SMTL ID : 5nue.2 (1 other biounit)

Cytosolic Malate Dehydrogenase 1 (peroxide-treated)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 25 residues within 4Å: Chain A: G.12, A.14, G.15, Q.16, I.17, L.42, D.43, I.44, V.88, G.89, G.90, F.91, P.92, I.109, Q.113, V.130, A.131, N.132, L.156, L.159, H.188, S.243, A.247 Ligands: SO4.2, PEO.7 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.17, A:A.247 Hydrogen bonds: A:G.12, A:Q.16, A:Q.16, A:I.17, A:G.90, A:Q.113, A:N.132, A:N.132, A:L.156 Water bridges: A:G.15, A:G.18, A:R.93 NAD.13: 25 residues within 4Å: Chain B: G.12, A.14, G.15, Q.16, I.17, L.42, D.43, I.44, V.88, G.89, G.90, F.91, P.92, I.109, Q.113, V.130, A.131, N.132, L.156, L.159, H.188, S.243, A.247 Ligands: SO4.14, PEO.19 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.17, B:A.247 Hydrogen bonds: B:G.12, B:Q.16, B:Q.16, B:I.17, B:G.90, B:Q.113, B:N.132, B:N.132, B:L.156 Water bridges: B:G.15, B:G.18, B:R.93

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

SO4.2: 7 residues within 4Å: Chain A: N.132, L.159, R.163, H.188, G.232, S.243 Ligands: NAD.1 8 PLIP interactions: 8 interactions with chain A Hydrogen bonds: A:N.132, A:S.243, A:S.243 Water bridges: A:R.163, A:G.232, A:S.243 Salt bridges: A:R.163, A:H.188 SO4.3: 4 residues within 4Å: Chain A: R.7, I.38, H.40, V.70 2 PLIP interactions: 2 interactions with chain A Salt bridges: A:R.7, A:H.40 SO4.4: 3 residues within 4Å: Chain A: A.122, P.123, N.124 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.83, A:N.124, A:N.124 SO4.14: 7 residues within 4Å: Chain B: N.132, L.159, R.163, H.188, G.232, S.243 Ligands: NAD.13 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.132, B:S.243, B:S.243 Water bridges: B:R.163, B:G.232, B:S.243 Salt bridges: B:R.163, B:H.188 SO4.15: 4 residues within 4Å: Chain B: R.7, I.38, H.40, V.70 2 PLIP interactions: 2 interactions with chain B Salt bridges: B:R.7, B:H.40 SO4.16: 3 residues within 4Å: Chain B: A.122, P.123, N.124 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.83, B:N.124, B:N.124

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: S.277, Y.278, Q.301, G.302 Ligands: EDO.12 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Y.278, A:Y.278, A:Q.301, A:G.302 Water bridges: A:S.277, A:S.279, A:S.279 GOL.17: 5 residues within 4Å: Chain B: S.277, Y.278, Q.301, G.302 Ligands: EDO.24 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:Y.278, B:Y.278, B:Q.301, B:G.302 Water bridges: B:S.277, B:S.279, B:S.279

8 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)

PEO.6: 6 residues within 4Å: Chain A: I.59, D.60 Chain B: R.163, G.166, Q.167, R.231 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.163, B:Q.167, B:Q.167, A:D.60 PEO.7: 3 residues within 4Å: Chain A: I.44, P.46 Ligands: NAD.1 1 PLIP interactions: 1 interactions with chain A Water bridges: A:P.46 PEO.8: 4 residues within 4Å: Chain A: I.59, F.63, L.66 Chain B: V.176 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain B Hydrogen bonds: A:F.63 Water bridges: A:A.62, A:L.66, B:S.169, B:S.169, B:S.169 PEO.9: 4 residues within 4Å: Chain A: Q.16, R.239, L.241 Chain B: Y.19 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.16, A:R.239 PEO.18: 6 residues within 4Å: Chain A: R.163, G.166, Q.167, R.231 Chain B: I.59, D.60 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.163, A:Q.167, A:Q.167, A:R.231 PEO.19: 3 residues within 4Å: Chain B: I.44, P.46 Ligands: NAD.13 1 PLIP interactions: 1 interactions with chain B Water bridges: B:P.46 PEO.20: 4 residues within 4Å: Chain A: V.176 Chain B: I.59, F.63, L.66 7 PLIP interactions: 4 interactions with chain B, 3 interactions with chain A Hydrogen bonds: B:L.66 Water bridges: B:I.59, B:A.62, B:F.63, A:S.169, A:S.169, A:E.170 PEO.21: 4 residues within 4Å: Chain A: Y.19 Chain B: Q.16, R.239, L.241 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.16, B:R.239

4 x FMT: FORMIC ACID(Non-functional Binders)

FMT.10: 2 residues within 4Å: Chain A: S.190, Q.230 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.190, A:Q.230 FMT.11: 5 residues within 4Å: Chain A: V.259, L.260, G.261, R.293, N.294 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.294 Water bridges: A:G.295, A:G.295 FMT.22: 2 residues within 4Å: Chain B: S.190, Q.230 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.190, B:Q.230 FMT.23: 5 residues within 4Å: Chain B: V.259, L.260, G.261, R.293, N.294 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:N.294 Water bridges: B:G.295, B:G.295

2 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)

EDO.12: 5 residues within 4Å: Chain A: Y.278, S.279, I.305, R.310 Ligands: GOL.5 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:S.279 Water bridges: A:S.279, A:G.302, A:R.310 EDO.24: 5 residues within 4Å: Chain B: Y.278, S.279, I.305, R.310 Ligands: GOL.17 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.279 Water bridges: B:S.279, B:G.302, B:R.310

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Huang, J. et al., Self-protection of cytosolic malate dehydrogenase against oxidative stress in Arabidopsis. J. Exp. Bot. (2018)

Release Date

2018-02-28

Peptides

Malate dehydrogenase 1, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
C

Malate dehydrogenase 1, cytoplasmic

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