MolNFT v1 · #169170 · protein
Crystal structure of MDIA2NES peptide bound to CRM1(E571K)
6X2Y · GTP-binding nuclear protein ran: “Crystal structure of MDIA2NES peptide bound to CRM1(E571K)”. X-ray diffraction, 2 ligands (GNP, MG), 14 pockets (best druggability 0.85). MolNFT v1 #169170 on GenesisL1: 3D structure, binding sites…
- PDB
- 6X2Y
- Type
- protein
- Length
- 1,333 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, Q9NSV4
- Ligands
- GNP, MG
- Pockets
- 14 · 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 | 205 | 33% helix, 22% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 123 | 14% helix, 49% strand | P41920 |
| C | Exportin-1 | protein | 994 | 78% helix, 0% strand | P30822 |
| D | Protein diaphanous homolog 3 | protein | 11 | 73% helix, 0% strand | Q9NSV4 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 3 copies · chains A, C
- EDO · 1,2-ethanediol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 899 | 0.85 | 0.87 | 110 | GOL |
| 2 | 702 | 0.67 | 0.75 | 63 | empty |
| 3 | 130 | 0.63 | 0.87 | 29 | GNP, MG |
| 4 | 270 | 0.61 | 0.80 | 43 | EDO |
| 5 | 115 | 0.57 | 0.84 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2050 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1993 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 667 Ų buried · 6 hydrogen bonds · protein-protein
- B–C · 179 Ų buried · 2 hydrogen bonds · protein-protein
Compared structures
- 6X2Y · Crystal Structure of mDia2NES peptide bound to CRM1(E571K) · 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
- Q9NSV4 · AlphaFold monomer V2.0 prediction for protein diaphanous homolog 3 (Q9NSV4) · a predicted model of the same protein · chain D against A, TM-score 0.68
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
- Every structure of UniProt Q9NSV4
- Elsewhere: RCSB PDB 6X2Y · PDBe 6X2Y · UniProt P62826 · UniProt P41920 · UniProt P30822 · UniProt Q9NSV4
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