SMTL ID : 5nuf.2 (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: SO4.2 15 PLIP interactions: 15 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:G.18, A:R.93 NAD.10: 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: SO4.12, ACT.14 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:I.17, B:A.247 Hydrogen bonds: B:G.12, B:A.14, B:Q.16, B:I.17, B:G.90, B:N.106, B:Q.113, B:N.132, B:N.132, B:L.156, B:S.242 Water bridges: B:G.15, B:G.18, B:S.242

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:G.232, A:S.243 Water bridges: A:R.163, 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 SO4.11: 4 residues within 4Å: Chain B: R.7, I.38, H.40, V.70 4 PLIP interactions: 4 interactions with chain B Water bridges: B:R.7, B:T.80 Salt bridges: B:R.7, B:H.40 SO4.12: 9 residues within 4Å: Chain B: R.93, R.99, N.132, L.159, R.163, H.188, G.232, S.243 Ligands: NAD.10 11 PLIP interactions: 11 interactions with chain B Hydrogen bonds: B:N.132, B:S.243 Water bridges: B:R.93, B:R.93, B:D.160, B:G.232, B:S.243 Salt bridges: B:R.93, B:R.99, B:R.163, B:H.188 SO4.13: 6 residues within 4Å: Chain B: R.93, E.98, R.99, S.189, S.190, Q.230 14 PLIP interactions: 14 interactions with chain B Hydrogen bonds: B:E.98, B:R.99, B:S.190, B:Q.229 Water bridges: B:R.93, 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

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

ACT.4: 3 residues within 4Å: Chain A: E.322, D.325, L.326 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:E.322 ACT.14: 5 residues within 4Å: Chain B: P.92, R.93, I.236, S.242 Ligands: NAD.10 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:P.92, B:I.236 Hydrogen bonds: B:R.93 Water bridges: B:N.132, B:N.132

7 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 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:G.15, B:Q.16, A:R.239 Water bridges: B:Q.16 GOL.6: 5 residues within 4Å: Chain A: Q.167, R.231 Chain B: M.56, I.59 Ligands: NA.8 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:Q.167, A:R.231, A:R.231 GOL.15: 6 residues within 4Å: Chain B: K.100, D.101, V.102, M.103, S.104, L.326 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:K.100, B:D.101, B:S.104, B:S.104 GOL.16: 5 residues within 4Å: Chain A: M.56, I.59 Chain B: Q.167, E.170, R.231 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:Q.167, B:R.231, B:R.231 Water bridges: B:Q.167, B:Q.167 GOL.17: 4 residues within 4Å: Chain B: S.277, Y.278, Q.301, G.302 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.277, B:Y.278, B:Q.301, B:G.302 GOL.18: 10 residues within 4Å: Chain B: L.117, E.118, A.121, A.122, P.123, N.124, C.125, S.147, I.148, P.149 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:A.122, B:N.124, B:C.125, B:S.147 GOL.19: 5 residues within 4Å: Chain B: K.142, P.146, I.148, P.149, E.150 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.142, B:I.148, B:E.150, B:E.150 Water bridges: B:I.148

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

FMT.7: 2 residues within 4Å: Chain A: P.149, E.150 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:E.150, A:E.150 Water bridges: A:K.142, A:K.142, A:K.151

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

NA.8: 2 residues within 4Å: Chain A: E.170 Ligands: GOL.6 1 PLIP interactions: 1 interactions with chain B Water bridges: B:K.55

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

EDO.9: 3 residues within 4Å: Chain A: L.260, G.261, P.263 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.264 EDO.21: 4 residues within 4Å: Chain B: K.215, D.216, D.217, A.218 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:D.216, B:D.217, B:D.217, B:A.218 EDO.22: 3 residues within 4Å: Chain A: G.15, Y.19 Chain B: R.239 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.239

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

PEO.20: 3 residues within 4Å: Chain B: S.108, K.111, S.332 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.111, B:S.332, B:S.332

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
B

B
C

Malate dehydrogenase 1, cytoplasmic

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