SMTL ID : 5nuf.1 (1 other biounit)

Cytosolic Malate Dehydrogenase 1

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-dimer

Ligands

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

NAD.1: 24 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: SO4.3 14 PLIP interactions: 14 interactions with chain A Hydrophobic interactions: A:I.17, A:A.247 Hydrogen bonds: A:G.12, A:A.14, 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:R.93 NAD.15: 24 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: SO4.17 14 PLIP interactions: 14 interactions with chain B Hydrophobic interactions: B:I.17, B:A.247 Hydrogen bonds: B:G.12, B:A.14, 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:R.93

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

SO4.2: 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 SO4.3: 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:G.232 Water bridges: A:R.163, A:A.233, A:A.233, A:S.243 Salt bridges: A:R.163, A:H.188 SO4.4: 3 residues within 4Å: Chain A: A.122, P.123, N.124 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.124, A:N.124 Water bridges: A:N.83, A:N.83 SO4.16: 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 SO4.17: 7 residues within 4Å: Chain B: N.132, L.159, R.163, H.188, G.232, S.243 Ligands: NAD.15 8 PLIP interactions: 8 interactions with chain B Hydrogen bonds: B:N.132, B:G.232 Water bridges: B:R.163, B:A.233, B:A.233, B:S.243 Salt bridges: B:R.163, B:H.188 SO4.18: 3 residues within 4Å: Chain B: A.122, P.123, N.124 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:N.124, B:N.124 Water bridges: B:N.83, B:N.83

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: R.239 Chain B: A.14, G.15, Q.16, Y.19 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.239 GOL.6: 5 residues within 4Å: Chain A: S.277, Y.278, Q.301, G.302 Ligands: PEG.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Y.278, A:Y.278, A:G.302 GOL.19: 5 residues within 4Å: Chain A: A.14, G.15, Q.16, Y.19 Chain B: R.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.239 GOL.20: 5 residues within 4Å: Chain B: S.277, Y.278, Q.301, G.302 Ligands: PEG.22 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Y.278, B:Y.278, B:G.302

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

PEO.7: 1 residues within 4Å: Chain A: T.73 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.73 PEO.21: 1 residues within 4Å: Chain B: T.73 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:T.73 Water bridges: B:T.73

2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.8: 6 residues within 4Å: Chain A: Y.278, S.279, L.303, I.305, R.310 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.310 PEG.22: 6 residues within 4Å: Chain B: Y.278, S.279, L.303, I.305, R.310 Ligands: GOL.20 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.310

4 x NA: SODIUM ION(Non-functional Binders)

NA.9: 2 residues within 4Å: Chain A: D.217, D.221 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:D.217 NA.10: 3 residues within 4Å: Chain A: D.275, S.277, Q.301 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.275, A:S.277, A:Q.301 Water bridges: A:I.299 NA.23: 2 residues within 4Å: Chain B: D.217, D.221 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.217, B:D.221 NA.24: 3 residues within 4Å: Chain B: D.275, S.277, Q.301 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.277, B:S.277, B:Q.301 Water bridges: B:I.299

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

EDO.11: 3 residues within 4Å: Chain A: L.260, G.261, T.262 2 PLIP interactions: 2 interactions with chain A Water bridges: A:T.262, A:T.262 EDO.12: 5 residues within 4Å: Chain A: D.221, I.225, S.226, Q.229, K.312 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.229, A:Q.229, A:K.312, A:K.312 EDO.13: 4 residues within 4Å: Chain A: Q.167, R.231 Chain B: M.56, I.59 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.167, A:R.231, A:R.231 EDO.14: 6 residues within 4Å: Chain A: S.169, E.170, S.173, V.174, P.175 Chain B: K.67 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:K.67, A:E.170 Water bridges: A:V.176 EDO.25: 3 residues within 4Å: Chain B: L.260, G.261, T.262 2 PLIP interactions: 2 interactions with chain B Water bridges: B:T.262, B:T.262 EDO.26: 5 residues within 4Å: Chain B: D.221, I.225, S.226, Q.229, K.312 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.229, B:Q.229, B:K.312, B:K.312 EDO.27: 4 residues within 4Å: Chain A: M.56, I.59 Chain B: Q.167, R.231 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:Q.167, B:R.231, B:R.231 EDO.28: 6 residues within 4Å: Chain A: K.67 Chain B: S.169, E.170, S.173, V.174, P.175 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Hydrogen bonds: A:K.67, B:E.170 Water bridges: B:V.176

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

2018-01-10

Peptides

Malate dehydrogenase 1, cytoplasmic: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

Malate dehydrogenase 1, cytoplasmic

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