SMTL ID : 4xgn.1 (1 other biounit)

Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-tetramer

Ligands

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

NAD.1: 26 residues within 4Å: Chain A: G.20, S.23, G.24, L.25, D.44, L.45, C.64, D.65, V.66, C.91, A.92, G.93, V.118, T.151, A.152, S.153, Y.166, K.170, P.196, G.197, I.198, F.199, T.201, P.202, M.203 Ligands: EDO.2 17 PLIP interactions: 17 interactions with chain A Hydrophobic interactions: A:P.196 Hydrogen bonds: A:G.20, A:S.23, A:L.25, A:L.45, A:D.65, A:V.66, A:A.92, A:G.93, A:K.170, A:F.199, A:F.199, A:T.201, A:M.203 Water bridges: A:G.26, A:N.46, A:K.114 NAD.4: 26 residues within 4Å: Chain B: G.20, S.23, G.24, L.25, D.44, L.45, C.64, D.65, V.66, C.91, A.92, G.93, V.118, T.151, A.152, S.153, Y.166, K.170, P.196, G.197, I.198, F.199, T.201, P.202, M.203 Ligands: EDO.5 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.196 Hydrogen bonds: B:S.23, B:L.25, B:L.45, B:D.65, B:D.65, B:V.66, B:A.92, B:G.93, B:Y.166, B:K.170, B:F.199, B:F.199, B:M.203 Water bridges: B:G.26, B:N.46 NAD.7: 26 residues within 4Å: Chain C: G.20, S.23, G.24, L.25, D.44, L.45, C.64, D.65, V.66, C.91, A.92, G.93, V.118, T.151, A.152, S.153, Y.166, K.170, P.196, G.197, I.198, F.199, T.201, P.202, M.203 Ligands: EDO.8 16 PLIP interactions: 16 interactions with chain C Hydrophobic interactions: C:P.196 Hydrogen bonds: C:S.23, C:S.23, C:L.25, C:L.45, C:D.65, C:V.66, C:A.92, C:G.93, C:K.170, C:F.199, C:F.199, C:T.201, C:M.203 Water bridges: C:G.26, C:N.46 NAD.11: 26 residues within 4Å: Chain D: G.20, S.23, G.24, L.25, D.44, L.45, C.64, D.65, V.66, C.91, A.92, G.93, V.118, T.151, A.152, S.153, Y.166, K.170, P.196, G.197, I.198, F.199, T.201, P.202, M.203 Ligands: EDO.12 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.196 Hydrogen bonds: D:G.20, D:S.23, D:L.25, D:L.45, D:D.65, D:D.65, D:V.66, D:A.92, D:G.93, D:Y.166, D:K.170, D:F.199, D:F.199, D:M.203 Water bridges: D:G.26, D:N.46

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

EDO.2: 7 residues within 4Å: Chain A: S.153, Y.166, G.197, I.198, M.203, L.204 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrogen bonds: A:S.153, A:S.153, A:Y.166 EDO.3: 6 residues within 4Å: Chain A: Q.160, M.218, I.255, R.256, M.257, Q.258 7 PLIP interactions: 7 interactions with chain A Hydrogen bonds: A:Q.160, A:Q.258 Water bridges: A:M.218, A:R.256, A:R.256, A:R.256, A:Q.258 EDO.5: 6 residues within 4Å: Chain B: S.153, Y.166, G.197, M.203, L.204 Ligands: NAD.4 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:S.153, B:S.153 EDO.6: 7 residues within 4Å: Chain B: Q.160, M.218, I.255, R.256, M.257, Q.258, K.260 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:Q.160, B:Q.258, B:K.260 Water bridges: B:Q.258 EDO.8: 6 residues within 4Å: Chain C: S.153, Y.166, I.198, M.203, L.204 Ligands: NAD.7 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.153, C:S.153, C:Y.166 EDO.12: 5 residues within 4Å: Chain D: S.153, Y.166, M.203, L.204 Ligands: NAD.11 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:S.153, D:S.153 EDO.13: 6 residues within 4Å: Chain D: Q.160, M.218, I.255, R.256, M.257, Q.258 8 PLIP interactions: 8 interactions with chain D Hydrogen bonds: D:Q.258 Water bridges: D:Q.160, D:M.218, D:R.256, D:R.256, D:R.256, D:Q.258, D:K.260

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.9: 4 residues within 4Å: Chain B: E.247, V.248 Chain C: E.247, V.248 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:E.247 Water bridges: B:E.247, B:V.248, C:V.248 GOL.10: 6 residues within 4Å: Chain A: E.247, V.248, R.250 Chain D: E.247, V.248, R.250 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:E.247, D:E.247

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Abendroth, J. et al., Crystal structure of 3-hydroxyacyl-CoA dehydrogenase in complex with NAD from Burkholderia thailandensis. to be published

Release Date

2015-01-14

Peptides

3-hydroxyacyl-CoA dehydrogenase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

3-hydroxyacyl-CoA dehydrogenase

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