SMTL ID : 4g1c.3 (2 other biounits)

Human SIRT5 bound to Succ-IDH2 and Carba-NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.94 Å

Oligo State

homo-dimer

Ligands

2 x ACE- ALA- VAL- SLL- CYS- ALA- NH2: Succinylated IDH2 peptide(Non-covalent)

ACE-ALA-VAL-SLL-CYS-ALA-NH2.1: 22 residues within 4Å: Chain A: Y.67, R.70, I.107, H.123, V.185, V.186, W.187, F.188, G.189, E.190, N.191, L.192, L.197, V.218, V.219, Y.220, P.221 Chain B: F.188 Ligands: ACE-ALA-VAL-SLL-CYS-ALA-NH2.2, ACE-ALA-VAL-SLL-CYS-ALA-NH2.2, ACE-ALA-VAL-SLL-CYS-ALA-NH2.2, CNA.4 Protein-ligand interaction information (PLIP) not available ACE-ALA-VAL-SLL-CYS-ALA-NH2.2: 25 residues within 4Å: Chain A: Q.48, F.188, G.189 Chain B: A.51, Y.67, R.70, I.107, H.123, V.185, V.186, W.187, F.188, G.189, E.190, N.191, L.192, L.197, V.218, V.219, Y.220, P.221 Ligands: ACE-ALA-VAL-SLL-CYS-ALA-NH2.1, ACE-ALA-VAL-SLL-CYS-ALA-NH2.1, ACE-ALA-VAL-SLL-CYS-ALA-NH2.1, ACE-ALA-VAL-SLL-CYS-ALA-NH2.1 Protein-ligand interaction information (PLIP) not available

2 x ZN: ZINC ION(Non-covalent)

ZN.3: 4 residues within 4Å: Chain A: C.131, C.134, C.172, C.177 4 PLIP interactions: 4 interactions with chain A Metal complexes: A:C.131, A:C.134, A:C.172, A:C.177 ZN.5: 4 residues within 4Å: Chain B: C.131, C.134, C.172, C.177 4 PLIP interactions: 4 interactions with chain B Metal complexes: B:C.131, B:C.134, B:C.172, B:C.177

1 x CNA: CARBA-NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

CNA.4: 28 residues within 4Å: Chain A: G.23, A.24, G.25, S.27, A.28, E.29, V.32, P.33, T.34, F.35, R.36, R.70, Q.105, N.106, I.107, D.108, H.123, G.214, T.215, S.216, F.239, N.240, T.241, E.242, G.256, P.257, C.258 Ligands: ACE-ALA-VAL-SLL-CYS-ALA-NH2.1 27 PLIP interactions: 27 interactions with chain A Hydrophobic interactions: A:A.24, A:F.35, A:F.35 Hydrogen bonds: A:A.24, A:G.25, A:E.29, A:T.34, A:F.35, A:R.36, A:Q.105, A:I.107, A:D.108, A:D.108, A:T.215, A:T.215, A:S.216, A:S.216, A:N.240, A:T.241, A:T.241, A:E.242, A:C.258 Water bridges: A:E.29, A:R.36, A:R.70, A:R.70 pi-Cation interactions: A:R.70

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Szczepankiewicz, B.G. et al., Synthesis of Carba-NAD and the Structures of Its Ternary Complexes with SIRT3 and SIRT5. J.Org.Chem. (2012)

Release Date

2012-08-15

Peptides

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

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

NAD-dependent protein deacylase sirtuin-5, mitochondrial

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