SMTL ID : 3iah.1

Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate.

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.83 Å

Oligo State

homo-dimer

Ligands

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.1: 31 residues within 4Å: Chain A: G.22, S.24, D.25, G.26, I.27, R.47, N.48, K.51, L.72, D.73, L.74, L.75, N.102, A.103, G.104, V.126, T.153, S.154, S.155, Y.168, K.172, N.197, P.198, G.199, G.200, T.201, T.203, S.204, M.205, R.206 Ligands: ACT.2 32 PLIP interactions: 32 interactions with chain A Hydrophobic interactions: A:P.198 Hydrogen bonds: A:G.22, A:S.24, A:S.24, A:S.24, A:D.25, A:I.27, A:R.47, A:D.73, A:D.73, A:L.74, A:L.75, A:N.102, A:G.104, A:Y.168, A:K.172, A:T.201, A:T.201, A:T.203, A:S.204, A:S.204 Water bridges: A:D.25, A:G.26, A:G.28, A:R.47, A:N.48, A:K.51, A:N.102, A:S.204 Salt bridges: A:R.47, A:K.51 pi-Cation interactions: A:R.47 NAP.7: 30 residues within 4Å: Chain B: G.22, S.24, D.25, G.26, I.27, R.47, N.48, K.51, L.72, D.73, L.74, L.75, N.102, A.103, G.104, V.126, T.153, S.154, S.155, Y.168, K.172, P.198, G.199, G.200, T.201, T.203, S.204, M.205, R.206 Ligands: ACT.8 26 PLIP interactions: 26 interactions with chain B Hydrophobic interactions: B:P.198 Hydrogen bonds: B:G.22, B:S.24, B:S.24, B:S.24, B:D.25, B:I.27, B:R.47, B:D.73, B:D.73, B:L.74, B:L.75, B:N.102, B:G.104, B:K.172, B:T.201, B:T.201, B:T.203 Water bridges: B:G.28, B:R.47, B:N.102, B:S.204, B:S.204 Salt bridges: B:R.47, B:K.51 pi-Cation interactions: B:R.47

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.2: 6 residues within 4Å: Chain A: S.155, W.165, Y.168, R.206 Ligands: NAP.1, EOH.4 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.155, A:Y.168 Water bridges: A:S.156 Salt bridges: A:R.206 ACT.3: 4 residues within 4Å: Chain A: R.162, W.165, F.210, G.253 4 PLIP interactions: 4 interactions with chain A Water bridges: A:A.163, A:A.163, A:W.165 Salt bridges: A:R.162 ACT.8: 5 residues within 4Å: Chain B: S.155, W.165, Y.168, R.206 Ligands: NAP.7 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:W.165 Hydrogen bonds: B:S.155, B:Y.168 Water bridges: B:S.156, B:R.206, B:R.206 Salt bridges: B:R.206

2 x EOH: ETHANOL(Non-functional Binders)

EOH.4: 8 residues within 4Å: Chain A: S.156, R.162, G.200, R.206, R.250, P.252, G.253 Ligands: ACT.2 6 PLIP interactions: 6 interactions with chain A Hydrogen bonds: A:G.200, A:R.206, A:R.206, A:R.250, A:G.253, A:G.253 EOH.5: 2 residues within 4Å: Chain A: T.212, D.214 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:D.214 Hydrogen bonds: A:T.212

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

CL.6: 3 residues within 4Å: Chain A: F.70, R.88, H.92 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Minasov, G. et al., Crystal Structure of Short Chain Dehydrogenase (yciK) from Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 in Complex with NADP and Acetate. TO BE PUBLISHED

Release Date

2009-07-21

Peptides

Short Chain Dehydrogenase yciK: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Short Chain Dehydrogenase yciK