SMTL ID : 3ub6.1

Periplasmic portion of the Helicobacter pylori chemoreceptor TlpB with urea bound

Coordinates

PDB Format

Method

X-RAY DIFFRACTION 1.38 Å

Oligo State

homo-dimer

Ligands

2 x URE: UREA(Non-functional Binders)

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

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

SO4.2: 7 residues within 4Å: Chain A: K.24, R.25, T.28, M.69, E.162 Chain B: K.24 Ligands: SO4.10 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Water bridges: A:Q.21, A:N.163, A:N.163 Salt bridges: A:K.24, A:R.25, B:K.24 Hydrogen bonds: B:T.28, B:T.28 SO4.4: 4 residues within 4Å: Chain A: Q.38, H.41 Chain B: R.62 Ligands: PEG.3 3 PLIP interactions: 2 interactions with chain A, 1 interactions with chain B Hydrogen bonds: A:Q.38 Salt bridges: A:H.41, B:R.62 SO4.10: 7 residues within 4Å: Chain A: K.24 Chain B: K.24, R.25, T.28, M.69, E.162 Ligands: SO4.2 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrogen bonds: B:T.28 Water bridges: B:N.163 Salt bridges: B:K.24, B:R.25, A:K.24

1 x PEG: DI(HYDROXYETHYL)ETHER(Non-functional Binders)

PEG.3: 4 residues within 4Å: Chain A: Q.38, H.41 Chain B: R.62 Ligands: SO4.4 No protein-ligand interaction detected (PLIP)

9 x GOL: GLYCEROL(Non-functional Binders)

GOL.5: 5 residues within 4Å: Chain A: G.68, M.69, D.158, T.161, E.162 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:G.68, A:E.162 Water bridges: A:K.127, A:K.127 GOL.6: 4 residues within 4Å: Chain A: E.18, Y.22, K.135, Y.156 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:Y.22 Water bridges: A:Y.156 GOL.7: 2 residues within 4Å: Chain A: K.89, Q.93 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:Q.93 Water bridges: A:K.89, A:K.89, A:Q.93 GOL.8: 2 residues within 4Å: Chain A: V.104, Y.105 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:Y.105 GOL.11: 6 residues within 4Å: Chain B: N.64, D.65, Y.71, K.127, Y.128 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:K.127 Water bridges: B:Y.71 GOL.12: 6 residues within 4Å: Chain B: K.67, G.68, M.69, D.158, T.161, E.162 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:E.162 GOL.13: 4 residues within 4Å: Chain B: E.18, Y.22, K.135, Y.156 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:E.18, B:E.18 Water bridges: B:Y.156, B:Y.156 GOL.14: 3 residues within 4Å: Chain B: K.67, Y.128 Ligands: GOL.15 2 PLIP interactions: 2 interactions with chain B Water bridges: B:Y.128, B:Y.128 GOL.15: 3 residues within 4Å: Chain B: Y.128 Ligands: GOL.11, GOL.14 No protein-ligand interaction detected (PLIP)

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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