Research workbench
Crystal structure of PKI(DE)NES peptide bound to CRM1
Analyse Crystal structure of PKI(DE)NES peptide bound to CRM1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6X2V
- Type
- protein
- Length
- 1,320 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, P61925
- Ligands
- GNP, MG
- Pockets
- 14 · best druggability 0.85
Structure
x-ray diffraction · 4 distinct chains · 64% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein ran | protein | 202 | 29% helix, 24% strand | P62826 |
| B | Ran-specific GTPase-activating protein 1 | protein | 120 | 14% helix, 55% strand | P41920 |
| C | Exportin-1 | protein | 982 | 78% helix, 0% strand | P30822 |
| D | Camp-dependent protein kinase inhibitor alpha | protein | 16 | 44% helix, 0% strand | P61925 |
Ligands and binding sites
- GNP · Phosphoaminophosphonic acid-guanylate ester · ligand · chains A
- MG · Magnesium ion · metal · chains A
- GOL · Glycerol · additive · 2 copies · chains A, 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 | 887 | 0.85 | 0.87 | 119 | GOL |
| 2 | 67 | 0.65 | 0.93 | 23 | empty |
| 3 | 117 | 0.64 | 0.88 | 30 | GNP, MG |
| 4 | 386 | 0.58 | 0.75 | 37 | empty |
| 5 | 123 | 0.55 | 0.82 | 20 | empty |
Interfaces
4 interfaces between chains.
- A–C · 2012 Ų buried · 16 hydrogen bonds · protein-protein
- A–B · 1873 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 875 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 169 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6X2V · Crystal Structure of PKI(DE)NES peptide bound to CRM1 · the same entry in another collection · chain C against C, 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
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 P61925
- Elsewhere: RCSB PDB 6X2V · PDBe 6X2V · UniProt P62826 · UniProt P41920 · UniProt P30822 · UniProt P61925
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