› 6aco

X-ray diffraction
1.71Å resolution

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120

Released:
DOI: 10.2210/pdb6aco/pdb
PDB entry 6aco coloured by chain, front view.
PDB entry 6aco coloured by chain, side view.
PDB entry 6aco 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-158703 (preferred)
Entry contents:
2 distinct polypeptide molecules
Macromolecules (2 distinct):
NAD-dependent protein deacylase sirtuin-5, mitochondrial Chain: A
Molecule details ›
Chain: A
Length: 270 amino acids
Theoretical weight: 29.37 KDa
Source organism: Homo sapiens
Expression system: Escherichia coli
UniProt:
  • Canonical: Q9NXA8 (Residues: 34-302; Coverage: 87%)
Gene names: SIR2L5, SIRT5
Sequence domains: Sir2 family
Histone H2B type 1-C/E/F/G/I Chain: B
Molecule details ›
Chain: B
Length: 7 amino acids
Theoretical weight: 869 Da
Source organism: Homo sapiens
Expression system: Not provided
UniProt:
  • Canonical: P62807 (Residues: 118-124; Coverage: 6%)
Gene names: H2BC10, H2BC4, H2BC6, H2BC7, H2BC8, H2BFA, H2BFG, H2BFH, H2BFK, H2BFL, HIST1H2BC, HIST1H2BE, HIST1H2BF, HIST1H2BG, HIST1H2BI

Ligands and Environments

3 bound ligands:
Ligand ZN 1 x ZN
Ligand CL 1 x CL
Ligand GOL 1 x GOL
1 modified residue:
Ligand SLL 1 x SLL

Experiments and Validation Details

Entry percentile scores
X-ray source: SSRF BEAMLINE BL17U1
Spacegroup: P21
Unit cell:
a: 33.885Å b: 64.877Å c: 55.564Å
α: 90° β: 95.92° γ: 90°
R-values:
R R work R free
0.164 0.161 0.217
Expression systems:
  • Escherichia coli
  • Not provided

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