Research workbench
Crystal structure of exportin-5:RANGTP complex
Analyse Crystal structure of exportin-5:RANGTP complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YU6
- Type
- protein
- Length
- 2,508 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exportin-5; 13-mer peptide; GTP-binding nuclear protein ran
- UniProt
- Q9HAV4, P62825
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exportin-5 | protein | 1069 | 73% helix, 1% strand | Q9HAV4 |
| E, F | 13-mer peptide | protein | 13 | 77% helix, 0% strand | — |
| B, D | GTP-binding nuclear protein ran | protein | 170 | 29% helix, 28% strand | P62825 |
| C | Exportin-5 | protein | 1073 | 73% helix, 1% strand | Q9HAV4 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains B, D
- MG · Magnesium ion · metal · 2 copies · chains B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 966 | 0.81 | 0.83 | 72 | empty |
| 2 | 983 | 0.80 | 0.82 | 77 | empty |
| 3 | 768 | 0.79 | 0.82 | 89 | empty |
| 4 | 948 | 0.76 | 0.79 | 65 | empty |
| 5 | 94 | 0.72 | 0.94 | 23 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1948 Ų buried · 24 hydrogen bonds · protein-protein
- C–D · 1515 Ų buried · 21 hydrogen bonds · protein-protein
- A–C · 745 Ų buried · 2 hydrogen bonds · protein-protein
- C–F · 346 Ų buried · 1 hydrogen bond · protein-protein
- A–E · 315 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 5YU6 · Crystal structure of exportin-5:RANGTP complex · the same entry in another collection · chain D against D, TM-score 1.00
- P62825 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein ran (P62825) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q9HAV4 · AlphaFold monomer V2.0 prediction for exportin-5 (Q9HAV4) · a predicted model of the same protein · chain C against A, TM-score 0.92
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 Q9HAV4
- Every structure of UniProt P62825
- Elsewhere: RCSB PDB 5YU6 · PDBe 5YU6 · UniProt Q9HAV4 · UniProt P62825
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