SMTL ID : 8iyg.1

Human neuronal gap junction channel connexin 36

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-12-mer

Ligands

48 x Y01: CHOLESTEROL HEMISUCCINATE(Non-covalent)

Y01.1: 4 residues within 4Å: Chain A: F.223, S.224, I.263 Ligands: LMT.8 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.223, A:F.223, A:F.223, A:I.263 Y01.2: 3 residues within 4Å: Chain A: L.91, T.95 Ligands: Y01.56 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:L.91, A:T.95 Y01.9: 6 residues within 4Å: Chain A: T.88, C.92, F.198, I.201, F.205 Chain F: I.22 5 PLIP interactions: 1 interactions with chain F, 4 interactions with chain A Hydrophobic interactions: F:I.22, A:F.198, A:I.201, A:F.205, A:F.205 Y01.10: 6 residues within 4Å: Chain A: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.13 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.35 Salt bridges: A:R.206 Y01.12: 4 residues within 4Å: Chain B: F.223, S.224, I.263 Ligands: LMT.19 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:F.223, B:F.223, B:I.263 Y01.13: 3 residues within 4Å: Chain B: L.91, T.95 Ligands: Y01.10 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:L.91, B:T.95 Y01.20: 6 residues within 4Å: Chain A: I.22 Chain B: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 4 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.198, B:I.201, B:F.205, B:F.205, A:I.22 Y01.21: 6 residues within 4Å: Chain B: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.24 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.35 Salt bridges: B:R.206 Y01.23: 4 residues within 4Å: Chain C: F.223, S.224, I.263 Ligands: LMT.30 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.223, C:F.223, C:F.223, C:I.263 Y01.24: 3 residues within 4Å: Chain C: L.91, T.95 Ligands: Y01.21 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:L.91, C:T.95 Y01.31: 6 residues within 4Å: Chain B: I.22 Chain C: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 4 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.198, C:I.201, C:F.205, C:F.205, B:I.22 Y01.32: 6 residues within 4Å: Chain C: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.35 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.35 Salt bridges: C:R.206 Y01.34: 4 residues within 4Å: Chain D: F.223, S.224, I.263 Ligands: LMT.41 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:F.223, D:F.223, D:I.263 Y01.35: 3 residues within 4Å: Chain D: L.91, T.95 Ligands: Y01.32 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:L.91, D:T.95 Y01.42: 6 residues within 4Å: Chain C: I.22 Chain D: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 1 interactions with chain C, 4 interactions with chain D Hydrophobic interactions: C:I.22, D:F.198, D:I.201, D:F.205, D:F.205 Y01.43: 6 residues within 4Å: Chain D: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.46 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.35 Salt bridges: D:R.206 Y01.45: 4 residues within 4Å: Chain E: F.223, S.224, I.263 Ligands: LMT.52 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:F.223, E:F.223, E:I.263 Y01.46: 3 residues within 4Å: Chain E: L.91, T.95 Ligands: Y01.43 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:L.91, E:T.95 Y01.53: 6 residues within 4Å: Chain D: I.22 Chain E: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 4 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.198, E:I.201, E:F.205, E:F.205, D:I.22 Y01.54: 6 residues within 4Å: Chain E: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.59 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.35 Salt bridges: E:R.206 Y01.56: 6 residues within 4Å: Chain F: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.2 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:I.35 Salt bridges: F:R.206 Y01.58: 4 residues within 4Å: Chain F: F.223, S.224, I.263 Ligands: LMT.65 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:F.223, F:F.223, F:I.263 Y01.59: 3 residues within 4Å: Chain F: L.91, T.95 Ligands: Y01.54 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:L.91, F:T.95 Y01.66: 6 residues within 4Å: Chain E: I.22 Chain F: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 4 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.198, F:I.201, F:F.205, F:F.205, E:I.22 Y01.67: 4 residues within 4Å: Chain G: F.223, S.224, I.263 Ligands: LMT.74 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.223, G:F.223, G:F.223, G:I.263 Y01.68: 3 residues within 4Å: Chain G: L.91, T.95 Ligands: Y01.122 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:L.91, G:T.95 Y01.75: 6 residues within 4Å: Chain G: T.88, C.92, F.198, I.201, F.205 Chain L: I.22 5 PLIP interactions: 4 interactions with chain G, 1 interactions with chain L Hydrophobic interactions: G:F.198, G:I.201, G:F.205, G:F.205, L:I.22 Y01.76: 6 residues within 4Å: Chain G: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.79 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.35 Salt bridges: G:R.206 Y01.78: 4 residues within 4Å: Chain H: F.223, S.224, I.263 Ligands: LMT.85 3 PLIP interactions: 3 interactions with chain H Hydrophobic interactions: H:F.223, H:F.223, H:I.263 Y01.79: 3 residues within 4Å: Chain H: L.91, T.95 Ligands: Y01.76 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:L.91, H:T.95 Y01.86: 6 residues within 4Å: Chain G: I.22 Chain H: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 4 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:F.198, H:I.201, H:F.205, H:F.205, G:I.22 Y01.87: 6 residues within 4Å: Chain H: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.90 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:I.35 Salt bridges: H:R.206 Y01.89: 4 residues within 4Å: Chain I: F.223, S.224, I.263 Ligands: LMT.96 3 PLIP interactions: 3 interactions with chain I Hydrophobic interactions: I:F.223, I:F.223, I:I.263 Y01.90: 3 residues within 4Å: Chain I: L.91, T.95 Ligands: Y01.87 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:L.91, I:T.95 Y01.97: 6 residues within 4Å: Chain H: I.22 Chain I: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 1 interactions with chain H, 4 interactions with chain I Hydrophobic interactions: H:I.22, I:F.198, I:I.201, I:F.205, I:F.205 Y01.98: 6 residues within 4Å: Chain I: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.101 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:I.35 Salt bridges: I:R.206 Y01.100: 4 residues within 4Å: Chain J: F.223, S.224, I.263 Ligands: LMT.107 4 PLIP interactions: 4 interactions with chain J Hydrophobic interactions: J:F.223, J:F.223, J:F.223, J:I.263 Y01.101: 3 residues within 4Å: Chain J: L.91, T.95 Ligands: Y01.98 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:L.91, J:T.95 Y01.108: 6 residues within 4Å: Chain I: I.22 Chain J: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain J Hydrophobic interactions: I:I.22, J:F.198, J:I.201, J:F.205, J:F.205 Y01.109: 6 residues within 4Å: Chain J: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.112 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:I.35 Salt bridges: J:R.206 Y01.111: 4 residues within 4Å: Chain K: F.223, S.224, I.263 Ligands: LMT.118 3 PLIP interactions: 3 interactions with chain K Hydrophobic interactions: K:F.223, K:F.223, K:I.263 Y01.112: 3 residues within 4Å: Chain K: L.91, T.95 Ligands: Y01.109 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:L.91, K:T.95 Y01.119: 6 residues within 4Å: Chain J: I.22 Chain K: T.88, C.92, F.198, I.201, F.205 4 PLIP interactions: 1 interactions with chain J, 3 interactions with chain K Hydrophobic interactions: J:I.22, K:I.201, K:F.205, K:F.205 Y01.120: 6 residues within 4Å: Chain K: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.125 2 PLIP interactions: 2 interactions with chain K Hydrophobic interactions: K:I.35 Salt bridges: K:R.206 Y01.122: 6 residues within 4Å: Chain L: T.28, I.35, S.90, Y.199, R.206 Ligands: Y01.68 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:I.35 Salt bridges: L:R.206 Y01.124: 4 residues within 4Å: Chain L: F.223, S.224, I.263 Ligands: LMT.131 3 PLIP interactions: 3 interactions with chain L Hydrophobic interactions: L:F.223, L:F.223, L:I.263 Y01.125: 3 residues within 4Å: Chain L: L.91, T.95 Ligands: Y01.120 2 PLIP interactions: 2 interactions with chain L Hydrophobic interactions: L:L.91, L:T.95 Y01.132: 6 residues within 4Å: Chain K: I.22 Chain L: T.88, C.92, F.198, I.201, F.205 5 PLIP interactions: 4 interactions with chain L, 1 interactions with chain K Hydrophobic interactions: L:F.198, L:I.201, L:F.205, L:F.205, K:I.22

84 x LMT: DODECYL-BETA-D-MALTOSIDE(Non-covalent)(Non-functional Binders)

LMT.3: 4 residues within 4Å: Chain A: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.4: 1 residues within 4Å: Chain A: F.81 Ligand excluded by PLIP LMT.5: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.6: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.7: 1 residues within 4Å: Chain A: Y.218 Ligand excluded by PLIP LMT.8: 2 residues within 4Å: Chain A: Y.218 Ligands: Y01.1 Ligand excluded by PLIP LMT.11: 3 residues within 4Å: Chain A: V.252, V.255, F.256 Ligand excluded by PLIP LMT.14: 4 residues within 4Å: Chain B: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.15: 1 residues within 4Å: Chain B: F.81 Ligand excluded by PLIP LMT.16: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.17: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.18: 1 residues within 4Å: Chain B: Y.218 Ligand excluded by PLIP LMT.19: 2 residues within 4Å: Chain B: Y.218 Ligands: Y01.12 Ligand excluded by PLIP LMT.22: 3 residues within 4Å: Chain B: V.252, V.255, F.256 Ligand excluded by PLIP LMT.25: 4 residues within 4Å: Chain C: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.26: 1 residues within 4Å: Chain C: F.81 Ligand excluded by PLIP LMT.27: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.28: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.29: 1 residues within 4Å: Chain C: Y.218 Ligand excluded by PLIP LMT.30: 2 residues within 4Å: Chain C: Y.218 Ligands: Y01.23 Ligand excluded by PLIP LMT.33: 3 residues within 4Å: Chain C: V.252, V.255, F.256 Ligand excluded by PLIP LMT.36: 4 residues within 4Å: Chain D: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.37: 1 residues within 4Å: Chain D: F.81 Ligand excluded by PLIP LMT.38: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.39: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.40: 1 residues within 4Å: Chain D: Y.218 Ligand excluded by PLIP LMT.41: 2 residues within 4Å: Chain D: Y.218 Ligands: Y01.34 Ligand excluded by PLIP LMT.44: 3 residues within 4Å: Chain D: V.252, V.255, F.256 Ligand excluded by PLIP LMT.47: 4 residues within 4Å: Chain E: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.48: 1 residues within 4Å: Chain E: F.81 Ligand excluded by PLIP LMT.49: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.50: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.51: 1 residues within 4Å: Chain E: Y.218 Ligand excluded by PLIP LMT.52: 2 residues within 4Å: Chain E: Y.218 Ligands: Y01.45 Ligand excluded by PLIP LMT.55: 3 residues within 4Å: Chain E: V.252, V.255, F.256 Ligand excluded by PLIP LMT.57: 3 residues within 4Å: Chain F: V.252, V.255, F.256 Ligand excluded by PLIP LMT.60: 4 residues within 4Å: Chain F: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.61: 1 residues within 4Å: Chain F: F.81 Ligand excluded by PLIP LMT.62: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.63: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.64: 1 residues within 4Å: Chain F: Y.218 Ligand excluded by PLIP LMT.65: 2 residues within 4Å: Chain F: Y.218 Ligands: Y01.58 Ligand excluded by PLIP LMT.69: 4 residues within 4Å: Chain G: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.70: 1 residues within 4Å: Chain G: F.81 Ligand excluded by PLIP LMT.71: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.72: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.73: 1 residues within 4Å: Chain G: Y.218 Ligand excluded by PLIP LMT.74: 2 residues within 4Å: Chain G: Y.218 Ligands: Y01.67 Ligand excluded by PLIP LMT.77: 3 residues within 4Å: Chain G: V.252, V.255, F.256 Ligand excluded by PLIP LMT.80: 4 residues within 4Å: Chain H: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.81: 1 residues within 4Å: Chain H: F.81 Ligand excluded by PLIP LMT.82: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.83: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.84: 1 residues within 4Å: Chain H: Y.218 Ligand excluded by PLIP LMT.85: 2 residues within 4Å: Chain H: Y.218 Ligands: Y01.78 Ligand excluded by PLIP LMT.88: 3 residues within 4Å: Chain H: V.252, V.255, F.256 Ligand excluded by PLIP LMT.91: 4 residues within 4Å: Chain I: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.92: 1 residues within 4Å: Chain I: F.81 Ligand excluded by PLIP LMT.93: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.94: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.95: 1 residues within 4Å: Chain I: Y.218 Ligand excluded by PLIP LMT.96: 2 residues within 4Å: Chain I: Y.218 Ligands: Y01.89 Ligand excluded by PLIP LMT.99: 3 residues within 4Å: Chain I: V.252, V.255, F.256 Ligand excluded by PLIP LMT.102: 4 residues within 4Å: Chain J: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.103: 1 residues within 4Å: Chain J: F.81 Ligand excluded by PLIP LMT.104: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.105: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.106: 1 residues within 4Å: Chain J: Y.218 Ligand excluded by PLIP LMT.107: 2 residues within 4Å: Chain J: Y.218 Ligands: Y01.100 Ligand excluded by PLIP LMT.110: 3 residues within 4Å: Chain J: V.252, V.255, F.256 Ligand excluded by PLIP LMT.113: 4 residues within 4Å: Chain K: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.114: 1 residues within 4Å: Chain K: F.81 Ligand excluded by PLIP LMT.115: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.116: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.117: 1 residues within 4Å: Chain K: Y.218 Ligand excluded by PLIP LMT.118: 2 residues within 4Å: Chain K: Y.218 Ligands: Y01.111 Ligand excluded by PLIP LMT.121: 3 residues within 4Å: Chain K: V.252, V.255, F.256 Ligand excluded by PLIP LMT.123: 3 residues within 4Å: Chain L: V.252, V.255, F.256 Ligand excluded by PLIP LMT.126: 4 residues within 4Å: Chain L: G.212, L.220, Y.221, S.224 Ligand excluded by PLIP LMT.127: 1 residues within 4Å: Chain L: F.81 Ligand excluded by PLIP LMT.128: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.129: 0 residues within 4Å: (No contacts) Ligand excluded by PLIP LMT.130: 1 residues within 4Å: Chain L: Y.218 Ligand excluded by PLIP LMT.131: 2 residues within 4Å: Chain L: Y.218 Ligands: Y01.124 Ligand excluded by PLIP

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Mao, W. et al., Assembly mechanisms of the neuronal gap junction channel connexin 36 elucidated by Cryo-EM. Arch.Biochem.Biophys. (2024)

Release Date

2024-04-10

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.
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Gap junction delta-2 protein