SMTL ID : 8hlw.1

Crystal structure of SIRT3 in complex with H4K16la peptide

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.50 Å

Oligo State

monomer

Ligands

1 x GLY- GLY- ALA- LYS- ARG- HIS- ARG- LYS: Histone H4 residues 20-27(Non-covalent)

GLY-GLY-ALA-LYS-ARG-HIS-ARG-LYS.1: 22 residues within 4Å: Chain A: Y.57, E.59, F.62, E.63, H.130, V.174, F.175, F.176, G.177, E.178, P.179, L.180, L.204, E.205, V.206, E.207, P.208, A.210, G.231, P.232, W.235 Ligands: 2OP.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:F.176, A:L.180, A:V.206 Hydrogen bonds: A:V.174, A:G.177, A:E.178, A:L.180, A:L.204, A:L.204, A:E.205, A:E.207, A:E.207 Salt bridges: A:E.207 pi-Stacking: A:F.176

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 7 residues within 4Å: Chain A: C.138, V.140, C.141, C.162, V.164, C.165, G.167 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.138, A:C.141, A:C.162, A:C.165

1 x 2OP: (2S)-2-HYDROXYPROPANOIC ACID(Non-covalent)

2OP.3: 8 residues within 4Å: Chain A: F.39, F.62, I.112, H.130, I.173, V.174, V.206 Ligands: GLY-GLY-ALA-LYS-ARG-HIS-ARG-LYS.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:I.173 Hydrogen bonds: A:H.130 Water bridges: A:Q.110

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Fan, Z. et al., Identification of SIRT3 as an eraser of H4K16la. Iscience (2023)

Release Date

2023-09-27

Peptides

NAD-dependent protein deacetylase sirtuin-3, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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