- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 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)
- 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
AB
A
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.80 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 6 x SO4: SULFATE ION(Non-functional Binders)
- 4 x GOL: GLYCEROL(Non-functional Binders)
- 2 x PEO: HYDROGEN PEROXIDE(Non-functional Binders)
- 2 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)
- 4 x NA: SODIUM ION(Non-functional Binders)
- 8 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 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
AB
A