SMTL ID : 2jap.1

CLAVULANIC ACID DEHYDROGENASE: STRUCTURAL AND BIOCHEMICAL ANALYSIS OF THE FINAL STEP IN THE BIOSYNTHESIS OF THE BETA-LACTAMASE INHIBITOR CLAVULANIC ACID

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.10 Å

Oligo State

homo-tetramer

Ligands

4 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.1: 31 residues within 4Å: Chain A: G.14, A.15, S.16, S.17, G.18, I.19, A.38, R.39, R.40, L.63, D.64, V.65, N.91, A.92, G.93, I.94, T.114, M.140, S.141, S.142, Y.155, K.159, P.185, G.186, T.187, T.188, T.190, E.191, L.192, H.195 Ligands: J01.2 37 PLIP interactions: 37 interactions with chain A Hydrophobic interactions: A:P.185, A:L.192 Hydrogen bonds: A:S.16, A:S.16, A:S.17, A:S.17, A:S.17, A:S.17, A:I.19, A:R.39, A:R.40, A:R.40, A:D.64, A:D.64, A:V.65, A:N.91, A:N.91, A:G.93, A:Y.155, A:K.159, A:T.188, A:T.188, A:T.190, A:E.191, A:L.192 Water bridges: A:G.18, A:G.20, A:R.39, A:R.39, A:R.39, A:R.39, A:R.40, A:H.195, A:Y.205 Salt bridges: A:R.39, A:R.40 pi-Cation interactions: A:R.39 NDP.3: 30 residues within 4Å: Chain B: G.14, A.15, S.16, S.17, G.18, I.19, A.38, R.39, R.40, L.63, D.64, V.65, N.91, A.92, G.93, T.114, M.140, S.141, S.142, Y.155, K.159, P.185, G.186, T.187, T.188, T.190, E.191, L.192, H.195 Ligands: J01.4 34 PLIP interactions: 34 interactions with chain B Hydrophobic interactions: B:P.185, B:L.192 Hydrogen bonds: B:S.16, B:S.16, B:S.17, B:S.17, B:S.17, B:S.17, B:I.19, B:R.39, B:R.40, B:R.40, B:D.64, B:V.65, B:N.91, B:N.91, B:G.93, B:T.114, B:K.159, B:T.188, B:T.188, B:T.190, B:T.190, B:E.191, B:L.192 Water bridges: B:G.20, B:R.39, B:R.39, B:R.39, B:T.190, B:E.191 Salt bridges: B:R.39, B:R.40 pi-Cation interactions: B:R.39 NDP.5: 30 residues within 4Å: Chain C: G.14, A.15, S.16, S.17, G.18, I.19, A.38, R.39, R.40, L.63, D.64, V.65, N.91, A.92, G.93, T.114, M.140, S.141, S.142, Y.155, K.159, P.185, G.186, T.187, T.188, T.190, E.191, L.192, H.195 Ligands: J01.6 33 PLIP interactions: 33 interactions with chain C Hydrophobic interactions: C:P.185, C:L.192 Hydrogen bonds: C:S.16, C:S.16, C:S.17, C:S.17, C:S.17, C:S.17, C:I.19, C:R.39, C:R.40, C:R.40, C:D.64, C:D.64, C:V.65, C:N.91, C:N.91, C:G.93, C:Y.155, C:K.159, C:T.188, C:T.188, C:T.190, C:E.191, C:L.192 Water bridges: C:G.20, C:R.39, C:R.40, C:T.190, C:H.195 Salt bridges: C:R.39, C:R.40 pi-Cation interactions: C:R.39 NDP.7: 28 residues within 4Å: Chain D: G.14, S.16, S.17, G.18, I.19, A.38, R.39, R.40, L.63, D.64, V.65, N.91, A.92, G.93, T.114, M.140, S.141, S.142, Y.155, K.159, P.185, G.186, T.187, T.188, T.190, E.191, L.192 Ligands: J01.8 29 PLIP interactions: 29 interactions with chain D Hydrophobic interactions: D:P.185, D:L.192 Hydrogen bonds: D:S.16, D:S.16, D:S.17, D:S.17, D:S.17, D:S.17, D:I.19, D:R.39, D:R.40, D:R.40, D:D.64, D:V.65, D:N.91, D:N.91, D:G.93, D:K.159, D:T.188, D:T.188, D:T.190, D:T.190, D:E.191, D:L.192 Water bridges: D:G.20, D:T.190 Salt bridges: D:R.39, D:R.40 pi-Cation interactions: D:R.39

4 x J01: (2R,3Z,5R)-3-(2-HYDROXYETHYLIDENE)-7-OXO-4-OXA-1-AZABICYCLO[3.2.0]HEPTANE-2-CARBOXYLIC ACID(Non-covalent)

J01.2: 14 residues within 4Å: Chain A: M.95, L.97, S.142, I.143, A.144, V.149, A.152, Y.155, Q.156, T.187, L.192, Y.205, R.208 Ligands: NDP.1 10 PLIP interactions: 10 interactions with chain A Hydrophobic interactions: A:A.144, A:A.152, A:Y.155 Hydrogen bonds: A:S.142, A:Y.155, A:R.208 Water bridges: A:T.187, A:R.208, A:Q.246 Salt bridges: A:R.208 J01.4: 14 residues within 4Å: Chain B: M.95, L.97, S.142, I.143, A.144, V.149, A.152, Y.155, Q.156, T.187, L.192, Y.205, R.208 Ligands: NDP.3 12 PLIP interactions: 12 interactions with chain B Hydrophobic interactions: B:A.144, B:A.152, B:Y.155 Hydrogen bonds: B:S.142, B:Y.155, B:Y.155, B:Y.205, B:R.208 Water bridges: B:T.187, B:T.187, B:R.208 Salt bridges: B:R.208 J01.6: 14 residues within 4Å: Chain C: M.95, L.97, S.142, I.143, A.144, V.149, A.152, Y.155, Q.156, T.187, L.192, Y.205, R.208 Ligands: NDP.5 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:A.144, C:A.152, C:Y.155 Hydrogen bonds: C:S.142, C:Y.155, C:R.208 Water bridges: C:T.187, C:R.208, C:Q.246 Salt bridges: C:R.208 J01.8: 14 residues within 4Å: Chain D: M.95, L.97, S.142, I.143, A.144, V.149, A.152, Y.155, Q.156, T.187, L.192, Y.205, R.208 Ligands: NDP.7 12 PLIP interactions: 12 interactions with chain D Hydrophobic interactions: D:A.144, D:A.152, D:Y.155 Hydrogen bonds: D:S.142, D:Y.155, D:Y.155, D:Y.205, D:R.208 Water bridges: D:T.187, D:T.187, D:R.208 Salt bridges: D:R.208

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mackenzie, A.K. et al., Clavulanic Acid Dehydrogenase: Structural and Biochemical Analysis of the Final Step in the Biosynthesis of the Beta-Lactamase Inhibitor Clavulanic Acid. Biochemistry (2007)

Release Date

2007-02-20

Peptides

CLAVALDEHYDE DEHYDROGENASE: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

CLAVALDEHYDE DEHYDROGENASE

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