SMTL ID : 5mha.1

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with a mixture of 2-ketohexanoic acid and 2-hydroxyhexanoic acid, and NADPH (1.57 A resolution)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.57 Å

Oligo State

homo-dimer

Ligands

7 x MG: MAGNESIUM ION(Non-covalent)(Non-functional Binders)

MG.1: 2 residues within 4Å: Chain A: E.202, E.204 No protein-ligand interaction detected (PLIP) MG.2: 1 residues within 4Å: Chain A: E.211 3 PLIP interactions: 1 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:E.211, H2O.2, H2O.2 MG.3: 2 residues within 4Å: Chain A: D.265 Chain B: H.120 5 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: B:H.120, A:D.265, H2O.2, H2O.5, H2O.5 MG.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.5: 3 residues within 4Å: Chain A: T.132, A.134, E.136 4 PLIP interactions: 3 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:T.132, A:T.132, A:A.134, H2O.3 MG.13: 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.16 MG.14: 1 residues within 4Å: Ligands: EDO.15 No protein-ligand interaction detected (PLIP)

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

EDO.6: 4 residues within 4Å: Chain A: S.26, V.30, P.31, V.32 No protein-ligand interaction detected (PLIP) EDO.7: 4 residues within 4Å: Chain A: P.73, V.74, G.75, V.76 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:V.74, A:G.75, A:V.76 EDO.8: 2 residues within 4Å: Chain A: A.188, T.214 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:T.214 EDO.9: 5 residues within 4Å: Chain A: D.152, A.155, A.156, N.173 Chain B: A.156 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:A.156, A:A.156, A:N.173 EDO.15: 5 residues within 4Å: Chain B: R.109, A.112, D.123, E.267 Ligands: MG.14 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:R.109, B:D.123, B:E.267 EDO.16: 2 residues within 4Å: Chain B: I.90, D.285 3 PLIP interactions: 3 interactions with chain B Water bridges: B:T.93, B:T.93, B:D.285 EDO.17: 2 residues within 4Å: Chain B: A.245, D.268 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:A.245 EDO.18: 5 residues within 4Å: Chain B: T.93, R.148, G.149, D.152, R.153 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:T.93, B:R.148, B:D.152, B:R.153, B:R.153

2 x 7N5: 2-Ketohexanoic acid(Non-covalent)

7N5.10: 9 residues within 4Å: Chain A: A.15, R.66, A.67, G.68, H.91, R.226, H.274, Y.282 Ligands: NDP.11 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.15, A:Y.282 Hydrogen bonds: A:A.67, A:G.68 Water bridges: A:R.66, A:R.66 Salt bridges: A:R.66, A:R.226, A:H.274 7N5.19: 9 residues within 4Å: Chain B: R.66, A.67, G.68, H.91, R.226, H.274, Y.282 Ligands: 7N6.20, NDP.21 6 PLIP interactions: 6 interactions with chain B Hydrophobic interactions: B:Y.282 Hydrogen bonds: B:A.67, B:G.68 Salt bridges: B:R.66, B:R.226, B:H.274

2 x NDP: NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NDP.11: 27 residues within 4Å: Chain A: A.67, G.68, T.88, H.91, G.142, L.143, G.144, T.145, L.146, V.164, R.165, R.166, S.167, 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: 7N5.10 25 PLIP interactions: 25 interactions with chain A Hydrophobic interactions: A:A.67, A:L.146, A:A.277 Hydrogen bonds: A:T.88, A:T.88, A:L.143, A:L.143, A:T.145, A:L.146, A:R.166, A:R.166, A:S.167, A:V.224, A:A.277 Water bridges: A:Y.69, A:G.89, A:G.144, A:G.147, A:R.166, A:R.166, A:L.199, A:L.199, A:E.202 Salt bridges: A:R.165 pi-Stacking: A:H.91 NDP.21: 28 residues within 4Å: Chain B: A.67, G.68, T.88, H.91, G.142, L.143, G.144, T.145, L.146, V.164, R.165, R.166, S.167, 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: 7N5.19, 7N6.20 25 PLIP interactions: 25 interactions with chain B Hydrophobic interactions: B:A.67, B:L.146, B:A.277 Hydrogen bonds: B:T.88, B:T.88, B:L.143, B:L.143, B:T.145, B:T.145, B:L.146, B:R.166, B:S.167, B:D.250, B:D.250 Water bridges: B:G.89, B:G.144, B:G.147, B:R.166, B:L.199, B:L.199, B:E.202, B:A.277 Salt bridges: B:R.165, B:R.166 pi-Stacking: B:H.91

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

SO4.12: 3 residues within 4Å: Chain A: R.148, R.165, P.170 3 PLIP interactions: 3 interactions with chain A Water bridges: A:R.148 Salt bridges: A:R.148, A:R.165

1 x 7N6: (2R)-2-hydroxyhexanoic acid(Non-covalent)

7N6.20: 11 residues within 4Å: Chain B: F.50, I.65, R.66, A.67, G.68, H.91, R.226, H.274, Y.282 Ligands: 7N5.19, NDP.21 10 PLIP interactions: 10 interactions with chain B Hydrophobic interactions: B:F.50, B:Y.282 Hydrogen bonds: B:R.66, B:R.66, B:A.67, B:G.68, B:R.226 Salt bridges: B:R.66, B:H.91, B:R.226

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

2018-05-09

Peptides

D-2-hydroxyacid dehydrogenase: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

D-2-hydroxyacid dehydrogenase

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