- 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, MG, ZN, CL
- Pockets
- 12 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 65% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 208 | 33% helix, 22% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 128 | 13% helix, 47% strand | P41920 |
| C | Exportin-1 | protein | 995 | 79% helix, 0% strand | P30822 |
| D | Engineered nuclear export signal peptide (HRIO2 nes reverse mutant) | protein | 16 | 63% helix, 0% strand | — |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- ZN · Zinc ion · metal · chains C
- CL · Chloride ion · ion · chains C
- GOL · Glycerol · additive · 4 copies · chains A, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 880 | 0.85 | 0.87 | 106 | GOL |
| 2 | 662 | 0.67 | 0.76 | 61 | empty |
| 3 | 141 | 0.65 | 0.87 | 29 | GNP, MG |
| 4 | 78 | 0.63 | 0.91 | 26 | empty |
| 5 | 119 | 0.57 | 0.83 | 17 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2108 Ų buried · 28 hydrogen bonds · protein-protein
- A–C · 2083 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 867 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 175 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (engineered).
Compared structures
- 5DI9 · Crystal Structure of hRio2 NES Reverse Mutant Peptide in complex with CRM1-Ran-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 5DI9 · PDBe 5DI9 · UniProt P62826 · UniProt P41920 · UniProt P30822
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