Research workbench
Crystal structure of exportin-5:RANGTP:PRE-miRNA complex
Analyse Crystal structure of exportin-5:RANGTP:PRE-miRNA complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3A6P
- Type
- protein + RNA
- Length
- 2,602 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exportin-5; 13-mer peptide; GTP-binding nuclear protein ran; Pre-microrna
- UniProt
- Q9HAV4, P62825
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.83
Structure
x-ray diffraction · 5 distinct chains · 66% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, F | Exportin-5 | protein | 1072 | 72% helix, 1% strand | Q9HAV4 |
| B, G | 13-mer peptide | protein | 13 | 69% helix, 0% strand | — |
| C, H | GTP-binding nuclear protein ran | protein | 170 | 28% helix, 26% strand | P62825 |
| D, I | Pre-microrna | rna | 22 | — | — |
| E, J | Pre-microrna | rna | 24 | — | — |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains C, H
- MG · Magnesium ion · metal · 2 copies · chains C, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 782 | 0.83 | 0.87 | 80 | empty |
| 2 | 940 | 0.83 | 0.85 | 76 | empty |
| 3 | 970 | 0.82 | 0.83 | 107 | empty |
| 4 | 956 | 0.81 | 0.83 | 72 | empty |
| 5 | 1013 | 0.81 | 0.82 | 79 | empty |
Interfaces
17 interfaces between chains.
- A–C · 1817 Ų buried · 23 hydrogen bonds · protein-protein
- F–H · 1609 Ų buried · 26 hydrogen bonds · protein-protein
- A–E · 1458 Ų buried · 16 hydrogen bonds · protein-nucleic
- F–J · 1106 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–E · 1076 Ų buried · 104 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 3A6P · Crystal structure of Exportin-5:RanGTP:pre-miRNA complex · the same entry in another collection · chain J against J, 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 C against A, TM-score 0.99
- Q9HAV4 · AlphaFold monomer V2.0 prediction for exportin-5 (Q9HAV4) · a predicted model of the same protein · chain A against A, TM-score 0.91
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 3A6P · PDBe 3A6P · UniProt Q9HAV4 · UniProt P62825
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