SMTL ID : 8gyo.1

Inner channel lipids regulated gating mechanism of human pannexins.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

7 x NAG: 2-acetamido-2-deoxy-beta-D-glucopyranose(Post Translational Modification)

NAG.1: 2 residues within 4Å: Chain A: R.254, N.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:R.254 NAG.4: 1 residues within 4Å: Chain B: N.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255 NAG.6: 1 residues within 4Å: Chain C: N.255 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:N.255 NAG.7: 1 residues within 4Å: Chain D: N.255 No protein-ligand interaction detected (PLIP) NAG.9: 1 residues within 4Å: Chain E: N.255 No protein-ligand interaction detected (PLIP) NAG.11: 1 residues within 4Å: Chain F: N.255 No protein-ligand interaction detected (PLIP) NAG.13: 1 residues within 4Å: Chain G: N.255 No protein-ligand interaction detected (PLIP)

3 x AJP: Digitonin(Non-covalent)

AJP.2: 11 residues within 4Å: Chain A: E.9, F.12, S.13, L.16, L.48, S.51, L.52 Chain B: L.47, L.114 Ligands: PC1.5, AJP.12 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.48, A:L.52 Hydrogen bonds: A:F.12 AJP.8: 9 residues within 4Å: Chain D: E.9, F.12, S.13, L.16, L.48 Chain E: L.47, L.114 Ligands: PC1.10, AJP.12 5 PLIP interactions: 2 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.47, E:L.114, D:F.12, D:L.48 Hydrogen bonds: D:F.12 AJP.12: 8 residues within 4Å: Chain F: F.12, S.13, L.48, S.51 Chain G: L.47 Ligands: AJP.2, PC1.3, AJP.8 5 PLIP interactions: 5 interactions with chain F Hydrophobic interactions: F:F.12, F:F.12, F:F.12, F:L.48 Hydrogen bonds: F:F.12

3 x PC1: 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

PC1.3: 5 residues within 4Å: Chain A: Y.10 Chain G: K.36, C.40, S.51 Ligands: AJP.12 No protein-ligand interaction detected (PLIP) PC1.5: 7 residues within 4Å: Chain B: K.36, S.51, F.54, I.58 Chain C: L.6, Y.10 Ligands: AJP.2 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.54, B:I.58 Salt bridges: B:K.36, B:K.36 PC1.10: 9 residues within 4Å: Chain D: I.58 Chain E: K.36, S.51, F.54, A.55, Y.121 Chain F: L.6, Y.10 Ligands: AJP.8 4 PLIP interactions: 2 interactions with chain E, 1 interactions with chain F, 1 interactions with chain D Hydrophobic interactions: E:F.54, F:L.6, D:I.58 Salt bridges: E:K.36

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cong, Y. et al., Inner channel lipids regulated gating mechanism of human pannexins. To Be Published

Release Date

2024-04-17

Peptides

Pannexin-1: ABCDEFG

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

Membrane

We predict this structure to be a membrane protein.
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Pannexin-1

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