› 8v3o

X-ray diffraction
2.3Å resolution

CCP5 in complex with Glu-P-peptide 1 transition state analog

Released:
DOI: 10.2210/pdb8v3o/pdb
PDB entry 8v3o coloured by chain, front view.
PDB entry 8v3o coloured by chain, side view.
PDB entry 8v3o coloured by chain, top view.
Source organism: Homo sapiens
Primary publication:
Tubulin code eraser CCP5 binds branch glutamates by substrate deformation.
Chen J, Zehr EA, Gruschus JM, Szyk A, Liu Y, Tanner ME, Tjandra N, Roll-Mecak A
Nature (2024)
PMID: 39020174

Function and Biology Details

Reaction catalysed: 
Delta-2-[tubulin] + H(2)O = Delta-3-[tubulin] + L-glutamate
Biochemical function:
  • not assigned
Biological process:
  • not assigned
Cellular component:
  • not assigned

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-247200 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
Cytosolic carboxypeptidase-like protein 5 Chain: A
Molecule details ›
Chain: A
Length: 524 amino acids
Theoretical weight: 59.17 KDa
Source organism: Homo sapiens
Expression system: Spodoptera frugiperda
UniProt:
  • Canonical: Q8NDL9 (Residues: 2-338, 425-605; Coverage: 59%)
Gene names: AGBL5, CCP5
Sequence domains:
Tubulin beta-2A chain Chain: I
Molecule details ›
Chain: I
Length: 15 amino acids
Theoretical weight: 1.91 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q13885 (Residues: 431-445; Coverage: 3%)
Gene names: TUBB2, TUBB2A

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand MLT 2 x MLT
Ligand K 1 x K
No modified residues

Experiments and Validation Details

Entry percentile scores
X-ray source: ALS BEAMLINE 8.2.1
Unit cell:
a: 65.429Å b: 81.372Å c: 104Å
α: 90° β: 90° γ: 90°
R-values:
R R work R free
0.204 0.203 0.227
Expression systems:
  • Spodoptera frugiperda
  • Not provided

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