SMTL ID : 4yqe.1

Crystal structure of E. coli WrbA in complex with benzoquinone

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.33 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 20 residues within 4Å: Chain A: S.9, M.10, Y.11, G.12, H.13, I.14, P.76, T.77, R.78, F.79, G.80, S.112, T.113, G.114, T.115, G.116, G.117 Chain B: D.91, H.132 Ligands: PLQ.3 18 PLIP interactions: 18 interactions with chain A Hydrophobic interactions: A:F.79, A:F.79 Hydrogen bonds: A:Y.11, A:G.12, A:H.13, A:I.14, A:T.77, A:T.77, A:F.79, A:G.80, A:S.112, A:S.112, A:T.113, A:G.114, A:G.116, A:G.117 Water bridges: A:G.117 Salt bridges: A:H.13 FMN.4: 20 residues within 4Å: Chain A: D.91, H.132 Chain B: S.9, M.10, Y.11, G.12, H.13, I.14, P.76, T.77, R.78, F.79, G.80, S.112, T.113, G.114, T.115, G.116, G.117 Ligands: PLQ.2 20 PLIP interactions: 20 interactions with chain B Hydrophobic interactions: B:F.79, B:F.79 Hydrogen bonds: B:Y.11, B:G.12, B:H.13, B:I.14, B:T.77, B:T.77, B:F.79, B:G.80, B:S.112, B:S.112, B:G.114, B:T.115, B:G.116, B:G.117, B:G.117 Water bridges: B:R.78, B:T.115 Salt bridges: B:H.13 FMN.5: 20 residues within 4Å: Chain C: S.9, M.10, Y.11, G.12, H.13, I.14, P.76, T.77, R.78, F.79, G.80, S.112, T.113, G.114, T.115, G.116, G.117 Chain D: D.91, H.132 Ligands: PLQ.7 17 PLIP interactions: 17 interactions with chain C Hydrophobic interactions: C:F.79, C:F.79 Hydrogen bonds: C:Y.11, C:G.12, C:H.13, C:I.14, C:T.77, C:T.77, C:F.79, C:G.80, C:S.112, C:S.112, C:G.114, C:G.116, C:G.117 Water bridges: C:T.113 Salt bridges: C:H.13 FMN.8: 20 residues within 4Å: Chain C: D.91, H.132 Chain D: S.9, M.10, Y.11, G.12, H.13, I.14, P.76, T.77, R.78, F.79, G.80, S.112, T.113, G.114, T.115, G.116, G.117 Ligands: PLQ.6 20 PLIP interactions: 19 interactions with chain D, 1 interactions with chain A Hydrophobic interactions: D:F.79, D:F.79 Hydrogen bonds: D:Y.11, D:G.12, D:H.13, D:I.14, D:T.77, D:T.77, D:F.79, D:G.80, D:S.112, D:S.112, D:G.114, D:T.115, D:G.116, D:G.117, D:G.117 Water bridges: D:R.78, A:Y.142 Salt bridges: D:H.13

4 x PLQ: 1,4-benzoquinone(Non-covalent)

PLQ.2: 6 residues within 4Å: Chain A: W.97, H.132 Chain B: F.79, T.115 Chain C: Y.142 Ligands: FMN.4 4 PLIP interactions: 2 interactions with chain A, 1 interactions with chain C, 1 interactions with chain B Hydrogen bonds: A:H.132 pi-Stacking: A:W.97 Hydrophobic interactions: C:Y.142, B:F.79 PLQ.3: 6 residues within 4Å: Chain A: F.79, G.116 Chain B: W.97, H.132 Chain D: Y.142 Ligands: FMN.1 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:F.79 pi-Stacking: B:W.97 PLQ.6: 6 residues within 4Å: Chain A: Y.142 Chain C: W.97, H.132 Chain D: F.79, T.115 Ligands: FMN.8 3 PLIP interactions: 1 interactions with chain A, 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: A:Y.142, D:F.79 pi-Stacking: C:W.97 PLQ.7: 6 residues within 4Å: Chain B: Y.142 Chain C: F.79, G.116 Chain D: W.97, H.132 Ligands: FMN.5 4 PLIP interactions: 1 interactions with chain C, 1 interactions with chain B, 2 interactions with chain D Hydrophobic interactions: C:F.79 Hydrogen bonds: B:Y.142, D:H.132 pi-Stacking: D:W.97

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Degtjarik, O. et al., Quantum Calculations Indicate Effective Electron Transfer between FMN and Benzoquinone in a New Crystal Structure of Escherichia coli WrbA. J.Phys.Chem.B (2016)

Release Date

2016-05-25

Peptides

NAD(P)H dehydrogenase (quinone): ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

NAD(P)H dehydrogenase (quinone)

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