SMTL ID : 5nue.1 (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: 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: SO4.2 15 PLIP interactions: 15 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, A:S.112 NAD.12: 27 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, N.106, I.109, Q.113, V.130, A.131, N.132, L.156, L.159, H.188, S.242, S.243, A.247 Ligands: SO4.15, PEO.22 17 PLIP interactions: 17 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:R.93, B:N.106, B:Q.113, B:N.132, B:N.132 Water bridges: B:G.15, B:G.18, B:R.93, B:S.112, B:L.156

5 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 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:N.132, 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 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.7 Salt bridges: A:R.7, A:H.40 SO4.13: 6 residues within 4Å: Chain B: R.93, E.98, R.99, S.189, S.190, Q.230 12 PLIP interactions: 12 interactions with chain B Hydrogen bonds: B:E.98, B:R.99, B:S.190 Water bridges: B:R.93, B:R.93, B:K.100, B:K.100, B:S.190, B:S.190, B:S.191 Salt bridges: B:R.93, B:R.99 SO4.14: 4 residues within 4Å: Chain B: R.7, I.38, H.40, V.70 5 PLIP interactions: 5 interactions with chain B Water bridges: B:R.7, B:H.40, B:T.80 Salt bridges: B:R.7, B:H.40 SO4.15: 10 residues within 4Å: Chain B: R.93, R.99, N.132, R.163, H.188, G.232, S.243 Ligands: NAD.12, PEO.22, EDO.28 7 PLIP interactions: 7 interactions with chain B Hydrogen bonds: B:N.132 Water bridges: B:R.93, B:R.93 Salt bridges: B:R.93, B:R.99, B:R.163, B:H.188

5 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: I.299, V.300, Q.301 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.301, A:Q.301 GOL.5: 3 residues within 4Å: Chain A: Q.202, G.206, E.207 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Q.202, A:E.207 GOL.16: 5 residues within 4Å: Chain A: M.56, I.59 Chain B: Q.167, E.170, R.231 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.167, B:R.231, B:R.231 Water bridges: B:Q.167 GOL.17: 4 residues within 4Å: Chain B: N.83, V.84, N.124, K.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:N.124, B:K.126 GOL.18: 5 residues within 4Å: Chain A: R.239 Chain B: A.14, G.15, Q.16, Y.19 4 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:G.15, A:R.239, A:R.239 Water bridges: B:Q.16

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

PEO.6: 6 residues within 4Å: Chain A: R.163, G.166, Q.167, R.231 Chain B: I.59, D.60 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.167, A:Q.167, B:D.60 PEO.7: 6 residues within 4Å: Chain A: N.162, D.253 Chain B: R.27, A.61, A.62, P.64 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain A Hydrogen bonds: B:R.27, B:R.27, B:A.62, A:N.162, A:D.253 Water bridges: A:R.158, A:R.256, A:R.256 PEO.8: 3 residues within 4Å: Chain A: K.142, E.143, P.146 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:K.142 Water bridges: A:K.142, A:K.142 PEO.19: 6 residues within 4Å: Chain A: I.59, D.60 Chain B: R.163, G.166, Q.167, R.231 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.163, B:Q.167, A:D.60 PEO.20: 3 residues within 4Å: Chain B: K.142, E.143, P.146 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.142 Water bridges: B:K.142 PEO.21: 3 residues within 4Å: Chain A: V.176 Chain B: F.63, L.66 8 PLIP interactions: 4 interactions with chain A, 4 interactions with chain B Water bridges: A:S.169, A:S.169, A:S.169, A:E.170, B:I.59, B:A.62, B:F.63 Hydrogen bonds: B:L.66 PEO.22: 7 residues within 4Å: Chain B: R.163, G.232, I.236, S.242, S.243 Ligands: NAD.12, SO4.15 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.163, B:S.243 Water bridges: B:R.93

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

FMT.9: 2 residues within 4Å: Chain A: S.190, Q.230 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.190, A:Q.230 Water bridges: A:Q.230 FMT.26: 3 residues within 4Å: Chain B: Q.202, G.206, E.207 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:Q.202, B:E.207 FMT.27: 4 residues within 4Å: Chain B: S.108, K.111, L.331, S.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.111, B:K.111, B:S.332

1 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.10: 4 residues within 4Å: Chain A: K.215, D.216, D.217, A.218 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:D.216, A:D.217, A:D.217, A:A.218

1 x ETX: 2-ETHOXYETHANOL(Non-covalent)

ETX.11: 5 residues within 4Å: Chain A: Q.167, E.170, 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

3 x ACT: ACETATE ION(Non-functional Binders)

ACT.23: 3 residues within 4Å: Chain B: D.216, D.217, A.218 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:D.217, B:A.218 ACT.24: 3 residues within 4Å: Chain B: I.148, P.149, E.150 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:E.150, B:E.150 Water bridges: B:K.151 ACT.25: 2 residues within 4Å: Chain B: P.281, S.282 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:S.282

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

EDO.28: 11 residues within 4Å: Chain B: R.93, R.99, D.160, R.163, Q.192, V.228, Q.229, Q.230, R.231, G.232 Ligands: SO4.15 9 PLIP interactions: 9 interactions with chain B Hydrogen bonds: B:R.93, B:R.99, B:D.160, B:R.163, B:Q.192, B:Q.192, B:G.232 Water bridges: B:Q.229, B:A.233 EDO.29: 3 residues within 4Å: Chain B: D.325, Y.328, S.329 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.329 Water bridges: B:D.325

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
A

B
B

Malate dehydrogenase 1, cytoplasmic

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