SMTL ID : 5mh6.1 (1 other biounit)

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-ketohexanoic acid and NAD+ (1.35 A resolution)

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.35 Å

Oligo State

homo-dimer

Ligands

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

EDO.1: 7 residues within 4Å: Chain A: W.264, D.265, F.266, E.267 Chain B: R.114, Q.117, H.118 7 PLIP interactions: 3 interactions with chain B, 4 interactions with chain A Hydrogen bonds: B:Q.117 Water bridges: B:H.118, B:H.118, A:D.265, A:D.265, A:D.265, A:D.265 EDO.2: 4 residues within 4Å: Chain A: R.14, A.15 Chain B: L.124, Y.127 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:R.14, B:Y.127 EDO.3: 3 residues within 4Å: Chain A: G.89, I.90, D.285 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.89 Water bridges: A:I.90, A:T.93, A:T.93 EDO.4: 4 residues within 4Å: Chain A: P.258, D.260, S.261, P.262 No protein-ligand interaction detected (PLIP) EDO.5: 5 residues within 4Å: Chain A: T.88, G.89, L.289, T.304, N.305 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:N.305, A:N.305 Water bridges: A:G.89 EDO.6: 5 residues within 4Å: Chain A: S.11, F.50, G.51, H.52, R.53 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.11, A:S.11, A:G.51 Water bridges: A:R.14, A:H.52 EDO.18: 7 residues within 4Å: Chain A: R.114, Q.117, H.118 Chain B: W.264, D.265, F.266, E.267 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.117, B:F.266 Water bridges: A:R.114 EDO.19: 4 residues within 4Å: Chain A: Y.127 Chain B: G.13, R.14, A.15 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:R.14 Water bridges: A:Y.127 EDO.20: 6 residues within 4Å: Chain A: H.120 Chain B: E.259, D.260, S.261, P.262, D.265 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:E.259 Water bridges: B:D.265 EDO.21: 5 residues within 4Å: Chain B: P.170, V.171, V.174, S.175, V.177 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:V.171 EDO.22: 3 residues within 4Å: Chain B: G.205, A.208, V.231 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:G.205 EDO.23: 4 residues within 4Å: Chain A: W.122, L.124 Chain B: P.273, H.274 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:H.274 Water bridges: B:H.274

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

SO4.7: 4 residues within 4Å: Chain A: R.165, R.166, S.167 Ligands: NAD.15 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:R.166, A:S.167 Water bridges: A:R.165, A:R.166, A:R.166 Salt bridges: A:R.165, A:R.166 SO4.24: 4 residues within 4Å: Chain B: R.165, R.166, S.167 Ligands: NAD.30 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.166, B:S.167, B:S.167 Salt bridges: B:R.165

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

MG.8: 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.4 MG.9: 1 residues within 4Å: Chain A: R.126 No protein-ligand interaction detected (PLIP) MG.10: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.11: 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.3, H2O.11 MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.13: 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.14 MG.14: 5 residues within 4Å: Chain A: G.227, P.228, V.230, E.232, S.253 5 PLIP interactions: 3 interactions with chain A, 2 Ligand-Water interactions Metal complexes: A:G.227, A:V.230, A:S.253, H2O.4, H2O.13 MG.17: 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.9, H2O.14, H2O.19 MG.25: 2 residues within 4Å: Chain B: H.184, 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.26: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.27: 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.26, H2O.29 MG.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.29: 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, E.202, T.203, V.224, A.225, R.226, D.250, V.251, H.274, S.276, A.277 Ligands: SO4.7, 7N5.16 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:A.67, A:L.146, A:A.277 Hydrogen bonds: A:L.143, A:L.143, A:T.145, A:T.145, A:L.146, A:R.166, A:D.250, A:A.277 Water bridges: A:D.70, A:G.89, A:G.144, A:T.145, A:G.147, A:L.199, A:T.200, A:E.202 pi-Cation interactions: A:R.166 NAD.30: 26 residues within 4Å: Chain B: A.67, G.68, T.88, H.91, G.142, 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: SO4.24, 7N5.31 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:A.67, B:L.146, B:A.277 Hydrogen bonds: B:T.88, B:T.145, B:L.146, B:R.166, B:R.166, B:D.250, B:A.277 Water bridges: B:D.70, B:G.89, B:L.143, B:G.144, B:G.147, B:R.165, B:L.199, 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 8 PLIP interactions: 8 interactions with chain A Hydrophobic interactions: 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 7N5.31: 9 residues within 4Å: Chain B: R.66, A.67, G.68, H.91, R.226, H.274, A.277, Y.282 Ligands: NAD.30 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

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
A

B
B

D-2-hydroxyacid dehydrogenase

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