SMTL ID : 5jy1.1

Crystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD

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: 24 residues within 4Å: Chain A: G.21, G.24, G.25, I.26, E.45, I.46, T.70, D.71, V.72, T.73, N.98, A.99, F.100, V.101, F.149, Y.150, S.151, Y.164, K.168, P.194, T.195, A.196, A.199 Ligands: ACT.4 21 PLIP interactions: 21 interactions with chain A Hydrogen bonds: A:G.21, A:G.23, A:G.24, A:I.26, A:I.46, A:D.71, A:V.72, A:T.73, A:N.98, A:F.100, A:K.168, A:A.196, A:A.196, A:A.199 Water bridges: A:G.27, A:E.45, A:T.50, A:K.168, A:G.198, A:G.198, A:T.200 NAD.7: 25 residues within 4Å: Chain B: G.21, G.23, G.24, G.25, I.26, E.45, I.46, T.70, D.71, V.72, N.98, A.99, F.100, V.101, F.149, Y.150, S.151, Y.164, K.168, P.194, T.195, A.196, G.198, A.199 Ligands: ACT.10 22 PLIP interactions: 22 interactions with chain B Hydrogen bonds: B:G.21, B:G.23, B:G.24, B:I.26, B:I.46, B:D.71, B:D.71, B:V.72, B:N.98, B:F.100, B:Y.164, B:K.168, B:A.196, B:A.196, B:A.199 Water bridges: B:G.27, B:T.50, B:G.198, B:G.198, B:T.200, B:T.200, B:F.201 NAD.11: 25 residues within 4Å: Chain C: G.21, G.23, G.24, G.25, I.26, E.45, I.46, T.70, D.71, V.72, N.98, A.99, F.100, V.101, F.149, Y.150, S.151, Y.164, K.168, P.194, T.195, A.196, G.198, A.199 Ligands: ACT.13 20 PLIP interactions: 20 interactions with chain C Hydrogen bonds: C:G.21, C:G.23, C:G.24, C:I.26, C:I.46, C:D.71, C:V.72, C:T.73, C:N.98, C:F.100, C:K.168, C:A.196, C:A.196, C:A.199 Water bridges: C:G.27, C:G.198, C:G.198, C:T.200, C:T.200, C:F.201 NAD.16: 26 residues within 4Å: Chain D: G.21, G.23, G.24, G.25, I.26, E.45, I.46, T.70, D.71, V.72, T.73, N.98, A.99, F.100, V.101, F.149, Y.150, S.151, Y.164, K.168, P.194, T.195, A.196, G.198, A.199 Ligands: ACT.17 25 PLIP interactions: 25 interactions with chain D Hydrogen bonds: D:G.21, D:G.23, D:G.24, D:I.26, D:I.46, D:D.71, D:D.71, D:V.72, D:T.73, D:N.98, D:F.100, D:Y.164, D:K.168, D:A.196, D:A.196, D:A.199 Water bridges: D:G.27, D:E.45, D:A.99, D:K.168, D:G.198, D:G.198, D:T.200, D:T.200, D:F.201

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

CL.2: 5 residues within 4Å: Chain A: T.195, A.196, R.219, S.224, G.225 Ligand excluded by PLIP CL.8: 5 residues within 4Å: Chain B: T.195, A.196, R.219, S.224, G.225 Ligand excluded by PLIP CL.14: 5 residues within 4Å: Chain C: T.195, A.196, R.219, S.224, G.225 Ligand excluded by PLIP CL.18: 5 residues within 4Å: Chain D: T.195, A.196, R.219, S.224, G.225 Ligand excluded by PLIP

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

EDO.3: 4 residues within 4Å: Chain A: F.100, P.102, T.103, Y.164 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:T.103, A:T.103, A:H.161 Water bridges: A:T.103 EDO.5: 2 residues within 4Å: Chain A: R.139 Chain C: E.109 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.139, A:R.139 EDO.9: 5 residues within 4Å: Chain B: F.100, P.102, T.103, H.161, Y.164 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:T.103, B:T.103, B:H.161 EDO.12: 6 residues within 4Å: Chain C: F.100, P.102, T.103, H.161, Y.164 Ligands: ACT.13 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:T.103, C:T.103, C:H.161 EDO.15: 2 residues within 4Å: Chain C: L.160, I.269 1 PLIP interactions: 1 interactions with chain C Water bridges: C:L.107 EDO.19: 6 residues within 4Å: Chain D: F.100, P.102, T.103, H.161, Y.164 Ligands: ACT.17 3 PLIP interactions: 3 interactions with chain D Hydrogen bonds: D:T.103, D:H.161 Water bridges: D:T.103 EDO.20: 4 residues within 4Å: Chain B: T.154, A.169, R.176 Chain D: R.176 5 PLIP interactions: 3 interactions with chain B, 2 interactions with chain D Hydrogen bonds: B:T.154, B:T.154, B:R.176, D:R.176 Water bridges: D:R.176

5 x ACT: ACETATE ION(Non-functional Binders)

ACT.4: 4 residues within 4Å: Chain A: F.100, Y.164, T.200 Ligands: NAD.1 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:F.100 Water bridges: A:S.151, A:Y.164 ACT.6: 4 residues within 4Å: Chain A: E.79, R.132, A.133, V.136 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:V.136 ACT.10: 4 residues within 4Å: Chain B: F.100, Y.164, T.200 Ligands: NAD.7 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.100 ACT.13: 4 residues within 4Å: Chain C: Y.164, T.200 Ligands: NAD.11, EDO.12 1 PLIP interactions: 1 interactions with chain C Water bridges: C:H.161 ACT.17: 5 residues within 4Å: Chain D: F.100, Y.164, T.200 Ligands: NAD.16, EDO.19 2 PLIP interactions: 2 interactions with chain D Hydrogen bonds: D:Y.164 Water bridges: D:S.151

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Seattle Structural Genomics Center for Infectious Disease (SSGCID) et al., Crystal Structure of putative short-chain dehydrogenase/reductase from Burkholderia xenovorans LB400 bound to NAD. To Be Published

Release Date

2016-05-25

Peptides

Putative short-chain dehydrogenase/reductase: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

Putative short-chain dehydrogenase/reductase