SMTL ID : 4p33.2 (2 other biounits)

Crystal structure of E. coli LptB-E163Q in complex with ATP-sodium

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.65 Å

Oligo State

homo-dimer

Ligands

2 x NA: SODIUM ION(Non-functional Binders)

NA.1: 4 residues within 4Å: Chain A: T.42, Q.84, Q.162 Ligands: ATP.2 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:T.42, A:Q.84, A:Q.84 Water bridges: B:G.139 NA.5: 4 residues within 4Å: Chain B: T.42, Q.84, Q.162 Ligands: ATP.6 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain B Water bridges: A:G.139 Hydrogen bonds: B:Q.84, B:Q.162

2 x ATP: ADENOSINE-5'-TRIPHOSPHATE(Non-covalent)

ATP.2: 20 residues within 4Å: Chain A: Y.12, R.15, V.17, P.36, N.37, G.38, A.39, G.40, K.41, T.42, T.43, Q.84, Q.162, H.194 Chain B: S.136, S.138, G.139, G.140, E.141 Ligands: NA.1 28 PLIP interactions: 22 interactions with chain A, 6 interactions with chain B Hydrogen bonds: A:R.15, A:R.15, A:N.37, A:G.38, A:G.38, A:A.39, A:G.40, A:K.41, A:T.42, A:T.42, A:T.43, A:Q.84, A:Q.162, B:S.138, B:S.138, B:G.139, B:G.140, B:E.141, B:E.141 Water bridges: A:T.42, A:T.42, A:Q.84, A:D.161, A:Q.162 Salt bridges: A:K.41, A:K.41, A:H.194 pi-Stacking: A:Y.12 ATP.6: 20 residues within 4Å: Chain A: S.136, S.138, G.139, G.140, E.141 Chain B: Y.12, R.15, V.17, P.36, N.37, G.38, A.39, G.40, K.41, T.42, T.43, Q.84, Q.162, H.194 Ligands: NA.5 32 PLIP interactions: 9 interactions with chain A, 23 interactions with chain B Hydrogen bonds: A:S.138, A:S.138, A:G.139, A:G.140, A:E.141, A:E.141, B:R.15, B:R.15, B:N.37, B:G.38, B:G.38, B:A.39, B:G.40, B:K.41, B:T.42, B:T.43, B:T.43, B:Q.84, B:Q.162 Water bridges: A:E.141, A:E.141, A:G.166, B:Y.12, B:T.42, B:T.42, B:T.42, B:Q.84, B:D.161 Salt bridges: B:K.41, B:K.41, B:H.194 pi-Stacking: B:Y.12

4 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 5 residues within 4Å: Chain A: R.91, L.92, S.93, D.96, M.133 5 PLIP interactions: 5 interactions with chain A Hydrogen bonds: A:S.93, A:D.96 Water bridges: A:S.93, A:D.96, A:D.96 GOL.4: 1 residues within 4Å: Chain A: R.91 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:R.91, A:R.91 GOL.7: 5 residues within 4Å: Chain B: R.91, L.92, S.93, D.96, M.133 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:S.93 Water bridges: B:S.93, B:D.96, B:D.96 GOL.8: 1 residues within 4Å: Chain B: R.91 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:R.91, B:R.91

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Sherman, D.J. et al., Decoupling catalytic activity from biological function of the ATPase that powers lipopolysaccharide transport. Proc.Natl.Acad.Sci.USA (2014)

Release Date

2014-03-26

Peptides

Lipopolysaccharide export system ATP-binding protein LptB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
B

B
B

Lipopolysaccharide export system ATP-binding protein LptB

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