› 6j7f

X-ray diffraction
2.88Å resolution

Complex of GGTaseIII, farnesyl-Ykt6 (C-terminal methylated), and GGPP

Released:
DOI: 10.2210/pdb6j7f/pdb
PDB entry 6j7f coloured by chain, front view.
PDB entry 6j7f coloured by chain, side view.
PDB entry 6j7f coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Goto-Ito S, Yamagata A, Sato Y, Fukai S

Function and Biology Details

Reaction catalysed: 
Geranylgeranyl diphosphate + protein-cysteine = S-geranylgeranyl-protein + diphosphate
Biochemical function:
Biological process:
Cellular component:
Sequence domains:

Structure analysis Details

Assembly composition:
hetero trimer (preferred)
PDBe Complex ID:
PDB-CPX-127496 (preferred)
Entry contents:
3 distinct polypeptide molecules
Macromolecules (3 distinct):
Protein prenyltransferase alpha subunit repeat-containing protein 1 Chain: A
Molecule details ›
Chain: A
Length: 327 amino acids
Theoretical weight: 37.99 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q7Z6K3 (Residues: 1-327; Coverage: 81%)
Gene name: PTAR1
Sequence domains: Protein prenyltransferase alpha subunit repeat
Geranylgeranyl transferase type-2 subunit beta Chain: B
Molecule details ›
Chain: B
Length: 336 amino acids
Theoretical weight: 37.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: P53611 (Residues: 1-331; Coverage: 100%)
Gene names: GGTB, RABGGTB
Sequence domains: Prenyltransferase and squalene oxidase repeat
Synaptobrevin homolog YKT6 Chain: C
Molecule details ›
Chain: C
Length: 195 amino acids
Theoretical weight: 22.15 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: O15498 (Residues: 1-195; Coverage: 99%)
Gene name: YKT6
Sequence domains:

Ligands and Environments

4 bound ligands:
Ligand TLA 1 x TLA
Ligand FAR 1 x FAR
Ligand GER 1 x GER
Ligand DPO 1 x DPO
1 modified residue:
Ligand CMT 1 x CMT

Experiments and Validation Details

Entry percentile scores
X-ray source: SPRING-8 BEAMLINE BL41XU
Spacegroup: P41212
Unit cell:
a: 119.415Å b: 119.415Å c: 210.649Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.208 0.206 0.249
Expression system: Escherichia coli

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