SMTL ID : 8xgd.1

Human Cx36/GJD2 gap junction channel with pore-lining N-terminal helices in porcine brain lipids.

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

60 x MC3: 1,2-DIMYRISTOYL-RAC-GLYCERO-3-PHOSPHOCHOLINE(Non-covalent)

MC3.1: 4 residues within 4Å: Chain A: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.2: 3 residues within 4Å: Chain A: F.223, V.255, F.258 Ligand excluded by PLIP MC3.3: 5 residues within 4Å: Chain A: V.15, Q.16, Q.17, H.18 Chain B: V.98 Ligand excluded by PLIP MC3.5: 7 residues within 4Å: Chain A: P.72, I.73, Y.78, F.81, L.220 Chain D: V.252 Ligands: MC3.6 Ligand excluded by PLIP MC3.6: 5 residues within 4Å: Chain A: Y.78, F.213, G.216, L.220 Ligands: MC3.5 Ligand excluded by PLIP MC3.7: 7 residues within 4Å: Chain A: V.252 Chain B: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.8 Ligand excluded by PLIP MC3.8: 5 residues within 4Å: Chain B: Y.78, F.213, G.216, L.220 Ligands: MC3.7 Ligand excluded by PLIP MC3.9: 4 residues within 4Å: Chain B: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.10: 3 residues within 4Å: Chain B: F.223, V.255, F.258 Ligand excluded by PLIP MC3.11: 5 residues within 4Å: Chain B: V.15, Q.16, Q.17, H.18 Chain G: V.98 Ligand excluded by PLIP MC3.13: 4 residues within 4Å: Chain C: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.14: 3 residues within 4Å: Chain C: F.223, V.255, F.258 Ligand excluded by PLIP MC3.15: 5 residues within 4Å: Chain C: V.15, Q.16, Q.17, H.18 Chain L: V.98 Ligand excluded by PLIP MC3.17: 7 residues within 4Å: Chain C: P.72, I.73, Y.78, F.81, L.220 Chain H: V.252 Ligands: MC3.18 Ligand excluded by PLIP MC3.18: 5 residues within 4Å: Chain C: Y.78, F.213, G.216, L.220 Ligands: MC3.17 Ligand excluded by PLIP MC3.19: 4 residues within 4Å: Chain D: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.20: 3 residues within 4Å: Chain D: F.223, V.255, F.258 Ligand excluded by PLIP MC3.21: 5 residues within 4Å: Chain A: V.98 Chain D: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.23: 7 residues within 4Å: Chain D: P.72, I.73, Y.78, F.81, L.220 Chain E: V.252 Ligands: MC3.24 Ligand excluded by PLIP MC3.24: 5 residues within 4Å: Chain D: Y.78, F.213, G.216, L.220 Ligands: MC3.23 Ligand excluded by PLIP MC3.25: 4 residues within 4Å: Chain E: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.26: 3 residues within 4Å: Chain E: F.223, V.255, F.258 Ligand excluded by PLIP MC3.27: 5 residues within 4Å: Chain D: V.98 Chain E: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.29: 7 residues within 4Å: Chain E: P.72, I.73, Y.78, F.81, L.220 Chain F: V.252 Ligands: MC3.30 Ligand excluded by PLIP MC3.30: 5 residues within 4Å: Chain E: Y.78, F.213, G.216, L.220 Ligands: MC3.29 Ligand excluded by PLIP MC3.31: 4 residues within 4Å: Chain F: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.32: 3 residues within 4Å: Chain F: F.223, V.255, F.258 Ligand excluded by PLIP MC3.33: 5 residues within 4Å: Chain E: V.98 Chain F: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.35: 7 residues within 4Å: Chain F: P.72, I.73, Y.78, F.81, L.220 Chain G: V.252 Ligands: MC3.36 Ligand excluded by PLIP MC3.36: 5 residues within 4Å: Chain F: Y.78, F.213, G.216, L.220 Ligands: MC3.35 Ligand excluded by PLIP MC3.37: 7 residues within 4Å: Chain B: V.252 Chain G: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.38 Ligand excluded by PLIP MC3.38: 5 residues within 4Å: Chain G: Y.78, F.213, G.216, L.220 Ligands: MC3.37 Ligand excluded by PLIP MC3.39: 4 residues within 4Å: Chain G: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.40: 3 residues within 4Å: Chain G: F.223, V.255, F.258 Ligand excluded by PLIP MC3.41: 5 residues within 4Å: Chain F: V.98 Chain G: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.43: 4 residues within 4Å: Chain H: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.44: 3 residues within 4Å: Chain H: F.223, V.255, F.258 Ligand excluded by PLIP MC3.45: 5 residues within 4Å: Chain C: V.98 Chain H: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.47: 7 residues within 4Å: Chain H: P.72, I.73, Y.78, F.81, L.220 Chain I: V.252 Ligands: MC3.48 Ligand excluded by PLIP MC3.48: 5 residues within 4Å: Chain H: Y.78, F.213, G.216, L.220 Ligands: MC3.47 Ligand excluded by PLIP MC3.49: 4 residues within 4Å: Chain I: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.50: 3 residues within 4Å: Chain I: F.223, V.255, F.258 Ligand excluded by PLIP MC3.51: 5 residues within 4Å: Chain H: V.98 Chain I: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.53: 7 residues within 4Å: Chain I: P.72, I.73, Y.78, F.81, L.220 Chain J: V.252 Ligands: MC3.54 Ligand excluded by PLIP MC3.54: 5 residues within 4Å: Chain I: Y.78, F.213, G.216, L.220 Ligands: MC3.53 Ligand excluded by PLIP MC3.55: 4 residues within 4Å: Chain J: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.56: 3 residues within 4Å: Chain J: F.223, V.255, F.258 Ligand excluded by PLIP MC3.57: 5 residues within 4Å: Chain I: V.98 Chain J: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.59: 7 residues within 4Å: Chain J: P.72, I.73, Y.78, F.81, L.220 Chain K: V.252 Ligands: MC3.60 Ligand excluded by PLIP MC3.60: 5 residues within 4Å: Chain J: Y.78, F.213, G.216, L.220 Ligands: MC3.59 Ligand excluded by PLIP MC3.61: 4 residues within 4Å: Chain K: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.62: 3 residues within 4Å: Chain K: F.223, V.255, F.258 Ligand excluded by PLIP MC3.63: 5 residues within 4Å: Chain J: V.98 Chain K: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP MC3.65: 7 residues within 4Å: Chain K: P.72, I.73, Y.78, F.81, L.220 Chain L: V.252 Ligands: MC3.66 Ligand excluded by PLIP MC3.66: 5 residues within 4Å: Chain K: Y.78, F.213, G.216, L.220 Ligands: MC3.65 Ligand excluded by PLIP MC3.67: 7 residues within 4Å: Chain C: V.252 Chain L: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.68 Ligand excluded by PLIP MC3.68: 5 residues within 4Å: Chain L: Y.78, F.213, G.216, L.220 Ligands: MC3.67 Ligand excluded by PLIP MC3.69: 4 residues within 4Å: Chain L: T.248, T.251, V.252, V.255 Ligand excluded by PLIP MC3.70: 3 residues within 4Å: Chain L: F.223, V.255, F.258 Ligand excluded by PLIP MC3.71: 5 residues within 4Å: Chain K: V.98 Chain L: V.15, Q.16, Q.17, H.18 Ligand excluded by PLIP

12 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.4: 13 residues within 4Å: Chain A: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain D: F.33 8 PLIP interactions: 1 interactions with chain D, 7 interactions with chain A Hydrophobic interactions: D:F.33, A:Y.96, A:F.198, A:I.201, A:F.205, A:F.205, A:L.209 Salt bridges: A:R.197 Y01.12: 13 residues within 4Å: Chain A: F.33 Chain B: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 8 PLIP interactions: 7 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:Y.96, B:F.198, B:I.201, B:F.205, B:F.205, B:L.209, A:F.33 Salt bridges: B:R.197 Y01.16: 13 residues within 4Å: Chain C: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain H: F.33 8 PLIP interactions: 7 interactions with chain C, 1 interactions with chain H Hydrophobic interactions: C:Y.96, C:F.198, C:I.201, C:F.205, C:F.205, C:L.209, H:F.33 Salt bridges: C:R.197 Y01.22: 13 residues within 4Å: Chain D: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain E: F.33 8 PLIP interactions: 7 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:Y.96, D:F.198, D:I.201, D:F.205, D:F.205, D:L.209, E:F.33 Salt bridges: D:R.197 Y01.28: 13 residues within 4Å: Chain E: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain F: F.33 8 PLIP interactions: 7 interactions with chain E, 1 interactions with chain F Hydrophobic interactions: E:Y.96, E:F.198, E:I.201, E:F.205, E:F.205, E:L.209, F:F.33 Salt bridges: E:R.197 Y01.34: 13 residues within 4Å: Chain F: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain G: F.33 8 PLIP interactions: 7 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:Y.96, F:F.198, F:I.201, F:F.205, F:F.205, F:L.209, G:F.33 Salt bridges: F:R.197 Y01.42: 13 residues within 4Å: Chain B: F.33 Chain G: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 8 PLIP interactions: 7 interactions with chain G, 1 interactions with chain B Hydrophobic interactions: G:Y.96, G:F.198, G:I.201, G:F.205, G:F.205, G:L.209, B:F.33 Salt bridges: G:R.197 Y01.46: 13 residues within 4Å: Chain H: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain I: F.33 8 PLIP interactions: 7 interactions with chain H, 1 interactions with chain I Hydrophobic interactions: H:Y.96, H:F.198, H:I.201, H:F.205, H:F.205, H:L.209, I:F.33 Salt bridges: H:R.197 Y01.52: 13 residues within 4Å: Chain I: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain J: F.33 8 PLIP interactions: 7 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:Y.96, I:F.198, I:I.201, I:F.205, I:F.205, I:L.209, J:F.33 Salt bridges: I:R.197 Y01.58: 13 residues within 4Å: Chain J: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain K: F.33 8 PLIP interactions: 7 interactions with chain J, 1 interactions with chain K Hydrophobic interactions: J:Y.96, J:F.198, J:I.201, J:F.205, J:F.205, J:L.209, K:F.33 Salt bridges: J:R.197 Y01.64: 13 residues within 4Å: Chain K: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 Chain L: F.33 8 PLIP interactions: 1 interactions with chain L, 7 interactions with chain K Hydrophobic interactions: L:F.33, K:Y.96, K:F.198, K:I.201, K:F.205, K:F.205, K:L.209 Salt bridges: K:R.197 Y01.72: 13 residues within 4Å: Chain C: F.33 Chain L: F.81, M.85, T.88, P.89, Y.96, R.197, F.198, I.201, Q.202, F.205, L.209, F.213 8 PLIP interactions: 7 interactions with chain L, 1 interactions with chain C Hydrophobic interactions: L:Y.96, L:F.198, L:I.201, L:F.205, L:F.205, L:L.209, C:F.33 Salt bridges: L:R.197

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Cho, H.J. et al., Mefloquine-induced conformational shift in Cx36 N-terminal helix leading to channel closure mediated by lipid bilayer. Nat Commun (2024)

Release Date

2024-11-06

Peptides

Gap junction delta-2 protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
F

C
G

D
B

E
C

F
D

G
E

H
H

I
I

J
J

K
K

L
L

Membrane

We predict this structure to be a membrane protein.
Show / Hide

Gap junction delta-2 protein

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