MolNFT v1 · #83956 · protein
Crystal structure of XPO1P-YRB2P-GSP1P-GTP complex
3WYF: “Crystal structure of XPO1P-YRB2P-GSP1P-GTP complex”. X-ray diffraction, 2 ligands (GTP, MG), 20 pockets (best druggability 0.85). MolNFT v1 #83956 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3WYF
- Type
- protein
- Length
- 2,705 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GSP1P; Ran-specific GTPase-activating protein 2; Exportin-1
- UniProt
- E7KFU1, P40517, P30822
- Ligands
- GTP, MG
- Pockets
- 20 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 64% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GSP1P | protein | 189 | 28% helix, 24% strand | E7KFU1 |
| B | Ran-specific GTPase-activating protein 2 | protein | 144 | 15% helix, 36% strand | P40517 |
| C | Exportin-1 | protein | 1040 | 78% helix, 1% strand | P30822 |
| D | GSP1P | protein | 185 | 28% helix, 25% strand | E7KFU1 |
| E | Ran-specific GTPase-activating protein 2 | protein | 142 | 13% helix, 37% strand | P40517 |
| F | Exportin-1 | protein | 1005 | 77% helix, 1% strand | P30822 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · 2 copies · chains A, D
- MG · Magnesium ion · metal · 2 copies · chains A, 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, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 891 | 0.85 | 0.87 | 119 | empty |
| 2 | 724 | 0.84 | 0.87 | 103 | empty |
| 3 | 1109 | 0.76 | 0.79 | 107 | empty |
| 4 | 676 | 0.75 | 0.81 | 99 | empty |
| 5 | 826 | 0.74 | 0.78 | 85 | empty |
Interfaces
10 interfaces between chains.
- A–C · 2014 Ų buried · 17 hydrogen bonds · protein-protein
- D–F · 1951 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 1757 Ų buried · 23 hydrogen bonds · protein-protein
- B–C · 1706 Ų buried · 13 hydrogen bonds · protein-protein
- E–F · 1670 Ų buried · 8 hydrogen bonds · protein-protein
Compared structures
- 3WYF · Crystal structure of Xpo1p-Yrb2p-Gsp1p-GTP complex · the same entry in another collection · chain F against F, TM-score 1.00
- P30822 · AlphaFold monomer V2.0 prediction for exportin-1 (P30822) · a predicted model of the same protein · chain F against A, TM-score 0.99
- P40517 · AlphaFold monomer V2.0 prediction for ran-specific GTPase-activating protein 2 (P40517) · a predicted model of the same protein · chain B against A, TM-score 0.84
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 E7KFU1
- Every structure of UniProt P40517
- Every structure of UniProt P30822
- Elsewhere: RCSB PDB 3WYF · PDBe 3WYF · UniProt E7KFU1 · UniProt P40517 · UniProt P30822
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