Research workbench
Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GTP.
Analyse Crystal structure of the S. cerevisiae Ski7 GTPase-like domain, bound to GTP. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZKE
- Type
- protein
- Length
- 473 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.251
- Source
- Saccharomyces cerevisiae
- Molecule
- Superkiller protein 7
- UniProt
- Q08491
- Ligands
- GTP, MG, NA
- Pockets
- 8 · best druggability 0.75
Structure
x-ray diffraction · resolution 2.251 · 1 distinct chain · 22% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Superkiller protein 7 | protein | 473 | 22% helix, 33% strand | Q08491 |
Ligands and binding sites
- GTP · Guanosine-5'-triphosphate · ligand · chains A
- MG · Magnesium ion · metal · chains A
- NA · Sodium ion · metal · chains A
- PGE · Triethylene glycol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 592 | 0.75 | 0.82 | 59 | empty |
| 2 | 372 | 0.65 | 0.79 | 43 | empty |
| 3 | 160 | 0.55 | 0.81 | 31 | MG, GTP, NA |
| 4 | 113 | 0.38 | 0.74 | 19 | empty |
| 5 | 87 | 0.37 | 0.75 | 12 | empty |
Compared structures
- 4ZKE · Crystal structure of the S. cerevisiae SKI7 GTPase-like domain, bound to GTP. · the same entry in another collection · chain A against A, TM-score 1.00
- Q08491 · AlphaFold monomer V2.0 prediction for superkiller protein 7 (Q08491) · a predicted model of the same protein · chain A against A, TM-score 1.00
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 Q08491
- Elsewhere: RCSB PDB 4ZKE · PDBe 4ZKE · UniProt Q08491
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