4F56: The bicyclic intermediate structure provides insights into the desuccinylation mechanism of SIRT5

PDB ID: 4F56Download
MMDB ID: 238374
PDB Deposition Date: 2012/5/11
Updated in MMDB: 2023/11
Experimental Method:
x-ray diffraction
Resolution: 1.7  Å
Source Organism:
Similar Structures:
Biological Unit for 4F56: dimeric; determined by author and by software (PISA)
Molecular Components in 4F56
Label Count Molecule
Proteins (2 molecules)
1
Nad-dependent Lysine Demalonylase and Desuccinylase Sirtuin-5, Mitochondrial
(Gene symbol: SIRT5)
Molecule annotation
1
Peptide From Histone H3.1
(Gene symbol: H3C1)
Molecule annotation
Chemicals and Non-standard biopolymers (2 molecules)
1
1
ZINC IONZINC ION
2
1
3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid3-[(2R,3aR,5R,6R,6aR)-5-({[(S)-{[(S)-{[(2R,3S,4R,5R)-5-(6-amino-9H-purin-9-yl)-3,4-dihydroxytetrahydrofuran-2-yl]methoxy}(hydroxy)phosphoryl]oxy}(hydroxy)phosphoryl]oxy}methyl)-2,6-dihydroxytetrahydrofuro[2,3-d][1,3]oxathiol-2-yl]propanoic acid
* Click molecule labels to explore molecular sequence information.
Citing MMDB
Madej T, Lanczycki CJ, Zhang D, Thiessen PA, Geer RC, Marchler-Bauer A, Bryant SH. " MMDB and VAST+: tracking structural similarities between macromolecular complexes. Nucleic Acids Res. 2014 Jan; 42(Database issue):D297-303