SMTL ID : 4p33.3 (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-tetramer

Ligands

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

NA.1: 4 residues within 4Å: Chain A: T.42, Q.84, Q.162 Ligands: ATP.2 3 PLIP interactions: 1 interactions with chain C, 2 interactions with chain A Water bridges: C:G.139 Hydrogen bonds: A:Q.84, A:Q.84 NA.6: 4 residues within 4Å: Chain B: T.42, Q.84, Q.162 Ligands: ATP.7 4 PLIP interactions: 3 interactions with chain B, 1 interactions with chain D Hydrogen bonds: B:T.42, B:Q.84, B:Q.162 Water bridges: D:G.139 NA.10: 4 residues within 4Å: Chain C: T.42, Q.84, Q.162 Ligands: ATP.11 4 PLIP interactions: 3 interactions with chain C, 1 interactions with chain A Hydrogen bonds: C:T.42, C:Q.84, C:Q.162 Water bridges: A:G.139 NA.15: 4 residues within 4Å: Chain D: T.42, Q.84, Q.162 Ligands: ATP.16 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain D Water bridges: B:G.139 Hydrogen bonds: D:Q.84, D:Q.162

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

ATP.2: 21 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 C: S.136, S.138, G.139, G.140, E.141 Ligands: NA.1, GOL.9 29 PLIP interactions: 6 interactions with chain C, 23 interactions with chain A Hydrogen bonds: C:S.138, C:S.138, C:G.139, C:G.140, C:E.141, C:E.141, A:R.15, A:R.15, A:N.37, A:G.38, A:G.38, A:A.39, A:G.40, A:G.40, A:K.41, A:T.42, A:T.43, A:T.43, A:Q.84 Water bridges: A:Y.12, A:T.42, A:T.42, A:Q.84, A:Q.162 Salt bridges: A:K.41, A:K.41, A:H.194 pi-Stacking: A:Y.12, A:Y.12 ATP.7: 21 residues within 4Å: 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 Chain D: S.136, S.138, G.139, G.140, E.141 Ligands: GOL.3, NA.6 30 PLIP interactions: 22 interactions with chain B, 7 interactions with chain D, 1 interactions with chain A Hydrogen bonds: 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.42, B:T.43, B:Q.84, B:Q.162, D:S.138, D:S.138, D:G.139, D:G.140, D:E.141, D:E.141 Water bridges: B:T.42, B:T.42, B:Q.84, B:D.161, B:Q.162, D:Q.135, A:R.91 Salt bridges: B:K.41, B:K.41, B:H.194 pi-Stacking: B:Y.12 ATP.11: 21 residues within 4Å: Chain A: S.136, S.138, G.139, G.140, E.141 Chain C: 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.10, GOL.18 26 PLIP interactions: 19 interactions with chain C, 7 interactions with chain A Hydrogen bonds: C:R.15, C:R.15, C:N.37, C:G.38, C:G.38, C:A.39, C:G.40, C:G.40, C:K.41, C:T.42, C:T.42, C:T.43, C:Q.84, A:S.138, A:S.138, A:G.139, A:G.140, A:E.141, A:E.141 Water bridges: C:Q.84, A:G.166 Salt bridges: C:K.41, C:K.41, C:H.194 pi-Stacking: C:Y.12, C:Y.12 ATP.16: 21 residues within 4Å: Chain B: S.136, S.138, G.139, G.140, E.141 Chain D: 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: GOL.12, NA.15 34 PLIP interactions: 23 interactions with chain D, 10 interactions with chain B, 1 interactions with chain C Hydrogen bonds: D:R.15, D:R.15, D:N.37, D:G.38, D:G.38, D:A.39, D:G.40, D:K.41, D:T.42, D:T.43, D:T.43, D:Q.84, D:Q.162, B:S.138, B:S.138, B:G.139, B:G.140, B:E.141, B:E.141 Water bridges: D:Y.12, D:T.42, D:T.42, D:T.42, D:Q.84, D:D.161, B:Q.135, B:E.141, B:E.141, B:G.166, C:R.91 Salt bridges: D:K.41, D:K.41, D:H.194 pi-Stacking: D:Y.12

10 x GOL: GLYCEROL(Non-functional Binders)

GOL.3: 6 residues within 4Å: Chain A: R.91 Chain B: T.42, Y.46 Chain D: Q.135, L.137 Ligands: ATP.7 5 PLIP interactions: 2 interactions with chain B, 2 interactions with chain A, 1 interactions with chain D Water bridges: B:Y.12, B:T.42 Hydrogen bonds: A:R.91, A:R.91, D:Q.135 GOL.4: 8 residues within 4Å: Chain A: R.91, L.92, S.93, D.96, M.133 Chain B: G.50, I.51, P.53 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:S.93 Water bridges: A:S.93 GOL.5: 6 residues within 4Å: Chain A: Y.81, P.83, S.87, E.146, R.149, A.150 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:E.146, A:R.149 GOL.8: 8 residues within 4Å: Chain A: G.50, I.51, P.53 Chain B: R.91, L.92, S.93, D.96, M.133 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:S.93, B:D.96 Water bridges: B:S.93, B:D.96, A:G.50 GOL.9: 6 residues within 4Å: Chain A: Y.46 Chain B: R.91 Chain C: Q.135, L.137, S.138 Ligands: ATP.2 4 PLIP interactions: 2 interactions with chain B, 1 interactions with chain C, 1 interactions with chain A Hydrogen bonds: B:R.91, B:R.91, C:Q.135 Water bridges: A:T.42 GOL.12: 6 residues within 4Å: Chain B: Q.135, L.137 Chain C: R.91 Chain D: T.42, Y.46 Ligands: ATP.16 6 PLIP interactions: 2 interactions with chain C, 1 interactions with chain B, 3 interactions with chain D Hydrogen bonds: C:R.91, C:R.91, B:Q.135 Water bridges: D:Y.12, D:T.42, D:T.42 GOL.13: 8 residues within 4Å: Chain C: R.91, L.92, S.93, D.96, M.133 Chain D: G.50, I.51, P.53 3 PLIP interactions: 3 interactions with chain C Hydrogen bonds: C:S.93, C:D.96 Water bridges: C:S.93 GOL.14: 6 residues within 4Å: Chain C: Y.81, P.83, S.87, E.146, R.149, A.150 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:E.146, C:R.149 GOL.17: 8 residues within 4Å: Chain C: G.50, I.51, P.53 Chain D: R.91, L.92, S.93, D.96, M.133 4 PLIP interactions: 3 interactions with chain D, 1 interactions with chain C Hydrogen bonds: D:S.93 Water bridges: D:S.93, D:D.96, C:G.50 GOL.18: 6 residues within 4Å: Chain A: Q.135, L.137, S.138 Chain C: Y.46 Chain D: R.91 Ligands: ATP.11 4 PLIP interactions: 2 interactions with chain D, 1 interactions with chain A, 1 interactions with chain C Hydrogen bonds: D:R.91, D:R.91, A:Q.135 Water bridges: C:T.42

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: ABCD

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
A

D
B

Lipopolysaccharide export system ATP-binding protein LptB

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