- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
EDO.2: 7 residues within 4Å:- Chain A: W.264, D.265, F.266, E.267
- Chain B: R.114, Q.117, H.118
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:Q.117, A:F.266
- Water bridges: B:R.114
EDO.3: 6 residues within 4Å:- Chain A: G.13, R.14, A.15, M.16, P.17
- Chain B: Y.127
3 PLIP interactions:2 interactions with chain B, 1 interactions with chain A- Hydrogen bonds: B:P.125, A:M.16
- Water bridges: B:Y.127
EDO.4: 6 residues within 4Å:- Chain A: E.259, D.260, S.261, P.262, D.265
- Chain B: H.120
2 PLIP interactions:2 interactions with chain A- Hydrogen bonds: A:E.259, A:D.265
EDO.5: 5 residues within 4Å:- Chain A: P.170, V.171, V.174, S.175, V.177
1 PLIP interactions:1 interactions with chain A- Hydrogen bonds: A:V.171
EDO.6: 4 residues within 4Å:- Chain A: E.204, G.205, A.208, V.231
1 PLIP interactions:1 interactions with chain A- Water bridges: A:G.205
EDO.7: 3 residues within 4Å:- Chain A: D.260, S.261, P.262
No protein-ligand interaction detected (PLIP)EDO.18: 7 residues within 4Å:- Chain A: R.114, Q.117, H.118
- Chain B: W.264, D.265, F.266, E.267
5 PLIP interactions:3 interactions with chain A, 2 interactions with chain B- Hydrogen bonds: A:Q.117, B:D.265, B:F.266
- Water bridges: A:R.114, A:H.118
EDO.19: 4 residues within 4Å:- Chain B: P.17, P.18, Q.19, R.20
1 PLIP interactions:1 interactions with chain B- Hydrogen bonds: B:Q.19
EDO.20: 3 residues within 4Å:- Chain B: G.89, I.90, D.285
4 PLIP interactions:4 interactions with chain B- Hydrogen bonds: B:G.89
- Water bridges: B:I.90, B:T.93, B:T.93
EDO.21: 4 residues within 4Å:- Chain A: P.273, H.274
- Chain B: W.122, L.124
3 PLIP interactions:3 interactions with chain A- Hydrogen bonds: A:H.274
- Water bridges: A:R.14, A:H.274
- 2 x SO4: SULFATE ION(Non-functional Binders)
SO4.8: 4 residues within 4Å:- Chain A: R.165, R.166, S.167
- Ligands: NAD.15
4 PLIP interactions:4 interactions with chain A- Hydrogen bonds: A:R.166, A:S.167
- Water bridges: A:R.165
- Salt bridges: A:R.165
SO4.22: 4 residues within 4Å:- Chain B: R.165, R.166, S.167
- Ligands: NAD.28
7 PLIP interactions:7 interactions with chain B- Hydrogen bonds: B:R.166, B:S.167
- Water bridges: B:R.165, B:R.165, B:R.165
- Salt bridges: B:R.165, B:R.166
- 11 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
MG.9: 2 residues within 4Å:- Chain A: H.184, E.211
3 PLIP interactions:1 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:E.211, H2O.2, H2O.2
MG.10: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.11: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.12: 2 residues within 4Å:- Chain A: T.132, A.134
5 PLIP interactions:3 interactions with chain A, 2 Ligand-Water interactions- Metal complexes: A:T.132, A:T.132, A:A.134, H2O.11, H2O.12
MG.13: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.14: 4 residues within 4Å:- Chain A: F.212, E.213, M.215, D.243
5 PLIP interactions:4 interactions with chain A, 1 Ligand-Water interactions- Metal complexes: A:F.212, A:E.213, A:M.215, A:D.243, H2O.13
MG.23: 1 residues within 4Å:- Chain B: E.211
5 PLIP interactions:1 interactions with chain B, 4 Ligand-Water interactions- Metal complexes: B:E.211, H2O.20, H2O.21, H2O.27, H2O.28
MG.24: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.25: 2 residues within 4Å:- Chain B: T.132, A.134
5 PLIP interactions:3 interactions with chain B, 2 Ligand-Water interactions- Metal complexes: B:T.132, B:T.132, B:A.134, H2O.20, H2O.25
MG.26: 0 residues within 4Å:- (No contacts)
No protein-ligand interaction detected (PLIP)MG.27: 4 residues within 4Å:- Chain B: F.212, E.213, M.215, D.243
5 PLIP interactions:4 interactions with chain B, 1 Ligand-Water interactions- Metal complexes: B:F.212, B:E.213, B:M.215, B:D.243, H2O.30
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
NAD.15: 25 residues within 4Å:- Chain A: A.67, G.68, T.88, H.91, G.142, L.143, G.144, T.145, L.146, R.166, A.196, T.197, P.198, T.203, V.224, A.225, R.226, D.250, V.251, H.274, S.276, A.277
- Ligands: NA.1, SO4.8, 7N5.16
18 PLIP interactions:18 interactions with chain A- Hydrophobic interactions: A:A.67, A:L.146, A:A.277
- Hydrogen bonds: A:T.88, A:L.143, A:T.145, A:L.146, A:D.250, A:A.277
- Water bridges: A:D.70, A:G.89, A:L.143, A:G.144, A:T.145, A:G.147, A:L.199, A:T.200
- pi-Stacking: A:H.91
NAD.28: 29 residues within 4Å:- Chain B: A.67, G.68, T.88, H.91, V.141, G.142, L.143, G.144, T.145, L.146, V.164, R.165, R.166, P.180, A.196, T.197, P.198, T.203, V.224, A.225, R.226, D.250, V.251, H.274, S.276, A.277
- Ligands: NA.17, SO4.22, 7N5.29
23 PLIP interactions:23 interactions with chain B- Hydrophobic interactions: B:A.67, B:L.146, B:A.277
- Hydrogen bonds: B:T.88, B:L.143, B:L.143, B:T.145, B:T.145, B:L.146, B:R.166, B:D.250, B:A.277
- Water bridges: B:Y.69, B:D.70, B:G.89, B:G.144, B:T.145, B:G.147, B:R.165, B:L.199, B:T.200, B:E.202
- pi-Stacking: B:H.91
- 2 x 7N5: 2-Ketohexanoic acid(Non-covalent)
7N5.16: 9 residues within 4Å:- Chain A: R.66, A.67, G.68, H.91, R.226, H.274, A.277, Y.282
- Ligands: NAD.15
7 PLIP interactions:7 interactions with chain A- Hydrophobic interactions: A:A.277, A:Y.282
- Hydrogen bonds: A:A.67, A:G.68
- Salt bridges: A:R.66, A:R.226, A:H.274
7N5.29: 9 residues within 4Å:- Chain B: R.66, A.67, G.68, H.91, R.226, H.274, A.277, Y.282
- Ligands: NAD.28
10 PLIP interactions:10 interactions with chain B- Hydrophobic interactions: B:A.277, B:Y.282
- Hydrogen bonds: B:A.67, B:G.68, B:Y.282
- Water bridges: B:R.66, B:R.66
- Salt bridges: B:R.66, B:R.226, B:H.274
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Domenech Perez, J. et al., Productive ternary complexes of D-2-hydroxyacid dehydrogenase provide insights into the chiral specificity of its reaction mechanism. To Be Published
- Release Date
- 2018-06-06
- Peptides
- D-2-hydroxyacid dehydrogenase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D
- Coordinates
- PDB Format
- Method
- X-RAY DIFFRACTION 1.35 Å
- Oligo State
- homo-dimer
- Ligands
- 2 x NA: SODIUM ION(Non-functional Binders)
- 10 x EDO: 1,2-ETHANEDIOL(Non-functional Binders)
- 2 x SO4: SULFATE ION(Non-functional Binders)
- 11 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)
- 2 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)
- 2 x 7N5: 2-Ketohexanoic acid(Non-covalent)
- Links
- RCSB PDBe PDBe-KB PDBj PDBsum CATH PLIP
- Citation
- Domenech Perez, J. et al., Productive ternary complexes of D-2-hydroxyacid dehydrogenase provide insights into the chiral specificity of its reaction mechanism. To Be Published
- Release Date
- 2018-06-06
- Peptides
- D-2-hydroxyacid dehydrogenase: AB
- SMTL:PDB
- SMTL Chain Id:
PDB Chain Id:A
CB
D