SMTL ID : 6d9y.1

Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum with partially occupied NAD

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-tetramer

Ligands

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

EDO.1: 4 residues within 4Å: Chain A: N.159, M.214, K.217, R.255 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:N.159, A:R.255 Water bridges: A:K.217, A:R.255 EDO.2: 3 residues within 4Å: Chain A: W.110, E.111 Chain B: L.140 1 PLIP interactions: 1 interactions with chain A Water bridges: A:E.111 EDO.12: 4 residues within 4Å: Chain C: N.159, M.214, K.217, R.255 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:N.159, C:R.255 Water bridges: C:K.217, C:R.255 EDO.13: 3 residues within 4Å: Chain C: W.110, E.111 Chain D: L.140 2 PLIP interactions: 2 interactions with chain C Water bridges: C:E.111, C:E.111

6 x OXM: OXAMIC ACID(Non-covalent)

OXM.3: 6 residues within 4Å: Chain A: R.118, D.122, I.126 Chain B: R.118, I.121, I.126 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.118 Water bridges: B:D.122 OXM.6: 2 residues within 4Å: Chain B: K.141, Q.142 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:K.141, B:K.141 Water bridges: B:Q.138, B:K.141, B:K.141 OXM.8: 11 residues within 4Å: Chain B: S.152, V.153, A.154, N.159, Y.165, P.195, A.196, A.197, M.214, R.255 Ligands: NAD.7 6 PLIP interactions: 6 interactions with chain B Hydrogen bonds: B:S.152, B:N.159, B:A.197, B:R.255, B:R.255 Water bridges: B:Y.165 OXM.14: 6 residues within 4Å: Chain C: R.118, D.122, I.126 Chain D: R.118, I.121, I.126 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:R.118 Water bridges: D:D.122 OXM.17: 2 residues within 4Å: Chain D: K.141, Q.142 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:K.141, D:K.141 Water bridges: D:Q.138, D:Q.138, D:K.141 OXM.19: 11 residues within 4Å: Chain D: S.152, V.153, A.154, N.159, Y.165, P.195, A.196, A.197, M.214, R.255 Ligands: NAD.18 5 PLIP interactions: 5 interactions with chain D Hydrogen bonds: D:S.152, D:N.159, D:A.197, D:R.255, D:R.255

10 x FMT: FORMIC ACID(Non-functional Binders)

FMT.4: 4 residues within 4Å: Chain A: V.18, F.90, G.91, A.92 1 PLIP interactions: 1 interactions with chain A Water bridges: A:G.16 FMT.5: 3 residues within 4Å: Chain A: K.75, A.77, Q.78 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.78 FMT.9: 3 residues within 4Å: Chain B: K.75, A.77, Q.78 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:Q.78 FMT.10: 3 residues within 4Å: Chain B: V.66, C.67, A.89 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:V.66 Water bridges: B:A.68 FMT.11: 4 residues within 4Å: Chain B: G.16, A.42, K.65, F.90 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.65 Water bridges: B:G.16, B:A.42 FMT.15: 4 residues within 4Å: Chain C: V.18, F.90, G.91, A.92 1 PLIP interactions: 1 interactions with chain C Water bridges: C:G.16 FMT.16: 3 residues within 4Å: Chain C: K.75, A.77, Q.78 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:Q.78 FMT.20: 3 residues within 4Å: Chain D: K.75, A.77, Q.78 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:Q.78 FMT.21: 3 residues within 4Å: Chain D: V.66, C.67, A.89 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:V.66 Water bridges: D:E.57, D:A.68 FMT.22: 4 residues within 4Å: Chain D: G.16, A.42, K.65, F.90 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:K.65 Water bridges: D:G.16, D:A.42

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

NAD.7: 27 residues within 4Å: Chain B: G.23, R.26, G.27, I.28, D.47, L.48, D.49, V.71, D.72, Q.73, C.99, A.100, G.101, V.123, I.150, A.151, S.152, Y.165, K.169, P.195, A.196, A.197, A.198, T.200, I.202, F.203 Ligands: OXM.8 16 PLIP interactions: 16 interactions with chain B Hydrophobic interactions: B:P.195 Hydrogen bonds: B:R.26, B:I.28, B:L.48, B:D.49, B:Q.73, B:K.169, B:A.198, B:T.200, B:T.200, B:I.202 Water bridges: B:G.23, B:A.25, B:R.26, B:R.26, B:G.29 NAD.18: 27 residues within 4Å: Chain D: G.23, R.26, G.27, I.28, D.47, L.48, D.49, V.71, D.72, Q.73, C.99, A.100, G.101, V.123, I.150, A.151, S.152, Y.165, K.169, P.195, A.196, A.197, A.198, T.200, I.202, F.203 Ligands: OXM.19 17 PLIP interactions: 17 interactions with chain D Hydrophobic interactions: D:P.195 Hydrogen bonds: D:R.26, D:I.28, D:L.48, D:D.49, D:D.72, D:Q.73, D:Y.165, D:K.169, D:A.198, D:T.200, D:I.202 Water bridges: D:G.23, D:A.25, D:R.26, D:R.26, D:G.29

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mayclin, S.J. et al., Crystal structure of a short chain dehydrogenase/reductase SDR from Burkholderia phymatum with partially occupied NAD. To be Published

Release Date

2018-06-06

Peptides

Short-chain dehydrogenase/reductase SDR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Short-chain dehydrogenase/reductase SDR