SMTL ID : 7xnh.1

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

Coordinates

PDB Format

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

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

MC3.1: 9 residues within 4Å: Chain A: V.225, P.247, T.248, T.251, V.252, V.255 Chain F: R.233 Ligands: MC3.2, MC3.3 Ligand excluded by PLIP MC3.2: 5 residues within 4Å: Chain A: F.223, T.251, F.258 Ligands: MC3.1, MC3.3 Ligand excluded by PLIP MC3.3: 2 residues within 4Å: Ligands: MC3.1, MC3.2 Ligand excluded by PLIP MC3.4: 3 residues within 4Å: Chain F: L.10, V.98 Ligands: MC3.5 Ligand excluded by PLIP MC3.5: 7 residues within 4Å: Chain A: V.15, R.24, T.28, I.32 Chain F: L.91, T.95 Ligands: MC3.4 Ligand excluded by PLIP MC3.6: 9 residues within 4Å: Chain A: R.233 Chain B: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.13, MC3.14 Ligand excluded by PLIP MC3.7: 6 residues within 4Å: Chain A: P.72, I.73, Y.78, F.81 Ligands: MC3.8, MC3.10 Ligand excluded by PLIP MC3.8: 6 residues within 4Å: Chain A: G.212, F.213, G.216, L.220 Ligands: MC3.7, MC3.9 Ligand excluded by PLIP MC3.9: 3 residues within 4Å: Chain A: G.212, F.219 Ligands: MC3.8 Ligand excluded by PLIP MC3.10: 1 residues within 4Å: Ligands: MC3.7 Ligand excluded by PLIP MC3.11: 6 residues within 4Å: Chain A: P.89, C.92, F.198, I.201, F.205 Ligands: MC3.12 Ligand excluded by PLIP MC3.12: 7 residues within 4Å: Chain A: C.92, T.95, Y.96, F.198 Chain B: M.21, I.25 Ligands: MC3.11 Ligand excluded by PLIP MC3.13: 5 residues within 4Å: Chain B: F.223, T.251, F.258 Ligands: MC3.6, MC3.14 Ligand excluded by PLIP MC3.14: 2 residues within 4Å: Ligands: MC3.6, MC3.13 Ligand excluded by PLIP MC3.15: 3 residues within 4Å: Chain A: L.10, V.98 Ligands: MC3.16 Ligand excluded by PLIP MC3.16: 6 residues within 4Å: Chain A: L.91 Chain B: V.15, R.24, T.28, I.32 Ligands: MC3.15 Ligand excluded by PLIP MC3.17: 10 residues within 4Å: Chain B: D.68, R.233 Chain C: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.24, MC3.25 Ligand excluded by PLIP MC3.18: 7 residues within 4Å: Chain B: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.19, MC3.21 Ligand excluded by PLIP MC3.19: 8 residues within 4Å: Chain B: Y.78, G.212, F.213, G.216, F.219, L.220 Ligands: MC3.18, MC3.20 Ligand excluded by PLIP MC3.20: 4 residues within 4Å: Chain B: G.212, V.215, F.219 Ligands: MC3.19 Ligand excluded by PLIP MC3.21: 1 residues within 4Å: Ligands: MC3.18 Ligand excluded by PLIP MC3.22: 7 residues within 4Å: Chain B: P.89, C.92, Y.96, F.198, I.201, F.205 Ligands: MC3.23 Ligand excluded by PLIP MC3.23: 7 residues within 4Å: Chain B: C.92, T.95, Y.96, F.198 Chain C: M.21, I.25 Ligands: MC3.22 Ligand excluded by PLIP MC3.24: 5 residues within 4Å: Chain C: F.223, T.251, F.258 Ligands: MC3.17, MC3.25 Ligand excluded by PLIP MC3.25: 2 residues within 4Å: Ligands: MC3.17, MC3.24 Ligand excluded by PLIP MC3.26: 3 residues within 4Å: Chain B: L.10, V.98 Ligands: MC3.27 Ligand excluded by PLIP MC3.27: 7 residues within 4Å: Chain B: L.91, I.94 Chain C: V.15, R.24, T.28, I.32 Ligands: MC3.26 Ligand excluded by PLIP MC3.28: 9 residues within 4Å: Chain C: R.233 Chain D: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.35, MC3.36 Ligand excluded by PLIP MC3.29: 6 residues within 4Å: Chain C: P.72, I.73, Y.78, F.81 Ligands: MC3.30, MC3.32 Ligand excluded by PLIP MC3.30: 7 residues within 4Å: Chain C: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.29, MC3.31 Ligand excluded by PLIP MC3.31: 3 residues within 4Å: Chain C: G.212, F.219 Ligands: MC3.30 Ligand excluded by PLIP MC3.32: 1 residues within 4Å: Ligands: MC3.29 Ligand excluded by PLIP MC3.33: 6 residues within 4Å: Chain C: P.89, C.92, F.198, I.201, F.205 Ligands: MC3.34 Ligand excluded by PLIP MC3.34: 7 residues within 4Å: Chain C: C.92, T.95, Y.96, F.198 Chain D: M.21, I.25 Ligands: MC3.33 Ligand excluded by PLIP MC3.35: 5 residues within 4Å: Chain D: F.223, T.251, F.258 Ligands: MC3.28, MC3.36 Ligand excluded by PLIP MC3.36: 2 residues within 4Å: Ligands: MC3.28, MC3.35 Ligand excluded by PLIP MC3.37: 3 residues within 4Å: Chain C: L.10, V.98 Ligands: MC3.38 Ligand excluded by PLIP MC3.38: 7 residues within 4Å: Chain C: L.91, T.95 Chain D: V.15, R.24, T.28, I.32 Ligands: MC3.37 Ligand excluded by PLIP MC3.39: 10 residues within 4Å: Chain D: D.68, R.233 Chain E: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.46, MC3.47 Ligand excluded by PLIP MC3.40: 7 residues within 4Å: Chain D: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.41, MC3.43 Ligand excluded by PLIP MC3.41: 7 residues within 4Å: Chain D: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.40, MC3.42 Ligand excluded by PLIP MC3.42: 3 residues within 4Å: Chain D: G.212, F.219 Ligands: MC3.41 Ligand excluded by PLIP MC3.43: 1 residues within 4Å: Ligands: MC3.40 Ligand excluded by PLIP MC3.44: 5 residues within 4Å: Chain D: P.89, C.92, Y.96, F.198 Ligands: MC3.45 Ligand excluded by PLIP MC3.45: 6 residues within 4Å: Chain D: C.92, T.95, Y.96 Chain E: M.21, I.25 Ligands: MC3.44 Ligand excluded by PLIP MC3.46: 5 residues within 4Å: Chain E: F.223, T.251, F.258 Ligands: MC3.39, MC3.47 Ligand excluded by PLIP MC3.47: 2 residues within 4Å: Ligands: MC3.39, MC3.46 Ligand excluded by PLIP MC3.48: 2 residues within 4Å: Chain D: L.10 Ligands: MC3.49 Ligand excluded by PLIP MC3.49: 5 residues within 4Å: Chain E: V.15, R.24, T.28, I.32 Ligands: MC3.48 Ligand excluded by PLIP MC3.50: 9 residues within 4Å: Chain E: R.233 Chain F: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.63, MC3.64 Ligand excluded by PLIP MC3.51: 6 residues within 4Å: Chain E: P.72, I.73, Y.78, F.81 Ligands: MC3.52, MC3.54 Ligand excluded by PLIP MC3.52: 5 residues within 4Å: Chain E: G.212, G.216, L.220 Ligands: MC3.51, MC3.53 Ligand excluded by PLIP MC3.53: 2 residues within 4Å: Chain E: G.212 Ligands: MC3.52 Ligand excluded by PLIP MC3.54: 1 residues within 4Å: Ligands: MC3.51 Ligand excluded by PLIP MC3.55: 4 residues within 4Å: Chain E: C.92, F.198, F.205 Ligands: MC3.56 Ligand excluded by PLIP MC3.56: 7 residues within 4Å: Chain E: C.92, T.95, Y.96, F.198 Chain F: M.21, I.25 Ligands: MC3.55 Ligand excluded by PLIP MC3.57: 7 residues within 4Å: Chain F: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.58, MC3.60 Ligand excluded by PLIP MC3.58: 7 residues within 4Å: Chain F: G.212, F.213, G.216, F.219, L.220 Ligands: MC3.57, MC3.59 Ligand excluded by PLIP MC3.59: 3 residues within 4Å: Chain F: G.212, F.219 Ligands: MC3.58 Ligand excluded by PLIP MC3.60: 1 residues within 4Å: Ligands: MC3.57 Ligand excluded by PLIP MC3.61: 6 residues within 4Å: Chain F: P.89, C.92, F.198, I.201, F.205 Ligands: MC3.62 Ligand excluded by PLIP MC3.62: 6 residues within 4Å: Chain A: M.21, I.25 Chain F: C.92, Y.96, F.198 Ligands: MC3.61 Ligand excluded by PLIP MC3.63: 5 residues within 4Å: Chain F: F.223, T.251, F.258 Ligands: MC3.50, MC3.64 Ligand excluded by PLIP MC3.64: 2 residues within 4Å: Ligands: MC3.50, MC3.63 Ligand excluded by PLIP MC3.65: 3 residues within 4Å: Chain E: L.10, V.98 Ligands: MC3.66 Ligand excluded by PLIP MC3.66: 6 residues within 4Å: Chain E: L.91 Chain F: V.15, R.24, T.28, I.32 Ligands: MC3.65 Ligand excluded by PLIP MC3.67: 10 residues within 4Å: Chain G: V.225, P.247, T.248, T.251, V.252, V.255 Chain L: D.68, R.233 Ligands: MC3.68, MC3.69 Ligand excluded by PLIP MC3.68: 5 residues within 4Å: Chain G: F.223, T.251, F.258 Ligands: MC3.67, MC3.69 Ligand excluded by PLIP MC3.69: 2 residues within 4Å: Ligands: MC3.67, MC3.68 Ligand excluded by PLIP MC3.70: 3 residues within 4Å: Chain L: L.10, V.98 Ligands: MC3.71 Ligand excluded by PLIP MC3.71: 7 residues within 4Å: Chain G: V.15, R.24, T.28, I.32 Chain L: L.91, I.94 Ligands: MC3.70 Ligand excluded by PLIP MC3.72: 10 residues within 4Å: Chain G: D.68, R.233 Chain H: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.79, MC3.80 Ligand excluded by PLIP MC3.73: 7 residues within 4Å: Chain G: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.74, MC3.76 Ligand excluded by PLIP MC3.74: 7 residues within 4Å: Chain G: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.73, MC3.75 Ligand excluded by PLIP MC3.75: 3 residues within 4Å: Chain G: G.212, F.219 Ligands: MC3.74 Ligand excluded by PLIP MC3.76: 1 residues within 4Å: Ligands: MC3.73 Ligand excluded by PLIP MC3.77: 7 residues within 4Å: Chain G: T.88, P.89, C.92, Y.96, F.198, I.201 Ligands: MC3.78 Ligand excluded by PLIP MC3.78: 7 residues within 4Å: Chain G: C.92, T.95, Y.96, F.198 Chain H: M.21, I.25 Ligands: MC3.77 Ligand excluded by PLIP MC3.79: 5 residues within 4Å: Chain H: F.223, T.251, F.258 Ligands: MC3.72, MC3.80 Ligand excluded by PLIP MC3.80: 2 residues within 4Å: Ligands: MC3.72, MC3.79 Ligand excluded by PLIP MC3.81: 2 residues within 4Å: Chain G: L.10 Ligands: MC3.82 Ligand excluded by PLIP MC3.82: 5 residues within 4Å: Chain H: V.15, R.24, T.28, I.32 Ligands: MC3.81 Ligand excluded by PLIP MC3.83: 9 residues within 4Å: Chain H: R.233 Chain I: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.90, MC3.91 Ligand excluded by PLIP MC3.84: 7 residues within 4Å: Chain H: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.85, MC3.87 Ligand excluded by PLIP MC3.85: 6 residues within 4Å: Chain H: G.212, F.213, G.216, L.220 Ligands: MC3.84, MC3.86 Ligand excluded by PLIP MC3.86: 3 residues within 4Å: Chain H: G.212, F.219 Ligands: MC3.85 Ligand excluded by PLIP MC3.87: 1 residues within 4Å: Ligands: MC3.84 Ligand excluded by PLIP MC3.88: 5 residues within 4Å: Chain H: P.89, C.92, Y.96, F.198 Ligands: MC3.89 Ligand excluded by PLIP MC3.89: 6 residues within 4Å: Chain H: C.92, T.95, Y.96 Chain I: M.21, I.25 Ligands: MC3.88 Ligand excluded by PLIP MC3.90: 5 residues within 4Å: Chain I: F.223, T.251, F.258 Ligands: MC3.83, MC3.91 Ligand excluded by PLIP MC3.91: 2 residues within 4Å: Ligands: MC3.83, MC3.90 Ligand excluded by PLIP MC3.92: 1 residues within 4Å: Ligands: MC3.93 Ligand excluded by PLIP MC3.93: 5 residues within 4Å: Chain I: V.15, R.24, T.28, I.32 Ligands: MC3.92 Ligand excluded by PLIP MC3.94: 9 residues within 4Å: Chain I: R.233 Chain J: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.101, MC3.102 Ligand excluded by PLIP MC3.95: 7 residues within 4Å: Chain I: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.96, MC3.98 Ligand excluded by PLIP MC3.96: 7 residues within 4Å: Chain I: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.95, MC3.97 Ligand excluded by PLIP MC3.97: 3 residues within 4Å: Chain I: G.212, F.219 Ligands: MC3.96 Ligand excluded by PLIP MC3.98: 1 residues within 4Å: Ligands: MC3.95 Ligand excluded by PLIP MC3.99: 7 residues within 4Å: Chain I: P.89, C.92, Y.96, F.198, I.201, F.205 Ligands: MC3.100 Ligand excluded by PLIP MC3.100: 7 residues within 4Å: Chain I: C.92, T.95, Y.96, F.198 Chain J: M.21, I.25 Ligands: MC3.99 Ligand excluded by PLIP MC3.101: 5 residues within 4Å: Chain J: F.223, T.251, F.258 Ligands: MC3.94, MC3.102 Ligand excluded by PLIP MC3.102: 2 residues within 4Å: Ligands: MC3.94, MC3.101 Ligand excluded by PLIP MC3.103: 2 residues within 4Å: Chain I: L.10 Ligands: MC3.104 Ligand excluded by PLIP MC3.104: 7 residues within 4Å: Chain I: L.91, I.94 Chain J: V.15, R.24, T.28, I.32 Ligands: MC3.103 Ligand excluded by PLIP MC3.105: 9 residues within 4Å: Chain J: R.233 Chain K: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.112, MC3.113 Ligand excluded by PLIP MC3.106: 6 residues within 4Å: Chain J: P.72, I.73, Y.78, F.81 Ligands: MC3.107, MC3.109 Ligand excluded by PLIP MC3.107: 5 residues within 4Å: Chain J: G.212, G.216, L.220 Ligands: MC3.106, MC3.108 Ligand excluded by PLIP MC3.108: 2 residues within 4Å: Chain J: G.212 Ligands: MC3.107 Ligand excluded by PLIP MC3.109: 1 residues within 4Å: Ligands: MC3.106 Ligand excluded by PLIP MC3.110: 5 residues within 4Å: Chain J: C.92, F.198, I.201, F.205 Ligands: MC3.111 Ligand excluded by PLIP MC3.111: 7 residues within 4Å: Chain J: C.92, T.95, Y.96, F.198 Chain K: M.21, I.25 Ligands: MC3.110 Ligand excluded by PLIP MC3.112: 5 residues within 4Å: Chain K: F.223, T.251, F.258 Ligands: MC3.105, MC3.113 Ligand excluded by PLIP MC3.113: 2 residues within 4Å: Ligands: MC3.105, MC3.112 Ligand excluded by PLIP MC3.114: 3 residues within 4Å: Chain J: L.10, V.98 Ligands: MC3.115 Ligand excluded by PLIP MC3.115: 6 residues within 4Å: Chain J: L.91 Chain K: V.15, R.24, T.28, I.32 Ligands: MC3.114 Ligand excluded by PLIP MC3.116: 10 residues within 4Å: Chain K: D.68, R.233 Chain L: V.225, P.247, T.248, T.251, V.252, V.255 Ligands: MC3.129, MC3.130 Ligand excluded by PLIP MC3.117: 7 residues within 4Å: Chain K: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.118, MC3.120 Ligand excluded by PLIP MC3.118: 7 residues within 4Å: Chain K: Y.78, G.212, F.213, G.216, L.220 Ligands: MC3.117, MC3.119 Ligand excluded by PLIP MC3.119: 3 residues within 4Å: Chain K: G.212, F.219 Ligands: MC3.118 Ligand excluded by PLIP MC3.120: 1 residues within 4Å: Ligands: MC3.117 Ligand excluded by PLIP MC3.121: 7 residues within 4Å: Chain K: P.89, C.92, Y.96, F.198, I.201, F.205 Ligands: MC3.122 Ligand excluded by PLIP MC3.122: 7 residues within 4Å: Chain K: C.92, T.95, Y.96, F.198 Chain L: M.21, I.25 Ligands: MC3.121 Ligand excluded by PLIP MC3.123: 7 residues within 4Å: Chain L: P.72, I.73, Y.78, F.81, L.220 Ligands: MC3.124, MC3.126 Ligand excluded by PLIP MC3.124: 8 residues within 4Å: Chain L: Y.78, G.212, F.213, G.216, F.219, L.220 Ligands: MC3.123, MC3.125 Ligand excluded by PLIP MC3.125: 4 residues within 4Å: Chain L: G.212, V.215, F.219 Ligands: MC3.124 Ligand excluded by PLIP MC3.126: 1 residues within 4Å: Ligands: MC3.123 Ligand excluded by PLIP MC3.127: 6 residues within 4Å: Chain L: P.89, C.92, F.198, I.201, F.205 Ligands: MC3.128 Ligand excluded by PLIP MC3.128: 7 residues within 4Å: Chain G: M.21, I.25 Chain L: C.92, T.95, Y.96, F.198 Ligands: MC3.127 Ligand excluded by PLIP MC3.129: 5 residues within 4Å: Chain L: F.223, T.251, F.258 Ligands: MC3.116, MC3.130 Ligand excluded by PLIP MC3.130: 2 residues within 4Å: Ligands: MC3.116, MC3.129 Ligand excluded by PLIP MC3.131: 3 residues within 4Å: Chain K: L.10, V.98 Ligands: MC3.132 Ligand excluded by PLIP MC3.132: 6 residues within 4Å: Chain K: L.91 Chain L: V.15, R.24, T.28, I.32 Ligands: MC3.131 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Lee, S.N. et al., Cryo-EM structures of human Cx36/GJD2 neuronal gap junction channel. Nat Commun (2023)

Release Date

2023-03-22

Peptides

Gap junction delta-2 protein: ABCDEFGHIJKL

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
C

D
D

E
E

F
F

G
G

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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