› 2gf9

X-ray diffraction
1.53Å resolution

Crystal structure of human RAB3D in complex with GDP

Released:
DOI: 10.2210/pdb2gf9/pdb
PDB entry 2gf9 coloured by chain, front view.
PDB entry 2gf9 coloured by chain, side view.
PDB entry 2gf9 coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Hong B, Wang J, Shen L, Tempel W, Landry R, Arrowsmith CH, Edwards AM, Sundstrom M, Weigelt J, Bochkarev A, Park H, Structural Genomics Consortium (SGC)

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-132000 (preferred)
Entry contents:
1 distinct polypeptide molecule
Macromolecule:
Ras-related protein Rab-3D Chain: A
Molecule details ›
Chain: A
Length: 189 amino acids
Theoretical weight: 21.67 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O95716 (Residues: 20-189; Coverage: 78%)
Gene names: GOV, RAB16, RAB3D
Sequence domains: Ras family
Structure domains: P-loop containing nucleotide triphosphate hydrolases

Ligands and Environments

3 bound ligands:
Ligand MG 1 x MG
Ligand UNX 2 x UNX
Ligand GDP 1 x GDP
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: RIGAKU
Spacegroup: P212121
Unit cell:
a: 35.7Å b: 63.222Å c: 67.695Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.155 0.153 0.185
Expression system: Escherichia coli

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