MolNFT v1 · #89250 · protein
Crystal structure of a nuclear GTP-binding protein from encephalitozoon cuniculi bound to GDP-MG2+
4DJT · GTP-binding nuclear protein GSP1: “Crystal structure of a nuclear GTP-binding protein from encephalitozoon cuniculi bound to GDP-MG2+”. X-ray diffraction, 3 ligands (GDP, MG, NA), 2 pockets (best druggability 0.75). MolNFT v1 #89250…
- PDB
- 4DJT
- Type
- protein
- Length
- 390 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- GTP-binding nuclear protein GSP1
- UniProt
- Q8SS11
- Ligands
- GDP, MG, NA
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 25% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | GTP-binding nuclear protein GSP1 | protein | 186 | 25% helix, 28% strand | Q8SS11 |
| B | GTP-binding nuclear protein GSP1 | protein | 204 | 24% helix, 26% strand | Q8SS11 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 796 | 0.75 | 0.79 | 57 | empty |
| 2 | 88 | 0.35 | 0.75 | 15 | empty |
Interfaces
1 interface between chains.
- A–B · 511 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4DJT · Crystal structure of a nuclear GTP-binding protein from Encephalitozoon cuniculi bound to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SS11 · AlphaFold monomer V2.0 prediction for GTP-binding nuclear protein GSP1 (Q8SS11) · a predicted model of the same protein · chain A against A, TM-score 0.98
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 Q8SS11
- Elsewhere: RCSB PDB 4DJT · PDBe 4DJT · UniProt Q8SS11
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