SMTL ID : 4iqg.1

Crystal structure of BPRO0239 oxidoreductase from Polaromonas sp. JS666 in NADP bound form

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.85 Å

Oligo State

homo-tetramer

Ligands

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

FMT.1: 5 residues within 4Å: Chain A: A.168, L.171, S.173, P.174, R.271 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.173, A:R.271 FMT.2: 8 residues within 4Å: Chain A: R.170, D.266, T.268, G.270, R.271 Chain D: T.261, G.262, A.263 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain D Hydrogen bonds: A:T.268, A:R.271 Water bridges: D:T.261 FMT.3: 3 residues within 4Å: Chain A: K.26, Q.48, Y.50 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Q.48 FMT.5: 8 residues within 4Å: Chain B: T.261, G.262, A.263 Chain C: R.170, D.266, T.268, G.270, R.271 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Water bridges: B:T.261 Hydrogen bonds: C:T.268 FMT.6: 8 residues within 4Å: Chain B: R.170, D.266, T.268, G.270, R.271 Chain C: L.192, T.261, G.262 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C Hydrogen bonds: B:T.268 Water bridges: B:R.170, C:T.261 FMT.10: 8 residues within 4Å: Chain C: S.166, A.167, A.168, P.210, G.211, I.212, R.271 Ligands: NAP.9 5 PLIP interactions: 5 interactions with chain C Hydrogen bonds: C:A.167, C:A.168, C:G.211, C:R.271 Water bridges: C:S.166 FMT.11: 3 residues within 4Å: Chain C: Q.48, G.49, Y.50 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.49 Water bridges: C:K.26 FMT.14: 4 residues within 4Å: Chain C: R.153, E.197 Chain D: R.119, G.175 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:R.119, C:R.153 FMT.15: 8 residues within 4Å: Chain A: L.192, T.261, G.262, A.263 Chain D: R.170, D.266, T.268, R.271 3 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A Hydrogen bonds: D:R.271 Water bridges: D:R.170, A:T.261

4 x NAP: NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE(Non-covalent)

NAP.4: 32 residues within 4Å: Chain A: G.32, G.33, S.34, R.35, G.36, I.37, N.55, Y.56, A.57, S.58, N.59, A.82, D.83, V.84, N.110, A.111, G.112, V.113, I.134, V.164, S.165, S.166, Y.180, K.184, P.210, G.211, I.212, I.213, T.215, D.216, I.217, H.218 28 PLIP interactions: 28 interactions with chain A Hydrophobic interactions: A:P.210 Hydrogen bonds: A:G.32, A:G.32, A:S.34, A:S.34, A:S.34, A:R.35, A:I.37, A:A.57, A:S.58, A:N.59, A:D.83, A:D.83, A:V.84, A:N.110, A:G.112, A:Y.180, A:K.184, A:I.213, A:T.215, A:D.216, A:I.217, A:H.218 Water bridges: A:R.35, A:G.38, A:N.110 Salt bridges: A:R.35, A:R.35 NAP.8: 28 residues within 4Å: Chain B: G.32, G.33, S.34, R.35, G.36, I.37, N.55, Y.56, A.57, S.58, N.59, A.82, D.83, V.84, N.110, A.111, G.112, V.113, I.134, V.164, S.165, S.166, Y.180, K.184, P.210, G.211, I.212, I.213 24 PLIP interactions: 24 interactions with chain B Hydrogen bonds: B:G.32, B:G.32, B:S.34, B:S.34, B:R.35, B:I.37, B:A.57, B:S.58, B:S.58, B:N.59, B:D.83, B:D.83, B:V.84, B:N.110, B:G.112, B:Y.180, B:K.184, B:I.213, B:I.213 Water bridges: B:R.35, B:G.38, B:N.110 Salt bridges: B:R.35, B:R.35 NAP.9: 33 residues within 4Å: Chain C: G.32, G.33, S.34, R.35, G.36, I.37, N.55, Y.56, A.57, S.58, N.59, A.82, D.83, V.84, N.110, A.111, G.112, V.113, I.134, V.164, S.165, S.166, Y.180, K.184, P.210, G.211, I.212, I.213, T.215, D.216, I.217, H.218 Ligands: FMT.10 31 PLIP interactions: 31 interactions with chain C Hydrophobic interactions: C:P.210 Hydrogen bonds: C:G.32, C:G.32, C:S.34, C:S.34, C:S.34, C:R.35, C:I.37, C:A.57, C:S.58, C:N.59, C:D.83, C:V.84, C:N.110, C:K.184, C:I.213, C:I.213, C:T.215, C:T.215, C:D.216, C:I.217 Water bridges: C:R.35, C:R.35, C:R.35, C:G.38, C:N.59, C:N.110, C:D.216, C:S.220 Salt bridges: C:R.35, C:R.35 NAP.12: 31 residues within 4Å: Chain D: G.32, G.33, S.34, R.35, G.36, I.37, N.55, Y.56, A.57, S.58, N.59, A.82, D.83, V.84, N.110, A.111, G.112, V.113, I.134, V.164, S.165, S.166, Y.180, K.184, P.210, G.211, I.212, I.213, T.215, I.217, H.218 31 PLIP interactions: 31 interactions with chain D Hydrophobic interactions: D:P.210 Hydrogen bonds: D:G.32, D:G.32, D:S.34, D:S.34, D:R.35, D:I.37, D:A.57, D:S.58, D:S.58, D:N.59, D:D.83, D:V.84, D:N.110, D:G.112, D:K.184, D:I.213, D:I.213, D:T.215, D:T.215, D:D.216, D:I.217 Water bridges: D:R.35, D:R.35, D:R.35, D:R.35, D:N.59, D:N.110, D:D.216 Salt bridges: D:R.35, D:R.35

1 x GOL: GLYCEROL(Non-functional Binders)

GOL.7: 7 residues within 4Å: Chain B: G.159, S.160, G.202, R.204, L.253, G.254, D.255 5 PLIP interactions: 5 interactions with chain B Hydrogen bonds: B:G.202, B:R.204, B:L.253, B:G.254 Water bridges: B:K.26

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.13: 6 residues within 4Å: Chain C: K.196 Chain D: A.168, L.171, S.173, P.174, R.271 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.173, D:R.226, C:K.196 Water bridges: D:R.271

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Niedzialkowska, E. et al., Crystal structure of oxidoreductase from Polaromonas sp. in NADP bound form. To be Published

Release Date

2013-01-30

Peptides

Short-chain dehydrogenase/reductase SDR: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
C

B
A

C
B

D
D

Short-chain dehydrogenase/reductase SDR