Research workbench
Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small COPII coat GTPase SAR1 from Encephalitozoon cuniculi in complex with GDP
Analyse Crystal structure of ADP RIBOSYLATION FACTOR-LIKE GTP BINDING PROTEIN /Small… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VS4
- Type
- protein
- Length
- 446 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.4
- Source
- Encephalitozoon cuniculi (strain GB-M1)
- Molecule
- Small COPII coat GTPase SAR1
- EC
- 3.6.5.-
- UniProt
- Q8SS09
- Ligands
- GDP, MG
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · resolution 2.4 · 2 distinct chains · 49% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Small COPII coat GTPase SAR1 (EC 3.6.5.-) | protein | 223 | 49% helix, 19% strand | Q8SS09 |
| B | Small COPII coat GTPase SAR1 (EC 3.6.5.-) | protein | 223 | 49% helix, 19% strand | Q8SS09 |
Ligands and binding sites
- GDP · Guanosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 50 | 0.40 | 0.82 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 886 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6VS4 · Crystal structure of ADP ribosylation factor-like GTP binding protein /small copii coat… · the same entry in another collection · chain A against A, TM-score 1.00
- Q8SS09 · AlphaFold monomer V2.0 prediction for small copii coat GTPase SAR1 (Q8SS09) · a predicted model of the same protein · chain A against A, TM-score 0.72
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 Q8SS09
- Elsewhere: RCSB PDB 6VS4 · PDBe 6VS4 · UniProt Q8SS09
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