SMTL ID : 3flk.2 (1 other biounit)

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

Coordinates

PDB Format

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.1, H2O.1 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 A, 1 interactions with chain B, 2 Ligand-Water interactions Metal complexes: A:D.225, B:D.249, H2O.15, H2O.15

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

NAI.2: 26 residues within 4Å: Chain A: I.16, F.75, A.77, V.78, G.79, P.81, D.86, L.94, E.281, V.283, H.284, G.285, S.286, A.287, P.288, D.289, I.290, A.296, N.297, D.342 Chain B: N.194, H.223, I.226, R.230 Ligands: OXL.3, NH4.4 14 PLIP interactions: 11 interactions with chain A, 3 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:D.289, A:N.297, A:N.297, B:N.194, B:R.230, B:R.230 Water bridges: A:R.98 NAI.10: 28 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: DTT.9, OXL.11, NH4.12 15 PLIP interactions: 12 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:V.78, B:D.86, B:E.281, B:G.285, B:G.285, B:S.286, B:A.287, B:D.289, B:N.297, B:N.297, A:N.194, A:R.230 Water bridges: B:S.89, B:R.98, A:R.230

2 x OXL: OXALATE ION(Non-covalent)

OXL.3: 9 residues within 4Å: Chain A: R.98, R.108, R.134, D.249, V.283 Chain B: K.192, D.225 Ligands: MG.1, NAI.2 11 PLIP interactions: 3 interactions with chain B, 8 interactions with chain A Water bridges: B:K.192, B:K.192, A:R.108, A:R.108, A:R.108 Salt bridges: B:K.192, A:R.98, A:R.108, A:R.134, A:R.134 Hydrogen bonds: A:D.249 OXL.11: 9 residues within 4Å: Chain A: K.192, D.225 Chain B: R.98, R.108, R.134, D.249, V.283 Ligands: MG.5, NAI.10 11 PLIP interactions: 8 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:D.249 Water bridges: B:R.98, B:R.98, B:R.108, B:R.108, A:K.192, A:N.194 Salt bridges: B:R.98, B:R.108, B:R.134, 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:E.281 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:H.284

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

SO4.6: 2 residues within 4Å: Chain A: T.152, E.153 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:E.153 SO4.7: 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 SO4.8: 6 residues within 4Å: Chain A: P.109, 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 SO4.13: 4 residues within 4Å: Chain B: K.57, P.60, D.61, D.62 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:D.61, B:D.62 Water bridges: B:D.62, B:D.62 Salt bridges: B:K.57 SO4.14: 2 residues within 4Å: Chain B: R.26, S.357 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.357 Water bridges: B:D.358, B:D.358 Salt bridges: B:R.26 SO4.15: 5 residues within 4Å: Chain B: R.111, W.303, L.307, H.323, L.327 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:W.303 Water bridges: B:R.111 Salt bridges: B:R.111, B:H.323 SO4.16: 2 residues within 4Å: Chain A: R.165 Chain B: N.151 2 PLIP interactions: 2 interactions with chain A Water bridges: A:R.206 Salt bridges: A:R.165

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

DTT.9: 7 residues within 4Å: Chain A: I.226, R.230, L.233, Q.234 Chain B: T.261, I.262 Ligands: NAI.10 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.234 DTT.17: 7 residues within 4Å: Chain B: D.14, G.15, L.18, C.49, D.50, W.80, F.291 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.15

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
C

B
D

Tartrate dehydrogenase/decarboxylase

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