SMTL ID : 5b4v.1

Crystal structure of D-3-hydroxybutyrate dehydrogenase from Alcaligenes faecalis complexed with NAD+ and an inhibitor methylmalonate

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.50 Å

Oligo State

homo-tetramer

Ligands

4 x NAD: NICOTINAMIDE-ADENINE-DINUCLEOTIDE(Non-covalent)

NAD.1: 30 residues within 4Å: Chain A: G.11, S.12, T.13, S.14, G.15, I.16, N.34, G.35, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: DXX.2 21 PLIP interactions: 21 interactions with chain A Hydrophobic interactions: A:P.185 Hydrogen bonds: A:G.11, A:T.13, A:S.14, A:S.14, A:I.16, A:F.36, A:F.36, A:D.63, A:L.64, A:S.65, A:N.90, A:G.92, A:K.159, A:V.188, A:V.188, A:T.190 Water bridges: A:S.14, A:S.14, A:G.17, A:N.90 NAD.7: 30 residues within 4Å: Chain B: G.11, S.12, T.13, S.14, G.15, I.16, N.34, G.35, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: DXX.8 21 PLIP interactions: 21 interactions with chain B Hydrophobic interactions: B:P.185 Hydrogen bonds: B:G.11, B:T.13, B:S.14, B:S.14, B:I.16, B:F.36, B:F.36, B:D.63, B:L.64, B:S.65, B:N.90, B:G.92, B:K.159, B:V.188, B:V.188, B:T.190 Water bridges: B:S.14, B:S.14, B:G.17, B:N.90 NAD.13: 30 residues within 4Å: Chain C: G.11, S.12, T.13, S.14, G.15, I.16, N.34, G.35, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: DXX.14 22 PLIP interactions: 22 interactions with chain C Hydrophobic interactions: C:P.185 Hydrogen bonds: C:G.11, C:T.13, C:S.14, C:S.14, C:I.16, C:F.36, C:F.36, C:D.63, C:D.63, C:L.64, C:S.65, C:N.90, C:G.92, C:Y.155, C:K.159, C:V.188, C:V.188 Water bridges: C:S.14, C:S.14, C:G.17, C:N.90 NAD.19: 30 residues within 4Å: Chain D: G.11, S.12, T.13, S.14, G.15, I.16, N.34, G.35, F.36, A.62, D.63, L.64, N.90, A.91, G.92, L.113, I.140, A.141, S.142, Y.155, K.159, P.185, G.186, W.187, V.188, T.190, P.191, L.192, V.193 Ligands: DXX.20 22 PLIP interactions: 22 interactions with chain D Hydrophobic interactions: D:P.185 Hydrogen bonds: D:G.11, D:T.13, D:S.14, D:S.14, D:I.16, D:F.36, D:F.36, D:D.63, D:D.63, D:L.64, D:S.65, D:N.90, D:G.92, D:Y.155, D:K.159, D:V.188, D:V.188 Water bridges: D:S.14, D:S.14, D:G.17, D:N.90

4 x DXX: METHYLMALONIC ACID(Non-covalent)

DXX.2: 10 residues within 4Å: Chain A: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.1 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:W.187, A:W.187, A:W.257 Hydrogen bonds: A:Q.94, A:S.142, A:Y.155, A:Q.196 Water bridges: A:S.149 Salt bridges: A:H.144, A:H.144, A:K.152 DXX.8: 10 residues within 4Å: Chain B: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.7 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:W.187, B:W.187, B:W.257 Hydrogen bonds: B:Q.94, B:S.142, B:Y.155, B:Q.196 Water bridges: B:S.149 Salt bridges: B:H.144, B:H.144, B:K.152 DXX.14: 10 residues within 4Å: Chain C: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.13 10 PLIP interactions: 10 interactions with chain C Hydrophobic interactions: C:W.187, C:W.187, C:W.257 Hydrogen bonds: C:Q.94, C:S.142, C:Q.196 Water bridges: C:S.149 Salt bridges: C:H.144, C:H.144, C:K.152 DXX.20: 10 residues within 4Å: Chain D: Q.94, S.142, H.144, K.152, Y.155, W.187, L.192, Q.196, W.257 Ligands: NAD.19 10 PLIP interactions: 10 interactions with chain D Hydrophobic interactions: D:W.187, D:W.187, D:W.257 Hydrogen bonds: D:Q.94, D:S.142, D:Q.196 Water bridges: D:S.149 Salt bridges: D:H.144, D:H.144, D:K.152

4 x CL: CHLORIDE ION(Non-functional Binders)

CL.3: 3 residues within 4Å: Chain A: S.149, V.150, K.219 Ligand excluded by PLIP CL.9: 3 residues within 4Å: Chain B: S.149, V.150, K.219 Ligand excluded by PLIP CL.15: 3 residues within 4Å: Chain C: S.149, V.150, K.219 Ligand excluded by PLIP CL.21: 3 residues within 4Å: Chain D: S.149, V.150, K.219 Ligand excluded by PLIP

12 x NA: SODIUM ION(Non-functional Binders)

NA.4: 5 residues within 4Å: Chain A: V.147, R.260 Chain C: V.147, R.260 Ligands: NA.16 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.260 NA.5: 6 residues within 4Å: Chain A: L.64, S.65, A.112, S.116, A.117, H.120 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.65 Water bridges: A:S.116 NA.6: 3 residues within 4Å: Chain A: G.4, K.6, D.85 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:K.6, A:D.85 NA.10: 5 residues within 4Å: Chain B: V.147, R.260 Chain D: V.147, R.260 Ligands: NA.22 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:R.260 NA.11: 6 residues within 4Å: Chain B: L.64, S.65, A.112, S.116, A.117, H.120 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:L.64 Water bridges: B:S.116 NA.12: 3 residues within 4Å: Chain B: G.4, K.6, D.85 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.6, B:D.85 NA.16: 5 residues within 4Å: Chain A: V.147, R.260 Chain C: V.147, R.260 Ligands: NA.4 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.260 NA.17: 6 residues within 4Å: Chain C: L.64, S.65, A.112, S.116, A.117, H.120 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:A.112 Water bridges: C:S.116 NA.18: 3 residues within 4Å: Chain C: G.4, K.6, D.85 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:K.6, C:D.85 NA.22: 5 residues within 4Å: Chain B: V.147, R.260 Chain D: V.147, R.260 Ligands: NA.10 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:R.260 NA.23: 6 residues within 4Å: Chain D: L.64, S.65, A.112, S.116, A.117, H.120 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:L.64 Water bridges: D:S.116 NA.24: 3 residues within 4Å: Chain D: G.4, K.6, D.85 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:G.4, D:K.6

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kanazawa, H. et al., Structural insights into the catalytic reaction trigger and inhibition of D-3-hydroxybutyrate dehydrogenase. Acta Crystallogr.,Sect.F (2016)

Release Date

2016-08-17

Peptides

3-hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

D
A

3-hydroxybutyrate dehydrogenase

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