SMTL ID : 3flk.1 (1 other biounit)

Crystal Structure of Tartrate Dehydrogenase from Pseudomonas putida in complex with NADH, oxalate and metal ion

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 2.00 Å

Oligo State

homo-dimer

Ligands

2 x MG: MAGNESIUM ION(Non-covalent)

MG.1: 4 residues within 4Å: Chain A: D.249, D.253 Chain B: D.225 Ligands: OXL.3 4 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.249, B:D.225, H2O.7, H2O.7 MG.5: 4 residues within 4Å: Chain A: D.225 Chain B: D.249, D.253 Ligands: OXL.11 4 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: B:D.249, A:D.225, H2O.16, H2O.16

2 x NAI: 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE(Non-covalent)

NAI.2: 27 residues within 4Å: Chain A: I.16, F.75, A.77, V.78, G.79, P.81, D.86, L.94, I.262, G.263, E.281, V.283, H.284, G.285, S.286, A.287, P.288, I.290, A.296, N.297, D.342 Chain B: N.194, H.223, I.226, R.230 Ligands: OXL.3, NH4.4 17 PLIP interactions: 13 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:V.78, A:D.86, A:E.281, A:G.285, A:G.285, A:S.286, A:A.287, A:N.297, A:N.297, B:N.194, B:R.230 Water bridges: A:D.86, A:D.86, A:R.98, A:A.287, B:R.230, B:R.230 NAI.10: 27 residues within 4Å: Chain A: N.194, H.223, I.226, R.230 Chain B: I.16, F.75, A.77, V.78, G.79, P.81, D.86, L.94, I.262, E.281, V.283, H.284, G.285, S.286, A.287, P.288, D.289, I.290, A.296, N.297, D.342 Ligands: OXL.11, NH4.12 17 PLIP interactions: 13 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:V.78, B:D.86, B:E.281, B:H.284, B:G.285, B:G.285, B:S.286, B:A.287, B:D.289, B:N.297, A:N.194, A:R.230 Water bridges: B:S.89, B:R.98, B:D.289, A:R.230, A:R.230

2 x OXL: OXALATE ION(Non-covalent)

OXL.3: 8 residues within 4Å: Chain A: R.98, R.108, R.134, D.249 Chain B: K.192, D.225 Ligands: MG.1, NAI.2 11 PLIP interactions: 4 interactions with chain B, 7 interactions with chain A Water bridges: B:K.192, B:N.194, A:R.108, A:R.108, A:D.249 Salt bridges: B:K.192, B:K.192, A:R.98, A:R.108, A:R.134 Hydrogen bonds: A:D.249 OXL.11: 10 residues within 4Å: Chain A: K.192, D.225 Chain B: L.90, R.98, R.108, R.134, D.249, V.283 Ligands: MG.5, NAI.10 14 PLIP interactions: 10 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:D.249 Water bridges: B:R.98, B:R.108, B:R.108, B:R.134, B:D.249, A:K.192, A:N.194 Salt bridges: B:R.98, B:R.108, B:R.134, B:R.134, A:K.192, A:K.192

2 x NH4: AMMONIUM ION(Non-functional Binders)

NH4.4: 6 residues within 4Å: Chain A: G.76, A.77, E.281, P.282, H.284 Ligands: NAI.2 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.281, A:H.284 NH4.12: 6 residues within 4Å: Chain B: G.76, A.77, E.281, P.282, H.284 Ligands: NAI.10 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.281

7 x SO4: SULFATE ION(Non-functional Binders)

SO4.6: 5 residues within 4Å: Chain A: R.111, W.303, L.307, H.323, L.327 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.111, A:H.323 SO4.7: 2 residues within 4Å: Chain A: Q.234, R.237 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.234, A:Q.234 Salt bridges: A:R.237 SO4.8: 4 residues within 4Å: Chain A: K.57, P.60, D.61, D.62 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:D.61, A:D.62 Salt bridges: A:K.57 SO4.9: 2 residues within 4Å: Chain A: R.182, E.183 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.183 Salt bridges: A:R.182 SO4.13: 5 residues within 4Å: Chain B: R.111, W.303, L.307, H.323, L.327 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.111, B:H.323 SO4.14: 3 residues within 4Å: Chain B: N.151, T.152, E.153 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.153 SO4.15: 2 residues within 4Å: Chain B: Q.234, R.237 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.234, B:Q.234 Salt bridges: B:R.237

1 x DTT: 2,3-DIHYDROXY-1,4-DITHIOBUTANE(Non-covalent)

DTT.16: 3 residues within 4Å: Chain B: R.165, R.206, H.213 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.165, B:R.165, B:R.206, B:R.206

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Malik, R. et al., Structural characterization of tartrate dehydrogenase: a versatile enzyme catalyzing multiple reactions. Acta Crystallogr.,Sect.D (2010)

Release Date

2009-12-22

Peptides

Tartrate dehydrogenase/decarboxylase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

Tartrate dehydrogenase/decarboxylase

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