› 6ace

X-ray diffraction
1.98Å resolution

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H3K122

Released:
DOI: 10.2210/pdb6ace/pdb
Model geometry
Fit model/data
PDB entry 6ace coloured by chain, front view.
PDB entry 6ace coloured by chain, side view.
PDB entry 6ace coloured by chain, top view.
Source organism: Homo sapiens
Entry authors: Hang TR, Chen WB

Function and Biology Details

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

Structure analysis Details

Assembly composition:
hetero dimer (preferred)
Assembly name:
PDBe Complex ID:
PDB-CPX-180742 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase sirtuin-5, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 267 amino acids
Theoretical weight: 29.05 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NXA8 (Residues: 36-302; Coverage: 86%)
Gene names: SIR2L5, SIRT5
Sequence domains: Sir2 family
Histone H3.2 Chain: B
Molecule details ›
Chain: B
Length: 8 amino acids
Theoretical weight: 1.05 KDa
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: Q71DI3 (Residues: 119-126; Coverage: 6%)
Gene names: H3C13, H3C14, H3C15, H3F2, H3FM, HIST2H3A, HIST2H3C, HIST2H3D

Ligands and Environments

2 bound ligands:
Ligand ZN 1 x ZN
Ligand GOL 2 x GOL
1 modified residue:
Ligand SLL 1 x SLL

Experiments and Validation Details

wwPDB Validation report is not available for this entry.
X-ray source: SSRF BEAMLINE BL19U1
Spacegroup: C2
Unit cell:
a: 123.227Å b: 41.169Å c: 55.854Å
α: 90° β: 94.69° γ: 90°
R-values:
R R work R free
0.206 0.203 0.266
Expression systems:
  • Escherichia coli
  • Not provided

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