SMTL ID : 3b6k.1

WrbA from Escherichia coli, Benzoquinone complex

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.99 Å

Oligo State

homo-tetramer

Ligands

4 x FMN: FLAVIN MONONUCLEOTIDE(Non-covalent)

FMN.1: 21 residues within 4Å: Chain A: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, G.81, S.113, T.114, G.115, T.116, G.117, G.118 Chain C: Y.143 Chain D: D.92, H.133 Ligands: PLQ.2 20 PLIP interactions: 19 interactions with chain A, 1 interactions with chain D Hydrophobic interactions: A:F.80 Hydrogen bonds: A:M.11, A:Y.12, A:G.13, A:H.14, A:I.15, A:T.78, A:T.78, A:R.79, A:F.80, A:G.81, A:S.113, A:S.113, A:G.115, A:T.116, A:G.117, A:G.118, A:G.118, D:H.133 Salt bridges: A:H.14 FMN.5: 21 residues within 4Å: Chain B: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, G.81, S.113, T.114, G.115, T.116, G.117, G.118 Chain C: D.92, H.133 Chain D: Y.143 Ligands: PLQ.6 21 PLIP interactions: 20 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:F.80, B:F.80 Hydrogen bonds: B:M.11, B:Y.12, B:G.13, B:H.14, B:I.15, B:T.78, B:T.78, B:R.79, B:F.80, B:G.81, B:S.113, B:S.113, B:G.115, B:T.116, B:G.117, B:G.118, B:G.118, D:Y.143 Salt bridges: B:H.14 FMN.9: 21 residues within 4Å: Chain A: Y.143 Chain B: D.92, H.133 Chain C: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, G.81, S.113, T.114, G.115, T.116, G.117, G.118 Ligands: PLQ.10 21 PLIP interactions: 20 interactions with chain C, 1 interactions with chain A Hydrophobic interactions: C:F.80 Hydrogen bonds: C:M.11, C:Y.12, C:G.13, C:H.14, C:I.15, C:T.78, C:T.78, C:R.79, C:F.80, C:G.81, C:S.113, C:S.113, C:G.115, C:T.116, C:G.117, C:G.118, C:G.118 Water bridges: C:T.116, A:Y.143 Salt bridges: C:H.14 FMN.13: 21 residues within 4Å: Chain A: D.92, H.133 Chain B: Y.143 Chain D: S.10, M.11, Y.12, G.13, H.14, I.15, P.77, T.78, R.79, F.80, G.81, S.113, T.114, G.115, T.116, G.117, G.118 Ligands: PLQ.14 23 PLIP interactions: 20 interactions with chain D, 1 interactions with chain A, 2 interactions with chain B Hydrophobic interactions: D:F.80, D:F.80 Hydrogen bonds: D:M.11, D:Y.12, D:G.13, D:H.14, D:I.15, D:T.78, D:T.78, D:R.79, D:F.80, D:G.81, D:S.113, D:S.113, D:G.115, D:T.116, D:G.117, D:G.118, D:G.118, A:H.133 Salt bridges: D:H.14 Water bridges: B:Y.143, B:Y.143

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

PLQ.2: 3 residues within 4Å: Chain D: G.95, W.98 Ligands: FMN.1 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:W.98 PLQ.6: 3 residues within 4Å: Chain C: G.95, W.98 Ligands: FMN.5 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:W.98 PLQ.10: 3 residues within 4Å: Chain B: G.95, W.98 Ligands: FMN.9 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:W.98 PLQ.14: 3 residues within 4Å: Chain A: G.95, W.98 Ligands: FMN.13 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:W.98

8 x 15P: POLYETHYLENE GLYCOL (N=34)(Non-functional Binders)

15P.3: 9 residues within 4Å: Chain A: W.98, A.99, S.100, G.101, Y.104 Chain B: Y.143, A.144, Q.146, F.149 3 PLIP interactions: 2 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:Q.146, B:Q.146 Water bridges: A:G.101 15P.4: 6 residues within 4Å: Chain A: Y.188, G.191, K.195 Chain B: G.105, L.196, N.197 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:K.195 Water bridges: A:G.191, B:N.197 15P.7: 8 residues within 4Å: Chain A: Y.143, A.144, F.149 Chain B: W.98, A.99, S.100, G.101, Y.104 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Water bridges: B:G.101, A:Q.146, A:Q.146 15P.8: 7 residues within 4Å: Chain A: G.105, L.196, N.197 Chain B: Y.188, G.191, L.192, K.195 2 PLIP interactions: 1 interactions with chain A, 1 interactions with chain B Water bridges: A:N.197 Hydrogen bonds: B:K.195 15P.11: 9 residues within 4Å: Chain C: W.98, A.99, S.100, G.101, Y.104 Chain D: Y.143, A.144, Q.146, F.149 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain D Water bridges: C:G.101 Hydrogen bonds: D:Q.146, D:Q.146 15P.12: 6 residues within 4Å: Chain C: Y.188, G.191, K.195 Chain D: G.105, L.196, N.197 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:N.197, C:G.191 Hydrogen bonds: C:K.195 15P.15: 8 residues within 4Å: Chain C: Y.143, A.144, F.149 Chain D: W.98, A.99, S.100, G.101, Y.104 3 PLIP interactions: 1 interactions with chain D, 2 interactions with chain C Water bridges: D:G.101, C:Q.146, C:Q.146 15P.16: 7 residues within 4Å: Chain C: G.105, L.196, N.197 Chain D: Y.188, G.191, L.192, K.195 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Water bridges: C:N.197 Hydrogen bonds: D:K.195

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Andrade, S.L. et al., Crystal structure of the NADH:quinone oxidoreductase WrbA from Escherichia coli. J.Bacteriol. (2007)

Release Date

2007-12-11

Peptides

Flavoprotein wrbA: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Flavoprotein wrbA

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