SMTL ID : 5ytk.1

Crystal structure of SIRT3 bound to a leucylated AceCS2

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.70 Å

Oligo State

homo-hexamer

Ligands

4 x ARG- SER- GLY- LYS- VAL- MET- ARG: AceCS2-KLeu(Non-covalent)

ARG-SER-GLY-LYS-VAL-MET-ARG.1: 10 residues within 4Å: Chain A: H.128, V.172, F.173, F.174, G.175, E.176, P.177, L.178 Ligands: ARG-SER-GLY-LYS-VAL-MET.2, LEU.15 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.172, A:P.177, A:L.178 Hydrogen bonds: A:E.61, A:E.61, A:V.172, A:G.175, A:E.176, A:L.178 ARG-SER-GLY-LYS-VAL-MET-ARG.2: 15 residues within 4Å: Chain A: E.203 Chain D: E.57, E.61, V.172, F.173, F.174, G.175, E.176, P.177, L.178, F.182, H.185, P.206 Ligands: ARG-SER-GLY-LYS-VAL-MET-ARG.1, LEU.16 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:L.178 Hydrogen bonds: D:E.61, D:V.172, D:G.175, D:E.176, D:L.178 Salt bridges: D:E.57, A:E.203 ARG-SER-GLY-LYS-VAL-MET-ARG.3: 15 residues within 4Å: Chain B: F.66 Chain E: H.128, V.172, F.173, F.174, G.175, E.176, P.177, L.178, F.182, H.185 Chain F: E.203, V.204, E.205 Ligands: LEU.17 9 PLIP interactions: 2 interactions with chain F, 7 interactions with chain E Hydrogen bonds: F:E.205, E:V.172, E:G.175, E:E.176, E:L.178 Salt bridges: F:E.203, E:E.57 Hydrophobic interactions: E:V.172, E:L.178 ARG-SER-GLY-LYS-VAL-MET-ARG.4: 16 residues within 4Å: Chain D: F.66 Chain E: E.203, V.204, E.205 Chain F: E.57, V.172, F.173, F.174, G.175, E.176, P.177, L.178, F.182, L.183, H.185 Ligands: LEU.18 10 PLIP interactions: 6 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:L.178, E:E.205 Hydrogen bonds: F:V.172, F:G.175, F:E.176, F:L.178, E:E.203, E:E.203, E:E.205 Salt bridges: F:E.57

6 x ZN: ZINC ION(Non-covalent)

ZN.5: 4 residues within 4Å: Chain A: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.136, A:C.139, A:C.160, A:C.163 ZN.6: 4 residues within 4Å: Chain B: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.136, B:C.139, B:C.160, B:C.163 ZN.9: 4 residues within 4Å: Chain C: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain C Metal complexes: C:C.136, C:C.139, C:C.160, C:C.163 ZN.12: 4 residues within 4Å: Chain D: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain D Metal complexes: D:C.136, D:C.139, D:C.160, D:C.163 ZN.13: 4 residues within 4Å: Chain E: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain E Metal complexes: E:C.136, E:C.139, E:C.160, E:C.163 ZN.14: 4 residues within 4Å: Chain F: C.136, C.139, C.160, C.163 4 PLIP interactions: 4 interactions with chain F Metal complexes: F:C.136, F:C.139, F:C.160, F:C.163

6 x LEU: LEUCINE(Non-covalent)

LEU.7: 8 residues within 4Å: Chain B: F.37, R.38, F.60, Q.108, I.110, H.128, F.174 Ligands: LYS.8 2 PLIP interactions: 2 interactions with chain B, Hydrophobic interactions: B:F.37, B:F.60 LEU.10: 7 residues within 4Å: Chain C: F.37, F.60, Q.108, H.128, I.171, V.172 Ligands: LYS.11 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.37, C:F.60 Hydrogen bonds: C:H.128 LEU.15: 7 residues within 4Å: Chain A: F.37, F.60, Q.108, H.128, V.172, F.174 Ligands: ARG-SER-GLY-LYS-VAL-MET-ARG.1 3 PLIP interactions: 3 interactions with chain A, Hydrophobic interactions: A:F.37, A:F.60 Hydrogen bonds: A:V.172 LEU.16: 6 residues within 4Å: Chain D: F.37, F.60, Q.108, H.128, F.174 Ligands: ARG-SER-GLY-LYS-VAL-MET.2 1 PLIP interactions: 1 interactions with chain D, Hydrophobic interactions: D:F.37 LEU.17: 8 residues within 4Å: Chain E: F.37, F.60, Q.108, H.128, I.171, V.172, F.174 Ligands: THR-ARG-SER-GLY-LYS-VAL-MET-ARG.3 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.37, E:F.60 Hydrogen bonds: E:V.172 LEU.18: 9 residues within 4Å: Chain F: F.37, F.60, Q.108, I.110, H.128, I.171, V.172, F.174 Ligands: THR-ARG-SER-GLY-LYS-VAL-MET-ARG.4 5 PLIP interactions: 5 interactions with chain F, Hydrophobic interactions: F:F.37, F:F.60, F:F.60, F:I.110 Hydrogen bonds: F:V.172

2 x LYS: LYSINE(Non-covalent)

LYS.8: 7 residues within 4Å: Chain B: H.128, V.172, F.173, F.174, G.175, E.176 Ligands: LEU.7 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:V.172 Hydrogen bonds: B:V.172, B:G.175 LYS.11: 7 residues within 4Å: Chain C: H.128, V.172, F.173, F.174, G.175, E.176 Ligands: LEU.10 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:V.172 Hydrogen bonds: C:H.128, C:G.175

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

He, X.D. et al., Sensing and Transmitting Intracellular Amino Acid Signals through Reversible Lysine Aminoacylations. Cell Metab. (2018)

Release Date

2017-12-27

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

NAD-dependent protein deacetylase sirtuin-3, mitochondrial

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