SMTL ID : 3nug.1

Crystal structure of wild type tetrameric pyridoxal 4-dehydrogenase from Mesorhizobium loti

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.79 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 27 residues within 4Å: Chain A: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:P.183 Hydrogen bonds: A:Q.16, A:I.18, A:I.38, A:D.60, A:D.60, A:I.61, A:N.87, A:Y.153, A:K.157, A:I.186, A:I.186, A:S.188, A:S.188, A:G.190 Water bridges: A:G.13, A:G.19, A:N.87 NAD.2: 27 residues within 4Å: Chain B: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 18 PLIP interactions: 18 interactions with chain B Hydrophobic interactions: B:P.183 Hydrogen bonds: B:Q.16, B:Q.16, B:I.18, B:I.38, B:D.60, B:I.61, B:N.87, B:K.157, B:I.186, B:I.186, B:S.188, B:S.188, B:G.190 Water bridges: B:G.13, B:G.19, B:N.39, B:N.87 NAD.3: 27 residues within 4Å: Chain C: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 19 PLIP interactions: 19 interactions with chain C Hydrophobic interactions: C:P.183 Hydrogen bonds: C:Q.16, C:I.18, C:I.38, C:D.60, C:I.61, C:N.87, C:S.89, C:K.157, C:I.186, C:I.186, C:S.188, C:S.188, C:G.190 Water bridges: C:G.13, C:G.19, C:G.19, C:D.37, C:V.91 NAD.5: 27 residues within 4Å: Chain D: G.13, A.15, Q.16, G.17, I.18, D.37, I.38, A.59, D.60, I.61, N.87, A.88, S.89, V.91, V.110, I.138, A.139, S.140, Y.153, K.157, P.183, G.184, L.185, I.186, S.188, G.190, V.191 21 PLIP interactions: 21 interactions with chain D Hydrophobic interactions: D:I.18, D:P.183 Hydrogen bonds: D:Q.16, D:I.18, D:I.38, D:D.60, D:D.60, D:I.61, D:N.87, D:S.89, D:Y.153, D:K.157, D:I.186, D:I.186, D:S.188, D:S.188, D:G.190 Water bridges: D:G.19, D:A.59, D:N.87, D:V.91

1 x ACY: ACETIC ACID(Non-functional Binders)

ACY.4: 4 residues within 4Å: Chain A: Q.214, E.216, H.217 Chain C: R.231 5 PLIP interactions: 3 interactions with chain A, 2 interactions with chain C Hydrophobic interactions: A:Q.214 Water bridges: A:H.217, C:R.231 Salt bridges: A:H.217, C:R.231

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Chu, H.N. et al., The crystal structure of SDR-type pyridoxal 4-dehydrogenase of Mesorhizobium loti. Biosci.Biotechnol.Biochem. (2011)

Release Date

2011-04-20

Peptides

3-oxoacyl-(Acyl-carrier protein) reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-oxoacyl-(Acyl-carrier protein) reductase

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