SMTL ID : 3ub7.1

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with acetamide bound

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.40 Å

Oligo State

homo-dimer

Ligands

2 x ACM: ACETAMIDE(Non-covalent)

ACM.1: 9 residues within 4Å: Chain A: V.73, D.84, V.86, N.87, Y.106, Y.110, Y.123, M.125, K.136 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:V.73, A:Y.106 Hydrogen bonds: A:D.84, A:N.87, A:Y.110, A:K.136 Water bridges: A:D.84, A:Y.155, A:Y.155 ACM.3: 9 residues within 4Å: Chain B: V.73, D.84, V.86, N.87, Y.106, Y.110, Y.123, M.125, K.136 8 PLIP interactions: 8 interactions with chain B Hydrophobic interactions: B:V.73, B:Y.106 Hydrogen bonds: B:D.84, B:N.87, B:Y.123, B:K.136 Water bridges: B:T.153, B:T.153

2 x SO4: SULFATE ION(Non-functional Binders)

SO4.2: 6 residues within 4Å: Chain A: K.24, R.25, T.28, M.69 Chain B: K.24 Ligands: SO4.5 9 PLIP interactions: 6 interactions with chain B, 3 interactions with chain A Water bridges: B:K.24, B:K.24, B:K.24, B:T.28, B:T.28, A:N.163 Salt bridges: B:K.24, A:K.24, A:R.25 SO4.5: 6 residues within 4Å: Chain A: K.24 Chain B: K.24, R.25, T.28, M.69 Ligands: SO4.2 9 PLIP interactions: 7 interactions with chain B, 2 interactions with chain A Hydrogen bonds: B:T.28 Water bridges: B:K.24, B:R.25, B:N.163, B:N.163, A:K.24 Salt bridges: B:K.24, B:R.25, A:K.24

2 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 6 residues within 4Å: Chain B: N.64, D.65, K.67, Y.71, K.127, Y.128 3 PLIP interactions: 3 interactions with chain B Hydrogen bonds: B:K.127, B:K.127 Water bridges: B:Y.71 GOL.6: 5 residues within 4Å: Chain B: K.67, G.68, M.69, D.158, E.162 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.67, B:G.68

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Goers Sweeney, E. et al., Structure and proposed mechanism for the pH-sensing Helicobacter pylori chemoreceptor TlpB. Structure (2012)

Release Date

2012-06-27

Peptides

chemoreceptor TlpB: AB

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

chemoreceptor TlpB

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