SMTL ID : 8dt1.1

Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.80 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: G.21, A.23, S.24, G.25, I.26, D.45, L.46, M.70, D.71, V.72, N.98, A.99, G.100, I.101, I.121, H.122, M.149, G.150, S.151, Y.164, K.168, P.194, G.195, F.196, V.197 Ligands: CIT.2 20 PLIP interactions: 20 interactions with chain A Hydrophobic interactions: A:I.26, A:P.194 Hydrogen bonds: A:G.21, A:A.23, A:S.24, A:I.26, A:L.46, A:D.71, A:D.71, A:V.72, A:N.98, A:G.100, A:Y.164, A:K.168, A:V.197 Water bridges: A:G.27, A:G.27, A:N.47, A:I.101, A:V.197 NAD.6: 30 residues within 4Å: Chain B: G.21, A.23, S.24, G.25, I.26, D.45, L.46, M.70, D.71, V.72, N.98, A.99, G.100, I.101, I.121, H.122, M.149, G.150, S.151, Y.164, K.168, P.194, G.195, F.196, V.197, T.199, P.200, L.201, V.202 Ligands: CIT.7 19 PLIP interactions: 19 interactions with chain B Hydrophobic interactions: B:I.26, B:P.194 Hydrogen bonds: B:G.21, B:A.23, B:S.24, B:I.26, B:L.46, B:D.71, B:V.72, B:N.98, B:G.100, B:Y.164, B:K.168, B:V.197, B:V.197, B:T.199, B:L.201 Water bridges: B:G.27, B:N.98 NAD.10: 27 residues within 4Å: Chain C: G.21, A.23, S.24, G.25, I.26, D.45, L.46, M.70, D.71, V.72, N.98, A.99, G.100, I.121, H.122, M.149, G.150, S.151, Y.164, K.168, P.194, G.195, F.196, V.197, T.199, V.202 Ligands: CIT.11 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:I.26, C:P.194 Hydrogen bonds: C:G.21, C:S.24, C:S.24, C:I.26, C:L.46, C:D.71, C:V.72, C:N.98, C:G.100, C:K.168, C:V.197, C:T.199 Water bridges: C:N.98, C:I.101 NAD.14: 26 residues within 4Å: Chain D: G.21, A.23, S.24, G.25, I.26, D.45, L.46, N.47, M.70, D.71, V.72, N.98, A.99, G.100, I.121, H.122, M.149, G.150, S.151, Y.164, K.168, P.194, G.195, F.196, V.197 Ligands: CIT.15 20 PLIP interactions: 20 interactions with chain D Hydrophobic interactions: D:P.194 Hydrogen bonds: D:G.21, D:A.23, D:S.24, D:I.26, D:L.46, D:N.47, D:D.71, D:D.71, D:V.72, D:N.98, D:G.100, D:K.168, D:V.197 Water bridges: D:G.27, D:N.47, D:N.98, D:I.101, D:H.122, D:V.197

4 x CIT: CITRIC ACID(Non-functional Binders)

CIT.2: 7 residues within 4Å: Chain A: Q.102, S.151, H.153, K.161, Y.164, F.196 Ligands: NAD.1 12 PLIP interactions: 12 interactions with chain A Hydrophobic interactions: A:F.196 Hydrogen bonds: A:Q.102, A:S.151, A:K.161, A:Y.164 Water bridges: A:H.153, A:H.153, A:K.161, A:Y.164 Salt bridges: A:H.153, A:K.161, A:K.161 CIT.7: 11 residues within 4Å: Chain B: Q.102, S.151, H.153, K.161, Y.164, F.196, L.201, V.202, Q.205, M.225 Ligands: NAD.6 13 PLIP interactions: 13 interactions with chain B Hydrophobic interactions: B:V.202 Hydrogen bonds: B:Q.102, B:S.151, B:K.161, B:Q.205 Water bridges: B:H.153, B:H.153, B:H.153, B:S.158 Salt bridges: B:H.153, B:H.153, B:K.161, B:K.161 CIT.11: 8 residues within 4Å: Chain C: Q.102, S.151, H.153, K.161, Y.164, F.196, V.202 Ligands: NAD.10 12 PLIP interactions: 12 interactions with chain C Hydrophobic interactions: C:F.196 Hydrogen bonds: C:Q.102, C:S.151, C:H.153, C:K.161, C:Y.164, C:Y.164, C:Y.164 Salt bridges: C:H.153, C:K.161, C:K.161, C:K.161 CIT.15: 7 residues within 4Å: Chain D: Q.102, S.151, H.153, K.161, Y.164, F.196 Ligands: NAD.14 9 PLIP interactions: 9 interactions with chain D Hydrogen bonds: D:Q.102, D:S.151, D:H.153, D:K.161, D:Y.164 Water bridges: D:V.197 Salt bridges: D:H.153, D:K.161, D:K.161

1 x PO4: PHOSPHATE ION(Non-functional Binders)

PO4.3: 4 residues within 4Å: Chain A: E.75, N.79, K.131, K.135 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.79 Water bridges: A:K.131, A:K.135 Salt bridges: A:K.131

8 x PG4: TETRAETHYLENE GLYCOL(Non-functional Binders)

PG4.4: 7 residues within 4Å: Chain A: K.15, D.93, R.142, G.143, V.145, S.248, F.250 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:K.15 PG4.5: 6 residues within 4Å: Chain A: L.32, K.36, I.58, A.61, G.62, G.63 No protein-ligand interaction detected (PLIP) PG4.8: 10 residues within 4Å: Chain B: K.15, D.93, R.142, G.143, G.144, V.145, R.188, S.248, A.249, F.250 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:K.15 PG4.9: 5 residues within 4Å: Chain B: A.35, K.36, I.58, A.61, G.63 No protein-ligand interaction detected (PLIP) PG4.12: 10 residues within 4Å: Chain C: K.15, D.93, R.142, G.143, G.144, V.145, R.188, S.248, A.249, F.250 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:K.15 PG4.13: 7 residues within 4Å: Chain C: L.32, A.35, K.36, I.58, A.61, G.62, G.63 No protein-ligand interaction detected (PLIP) PG4.16: 8 residues within 4Å: Chain D: K.15, D.93, R.142, G.143, V.145, R.188, S.248, F.250 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:K.15 Water bridges: D:G.144 PG4.17: 7 residues within 4Å: Chain D: L.32, A.35, K.36, I.58, A.61, G.62, G.63 No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal Structure of a Putative D-beta-hydroxybutyrate dehydrogenase from Burkholderia cenocepacia J2315 in complex with NAD. To Be Published

Release Date

2022-08-17

Peptides

3-hydroxybutyrate dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-hydroxybutyrate dehydrogenase

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