SMTL ID : 8hly.1

Crystal structure of SIRT3 in complex with H3K23la peptide

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

monomer

Ligands

1 x ALA- THR- LYS- ALA- ALA- ARG: H3K23la peptide(Non-covalent)

ALA-THR-LYS-ALA-ALA-ARG.1: 23 residues within 4Å: Chain A: R.40, E.59, F.62, 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: GOL.2, 2OP.6, GOL.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:V.174, A:F.176, 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 Water bridges: A:E.207 Salt bridges: A:E.207

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.2: 12 residues within 4Å: Chain A: G.27, A.28, F.39, R.40, Q.110, H.130, T.202, S.203, L.204, V.206 Ligands: ALA-THR-LYS-ALA-ALA-ARG.1, 2OP.6 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:A.28, A:Q.110, A:H.130, A:T.202, A:T.202, A:S.203 Water bridges: A:G.29, A:S.203 GOL.5: 11 residues within 4Å: Chain A: A.28, I.36, P.37, D.38, F.39, Y.47, F.62, L.77, L.81, I.112 Ligands: 2OP.6 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:P.37, A:F.39, A:Y.47 Water bridges: A:I.112 GOL.7: 2 residues within 4Å: Ligands: ALA-THR-LYS-ALA-ALA-ARG.1, ALA-THR-LYS-ALA-ALA-ARG.1 No protein-ligand interaction detected (PLIP)

1 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.3: 4 residues within 4Å: Chain A: P.179, L.180, P.181, Q.182 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:L.180, A:Q.182

1 x ZN: ZINC ION(Non-covalent)

ZN.4: 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.6: 9 residues within 4Å: Chain A: F.39, F.62, I.112, H.130, I.173, V.206 Ligands: ALA-THR-LYS-ALA-ALA-ARG.1, GOL.2, GOL.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.112, A:H.130

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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