SMTL ID : 6aco.1

histone lysine desuccinylase Sirt5 in complex with succinyl peptide H2BK120

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.71 Å

Oligo State

monomer

Ligands

1 x ALA- VAL- THR- SLL- TYR- THR- SER: succinyl peptide H2BK120(Non-covalent)

ALA-VAL-THR-SLL-TYR-THR-SER.1: 20 residues within 4Å: Chain A: Q.51, A.54, Y.70, R.73, I.110, H.126, V.188, V.189, W.190, F.191, G.192, E.193, N.194, L.195, L.200, V.221, V.222, Y.223, P.224 Ligands: GOL.4 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:Q.51, A:V.188, A:V.189, A:F.191, A:F.191, A:N.194, A:L.200, A:Y.223, A:Y.223, A:P.224 Hydrogen bonds: A:Y.70, A:Y.70, A:V.189, A:G.192, A:E.193, A:L.195, A:V.221, A:V.221, A:Y.223, A:Y.223 Water bridges: A:N.194, A:N.194, A:N.194, A:L.195, A:S.220, A:Y.223 Salt bridges: A:R.73

1 x ZN: ZINC ION(Non-covalent)

ZN.2: 4 residues within 4Å: Chain A: C.134, C.137, C.175, C.180 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.134, A:C.137, A:C.175, A:C.180

1 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 6 residues within 4Å: Chain A: G.26, A.27, R.39, Q.108, T.218, S.219 Ligand excluded by PLIP

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Ligands: ALA-VAL-THR-SLL-TYR-THR-SER.1, ALA-VAL-THR-SLL-TYR-THR-SER.1, ALA-VAL-THR-SLL-TYR-THR-SER.1 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hang, T.R. et al., complex structure of histone lysine desuccinylase Sirt5 with succinyl peptide H2BK120. To Be Published

Release Date

2019-07-24

Peptides

NAD-dependent protein deacylase sirtuin-5, mitochondrial: A

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

NAD-dependent protein deacylase sirtuin-5, mitochondrial