SMTL ID : 4iin.1

Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Helicobacter pylori 26695 complexed with NAD+

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.40 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 25 residues within 4Å: Chain A: G.36, S.38, K.39, G.40, I.41, G.42, N.59, R.61, F.86, D.87, A.88, N.114, A.115, G.116, V.117, N.137, V.164, A.165, S.166, Y.179, K.183, P.209, G.210, I.212, T.214 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:I.41, A:P.209 Hydrogen bonds: A:K.39, A:K.39, A:K.39, A:I.41, A:G.42, A:A.88, A:A.89, A:N.114, A:G.116, A:N.137, A:Y.179, A:K.183, A:I.212, A:T.214 Water bridges: A:R.61, A:G.116 NAD.3: 26 residues within 4Å: Chain B: G.36, S.38, K.39, G.40, I.41, N.59, R.61, F.86, D.87, A.88, A.89, N.114, A.115, G.116, V.117, N.137, V.164, A.165, S.166, Y.179, K.183, P.209, G.210, F.211, I.212 Ligands: ACT.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.41, B:P.209 Hydrogen bonds: B:G.36, B:K.39, B:I.41, B:A.88, B:A.89, B:N.114, B:G.116, B:N.137, B:K.183, B:I.212, B:I.212 Water bridges: B:G.42, B:G.42 Salt bridges: B:K.39 NAD.6: 23 residues within 4Å: Chain C: G.36, G.40, I.41, N.59, R.61, F.86, D.87, A.88, A.89, N.114, A.115, G.116, V.117, N.137, V.164, A.165, S.166, Y.179, K.183, P.209, G.210, I.212 Ligands: ACT.7 15 PLIP interactions: 15 interactions with chain C Hydrophobic interactions: C:P.209 Hydrogen bonds: C:I.41, C:R.61, C:D.87, C:A.88, C:A.89, C:N.114, C:G.116, C:N.137, C:Y.179, C:K.183, C:I.212 Water bridges: C:G.42, C:G.42 pi-Cation interactions: C:R.61 NAD.8: 25 residues within 4Å: Chain D: G.36, K.39, G.40, I.41, N.59, R.61, F.86, D.87, A.88, A.89, N.114, A.115, G.116, V.117, N.137, V.164, A.165, S.166, Y.179, K.183, P.209, G.210, I.212, T.214 Ligands: ACT.9 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:I.41, D:P.209 Hydrogen bonds: D:I.41, D:R.61, D:R.61, D:D.87, D:A.88, D:A.89, D:N.114, D:G.116, D:N.137, D:Y.179, D:K.183, D:I.212 Water bridges: D:G.42, D:G.42 pi-Cation interactions: D:R.61

2 x K: POTASSIUM ION(Non-covalent)

K.2: 4 residues within 4Å: Chain A: E.261, T.262 Chain D: E.261, T.262 5 PLIP interactions: 2 interactions with chain A, 2 interactions with chain D, 1 Ligand-Water interactions Metal complexes: A:E.261, A:T.262, D:E.261, D:T.262, H2O.5 K.4: 4 residues within 4Å: Chain B: E.261, T.262 Chain C: E.261, T.262 5 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 1 Ligand-Water interactions Metal complexes: C:E.261, C:T.262, B:E.261, B:T.262, H2O.4

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

ACT.5: 5 residues within 4Å: Chain B: S.166, Y.179, G.210, F.211 Ligands: NAD.3 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.211 Hydrogen bonds: B:S.166, B:Y.179 ACT.7: 6 residues within 4Å: Chain C: S.166, I.168, Y.179, G.210, F.211 Ligands: NAD.6 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:F.211 Hydrogen bonds: C:S.166 Water bridges: C:Q.176 ACT.9: 5 residues within 4Å: Chain D: S.166, Y.179, G.210, F.211 Ligands: NAD.8 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.211 Hydrogen bonds: D:S.166, D:S.166

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Hou, J. et al., Crystal structure of a putative 3-oxoacyl-[acyl-carrier protein]reductase from Helicobacter pylori 26695 complexed with NAD+. To be Published

Release Date

2013-01-09

Peptides

3-ketoacyl-acyl carrier protein reductase (FabG): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-ketoacyl-acyl carrier protein reductase (FabG)

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