SMTL ID : 5mh5.1

D-2-hydroxyacid dehydrogenases (D2-HDH) from Haloferax mediterranei in complex with 2-keto-hexanoic acid and NADP+ (1.4 A resolution)

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

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

MG.1: 1 residues within 4Å: Chain A: E.204 No protein-ligand interaction detected (PLIP) MG.2: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.3: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.4: 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.4, H2O.5 MG.5: 1 residues within 4Å: Chain A: E.202 2 PLIP interactions: 1 interactions with chain A, 1 Ligand-Water interactions Metal complexes: A:E.202, H2O.6 MG.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Chain A: E.302 No protein-ligand interaction detected (PLIP) MG.8: 1 residues within 4Å: Chain A: D.172 4 PLIP interactions: 1 interactions with chain A, 3 Ligand-Water interactions Metal complexes: A:D.172, H2O.2, H2O.7, H2O.12 MG.9: 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.5 MG.10: 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.10 MG.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.12: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.16: 2 residues within 4Å: Chain A: H.120 Chain B: D.265 6 PLIP interactions: 1 interactions with chain B, 1 interactions with chain A, 4 Ligand-Water interactions Metal complexes: B:D.265, A:H.120, H2O.2, H2O.9, H2O.14, H2O.19 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.6, H2O.8, H2O.14 MG.18: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) MG.19: 2 residues within 4Å: Chain B: E.213, T.214 No protein-ligand interaction detected (PLIP) MG.20: 2 residues within 4Å: Chain B: P.170, V.177 No protein-ligand interaction detected (PLIP) MG.21: 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.24 MG.22: 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.16, H2O.22 MG.23: 1 residues within 4Å: Chain B: E.267 No protein-ligand interaction detected (PLIP) MG.24: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

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

7N5.13: 9 residues within 4Å: Chain A: R.66, A.67, G.68, H.91, R.226, H.274, A.277, Y.282 Ligands: NAP.14 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:A.277, 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 7N5.25: 9 residues within 4Å: Chain B: R.66, A.67, G.68, H.91, R.226, H.274, A.277, Y.282 Ligands: NAP.26 7 PLIP interactions: 7 interactions with chain B Hydrophobic interactions: B:Y.282 Hydrogen bonds: B:A.67, B:G.68 Water bridges: B:R.66 Salt bridges: B:R.66, B:R.226, B:H.274

2 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.14: 28 residues within 4Å: Chain A: 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, 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: 7N5.13 30 PLIP interactions: 30 interactions with chain A Hydrophobic interactions: A:A.67, A:L.146, A:A.277 Hydrogen bonds: A:T.88, A:L.143, A:L.143, A:T.145, A:T.145, A:L.146, A:R.166, A:S.167, A:D.250, A:A.277 Water bridges: A:Y.69, A:T.88, A:G.89, A:G.144, A:G.147, A:R.165, A:R.166, A:R.166, A:R.166, A:R.166, A:R.166, A:L.199, A:L.199, A:E.202 Salt bridges: A:R.165, A:R.166 pi-Stacking: A:H.91 NAP.26: 27 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: 7N5.25 29 PLIP interactions: 29 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:T.145, B:L.146, B:R.166, B:S.167, B:D.250, B:D.250, B:A.277 Water bridges: B:T.88, B:G.89, B:G.144, B:G.147, B:R.166, B:R.166, B:R.166, B:R.166, B:L.199, B:L.199, B:E.202 Salt bridges: B:R.165, B:R.166 pi-Stacking: B:H.91

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

SO4.15: 3 residues within 4Å: Chain A: R.148, R.165, P.170 7 PLIP interactions: 7 interactions with chain A Water bridges: A:R.148, A:R.148, A:R.148, A:R.165, A:S.167 Salt bridges: A:R.148, A:R.165 SO4.27: 3 residues within 4Å: Chain B: R.148, R.165, D.169 6 PLIP interactions: 6 interactions with chain B Water bridges: B:R.148, B:R.148, B:S.167, B:D.169 Salt bridges: B:R.148, B:R.165

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

2018-05-02

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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