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Crystal structure of a CRM1-rangtp-SPN1 export complex bound to a 113 amino acid fg-repeat containing fragment of NUP214
Analyse Crystal structure of a CRM1-rangtp-SPN1 export complex bound to a 113 amino… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5DIS
- Type
- protein
- Length
- 1,863 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Exportin-1; GTP-binding nuclear protein ran; Snurportin-1; Maltose-binding periplasmic…
- UniProt
- O14980, P62826, O95149, P0AEX9, P35658
- Ligands
- PRO, GTP, GLC, MG
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 58% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Exportin-1 | protein | 1032 | 78% helix, 1% strand | O14980 |
| B | GTP-binding nuclear protein ran | protein | 172 | 30% helix, 27% strand | P62826 |
| C | Snurportin-1 | protein | 264 | 27% helix, 28% strand | O95149 |
| D | Maltose-binding periplasmic PROTEIN,NUCLEAR pore complex protein NUP214 | protein | 395 | 37% helix, 10% strand | P0AEX9, P35658 |
Ligands and binding sites
- PRO · Proline · ligand · 2 copies · chains A, C
- GTP · Guanosine-5'-triphosphate · ligand · chains B
- GLC · alpha-D-glucopyranose · sugar · 2 copies · chains A
- MG · Magnesium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.86 | 0.91 | 109 | GTP, MG |
| 2 | 952 | 0.83 | 0.84 | 86 | empty |
| 3 | 966 | 0.81 | 0.82 | 75 | empty |
| 4 | 1010 | 0.81 | 0.82 | 96 | PRO |
| 5 | 243 | 0.76 | 0.89 | 32 | empty |
Interfaces
4 interfaces between chains.
- A–D · 2900 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 2436 Ų buried · 30 hydrogen bonds · protein-protein
- A–C · 1976 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 67 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5DIS · Crystal structure of a CRM1-RanGTP-SPN1 export complex bound to a 113 amino acid… · the same entry in another collection · chain B against B, TM-score 1.00
- P62826 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein ran (P62826) · a predicted model of the same protein · chain B against A, TM-score 0.99
- O14980 · AlphaFold monomer V2.0 prediction for exportin-1 (O14980) · a predicted model of the same protein · chain A against A, TM-score 0.99
- O95149 · AlphaFold monomer V2.0 prediction for snurportin-1 (O95149) · a predicted model of the same protein · chain C against A, TM-score 0.98
- P0AEX9 · AlphaFold monomer V2.0 prediction for MALTOSE/MALTODEXTRIN-binding periplasmic protein… · a predicted model of the same protein · chain D against A, TM-score 0.82
- P35658 · AlphaFold monomer V2.0 prediction for nuclear pore complex protein NUP214 (P35658) · a predicted model of the same protein · chain D against A, TM-score 0.27
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 O14980
- Every structure of UniProt P62826
- Every structure of UniProt O95149
- Every structure of UniProt P0AEX9
- Every structure of UniProt P35658
- Elsewhere: RCSB PDB 5DIS · PDBe 5DIS · UniProt O14980 · UniProt P62826 · UniProt O95149 · UniProt P0AEX9 · UniProt P35658
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