› 1n6k

X-ray diffraction
1.55Å resolution

Crystal Structure of Human Rab5a A30P mutant complex with GDP and aluminum fluoride

Released:
DOI: 10.2210/pdb1n6k/pdb
PDB entry 1n6k coloured by chain, front view.
PDB entry 1n6k coloured by chain, side view.
PDB entry 1n6k coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
High resolution crystal structures of human Rab5a and five mutants with substitutions in the catalytically important phosphate-binding loop.
Zhu G, Liu J, Terzyan S, Zhai P, Li G, Zhang XC
J Biol Chem 278 2452-60 (2003)
PMID: 12433916

Function and Biology Details

Reaction catalysed: 
GTP + H(2)O = GDP + phosphate
Biochemical function:
Biological process:
  • not assigned
Cellular component:
  • not assigned
Sequence domains:
Structure domain:

Structure analysis Details

Assembly composition:
monomeric (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-539467 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ras-related protein Rab-5A Chain: A
Molecule details ›
Chain: A
Length: 170 amino acids
Theoretical weight: 19.01 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli BL21(DE3)
UniProt:
  • Canonical: P20339 (Residues: 15-184; Coverage: 79%)
Gene names: RAB5, RAB5A
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

4 bound ligands:
Ligand MG 1 x MG
Ligand GDP 1 x GDP
Ligand AF3 1 x AF3
Ligand BME 1 x BME
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 35.84Å b: 64.04Å c: 65.88Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.18 0.177 0.2
Expression system: Escherichia coli BL21(DE3)

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Citations

4 review citations

GTP hydrolysis mechanism of Ras-like GTPases.
Li et al. (2004)
3 more

1 mention without citation

Metal Fluorides: Tools for Structural and Computational Analysis of Phosphoryl Transfer Enzymes.
Jin et al. (2017)