› 4phf

X-ray diffraction
1.95Å resolution

Crystal structure of Ypt7 covalently modified with GDP

Released:
DOI: 10.2210/pdb4phf/pdb
PDB entry 4phf coloured by chain, front view.
PDB entry 4phf coloured by chain, side view.
PDB entry 4phf coloured by chain, top view.
Source organism: Saccharomyces cerevisiae S288C
Primary publication:
Locking GTPases covalently in their functional states.
Wiegandt D, Vieweg S, Hofmann F, Koch D, Li F, Wu YW, Itzen A, Müller MP, Goody RS
Nat Commun 6 7773 (2015)
PMID: 26178622

Function and Biology Details

Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-152517 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ypt/Rab-type GTPase YPT7 Chain: A
Molecule details ›
Chain: A
Length: 184 amino acids
Theoretical weight: 20.33 KDa
Source organism: Saccharomyces cerevisiae S288C
Expression system: Escherichia coli
UniProt:
  • Canonical: P32939 (Residues: 1-182; Coverage: 88%)
Gene names: VAM4, YM8270.02, YML001W, YPT7
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand 2UH 1 x 2UH
Ligand MG 1 x MG
Ligand NO3 1 x NO3
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: SLS BEAMLINE X10SA
Spacegroup: P212121
Unit cell:
a: 49.31Å b: 54.9Å c: 60.47Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.199 0.196 0.245
Expression system: Escherichia coli

Quick links

Citations

4 review citations

Rab GTPases take centre stage in understanding Entamoeba histolytica biology.
Verma et al. (2020)
3 more

2 mentions without citation

Locking GTPases covalently in their functional states.
Wiegandt et al. (2015)
1 more