SMTL ID : 6nsj.1

CryoEM structure of Helicobacter pylori urea channel in closed state

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-hexamer

Ligands

18 x XP4: 1,2-DIMYRISTOYL-SN-GLYCERO-3-PHOSPHATE(Non-functional Binders)(Non-covalent)

XP4.1: 2 residues within 4Å: Ligands: XP4.3, XP4.16 Ligand excluded by PLIP XP4.2: 4 residues within 4Å: Chain A: T.49, Y.50, L.53 Chain B: V.42 Ligand excluded by PLIP XP4.3: 12 residues within 4Å: Chain A: I.41, I.99, F.103 Chain B: K.27, F.34, F.35, G.38, L.39, T.102, F.103 Ligands: XP4.1, XP4.4 Ligand excluded by PLIP XP4.4: 2 residues within 4Å: Ligands: XP4.3, XP4.6 Ligand excluded by PLIP XP4.5: 2 residues within 4Å: Chain B: T.49, L.53 Ligand excluded by PLIP XP4.6: 11 residues within 4Å: Chain B: I.41, I.99, F.103 Chain C: F.34, F.35, G.38, L.39, T.102, F.103 Ligands: XP4.4, XP4.7 Ligand excluded by PLIP XP4.7: 2 residues within 4Å: Ligands: XP4.6, XP4.9 Ligand excluded by PLIP XP4.8: 3 residues within 4Å: Chain C: T.49, Y.50, L.53 Ligand excluded by PLIP XP4.9: 11 residues within 4Å: Chain C: I.41, I.99, F.103 Chain D: K.27, F.34, G.38, L.39, T.102, F.103 Ligands: XP4.7, XP4.10 Ligand excluded by PLIP XP4.10: 2 residues within 4Å: Ligands: XP4.9, XP4.12 Ligand excluded by PLIP XP4.11: 4 residues within 4Å: Chain D: T.49, Y.50, L.53 Chain E: V.42 Ligand excluded by PLIP XP4.12: 12 residues within 4Å: Chain D: I.41, I.99, F.103 Chain E: K.27, F.34, F.35, G.38, L.39, T.102, F.103 Ligands: XP4.10, XP4.13 Ligand excluded by PLIP XP4.13: 2 residues within 4Å: Ligands: XP4.12, XP4.15 Ligand excluded by PLIP XP4.14: 2 residues within 4Å: Chain E: T.49, L.53 Ligand excluded by PLIP XP4.15: 11 residues within 4Å: Chain E: I.41, I.99, F.103 Chain F: F.34, F.35, G.38, L.39, T.102, F.103 Ligands: XP4.13, XP4.17 Ligand excluded by PLIP XP4.16: 11 residues within 4Å: Chain A: K.27, F.34, G.38, L.39, T.102, F.103 Chain F: I.41, I.99, F.103 Ligands: XP4.1, XP4.17 Ligand excluded by PLIP XP4.17: 2 residues within 4Å: Ligands: XP4.15, XP4.16 Ligand excluded by PLIP XP4.18: 3 residues within 4Å: Chain F: T.49, Y.50, L.53 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cui, Y. et al., pH-dependent gating mechanism of theHelicobacter pyloriurea channel revealed by cryo-EM. Sci Adv (2019)

Release Date

2019-04-03

Peptides

Acid-activated urea channel: ABCDEF

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

Membrane

We predict this structure to be a membrane protein.
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Acid-activated urea channel