SMTL ID : 8gn7.1

structure of human connexin 40.1 intercellular gap junction channel by cryoEM

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-10-mer

Ligands

30 x CLR: CHOLESTEROL(Non-covalent)

CLR.1: 5 residues within 4Å: Chain A: V.72, I.80 Chain B: E.193, L.197 Ligands: CLR.7 3 PLIP interactions: 1 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:L.197, A:V.72, A:I.80 CLR.2: 3 residues within 4Å: Chain A: C.84, F.157 Ligands: CLR.7 1 PLIP interactions: 1 interactions with chain A Hydrophobic interactions: A:F.157 CLR.5: 4 residues within 4Å: Chain A: F.200, A.203 Ligands: CLR.23, CLR.24 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.200, A:A.203 CLR.7: 4 residues within 4Å: Chain B: F.200, A.203 Ligands: CLR.1, CLR.2 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.200, B:A.203 CLR.8: 4 residues within 4Å: Chain B: I.80 Chain C: E.193, L.197 Ligands: CLR.12 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain C Hydrophobic interactions: B:I.80, C:L.197 CLR.9: 3 residues within 4Å: Chain B: C.84, F.157 Ligands: CLR.12 1 PLIP interactions: 1 interactions with chain B Hydrophobic interactions: B:F.157 CLR.12: 4 residues within 4Å: Chain C: F.200, A.203 Ligands: CLR.8, CLR.9 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.200, C:A.203 CLR.13: 4 residues within 4Å: Chain C: I.80 Chain D: E.193, L.197 Ligands: CLR.17 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:I.80, D:L.197 CLR.14: 3 residues within 4Å: Chain C: C.84, F.157 Ligands: CLR.17 1 PLIP interactions: 1 interactions with chain C Hydrophobic interactions: C:F.157 CLR.17: 4 residues within 4Å: Chain D: F.200, A.203 Ligands: CLR.13, CLR.14 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.200, D:A.203 CLR.18: 3 residues within 4Å: Chain D: C.84, F.157 Ligands: CLR.22 1 PLIP interactions: 1 interactions with chain D Hydrophobic interactions: D:F.157 CLR.20: 4 residues within 4Å: Chain D: I.80 Chain E: E.193, L.197 Ligands: CLR.22 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:I.80, E:L.197 CLR.22: 4 residues within 4Å: Chain E: F.200, A.203 Ligands: CLR.18, CLR.20 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.200, E:A.203 CLR.23: 4 residues within 4Å: Chain A: L.197 Chain E: V.72, I.80 Ligands: CLR.5 3 PLIP interactions: 2 interactions with chain E, 1 interactions with chain A Hydrophobic interactions: E:V.72, E:I.80, A:L.197 CLR.24: 2 residues within 4Å: Chain E: C.84 Ligands: CLR.5 No protein-ligand interaction detected (PLIP) CLR.26: 3 residues within 4Å: Chain F: C.84, F.157 Ligands: CLR.32 1 PLIP interactions: 1 interactions with chain F Hydrophobic interactions: F:F.157 CLR.29: 4 residues within 4Å: Chain F: F.200, A.203 Ligands: CLR.48, CLR.49 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:F.200, F:A.203 CLR.30: 4 residues within 4Å: Chain F: I.80 Chain G: E.193, L.197 Ligands: CLR.32 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:L.197, F:I.80 CLR.32: 4 residues within 4Å: Chain G: F.200, A.203 Ligands: CLR.26, CLR.30 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.200, G:A.203 CLR.33: 4 residues within 4Å: Chain G: I.80 Chain H: E.193, L.197 Ligands: CLR.37 2 PLIP interactions: 1 interactions with chain H, 1 interactions with chain G Hydrophobic interactions: H:L.197, G:I.80 CLR.34: 3 residues within 4Å: Chain G: C.84, F.157 Ligands: CLR.37 1 PLIP interactions: 1 interactions with chain G Hydrophobic interactions: G:F.157 CLR.37: 4 residues within 4Å: Chain H: F.200, A.203 Ligands: CLR.33, CLR.34 2 PLIP interactions: 2 interactions with chain H Hydrophobic interactions: H:F.200, H:A.203 CLR.38: 3 residues within 4Å: Chain H: C.84, F.157 Ligands: CLR.42 1 PLIP interactions: 1 interactions with chain H Hydrophobic interactions: H:F.157 CLR.40: 4 residues within 4Å: Chain H: I.80 Chain I: E.193, L.197 Ligands: CLR.42 2 PLIP interactions: 1 interactions with chain I, 1 interactions with chain H Hydrophobic interactions: I:L.197, H:I.80 CLR.42: 4 residues within 4Å: Chain I: F.200, A.203 Ligands: CLR.38, CLR.40 2 PLIP interactions: 2 interactions with chain I Hydrophobic interactions: I:F.200, I:A.203 CLR.43: 4 residues within 4Å: Chain I: V.72, I.80 Chain J: L.197 Ligands: CLR.47 3 PLIP interactions: 2 interactions with chain I, 1 interactions with chain J Hydrophobic interactions: I:V.72, I:I.80, J:L.197 CLR.44: 3 residues within 4Å: Chain I: C.84, F.157 Ligands: CLR.47 1 PLIP interactions: 1 interactions with chain I Hydrophobic interactions: I:F.157 CLR.47: 4 residues within 4Å: Chain J: F.200, A.203 Ligands: CLR.43, CLR.44 2 PLIP interactions: 2 interactions with chain J Hydrophobic interactions: J:F.200, J:A.203 CLR.48: 5 residues within 4Å: Chain F: E.193, L.197 Chain J: V.72, I.80 Ligands: CLR.29 3 PLIP interactions: 1 interactions with chain F, 2 interactions with chain J Hydrophobic interactions: F:L.197, J:V.72, J:I.80 CLR.49: 2 residues within 4Å: Chain J: C.84 Ligands: CLR.29 No protein-ligand interaction detected (PLIP)

10 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.3: 7 residues within 4Å: Chain A: L.87, Y.95, A.141, I.145, H.146, L.149, L.153 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.87, A:H.146, A:L.149, A:L.153 Hydrogen bonds: A:Y.95 PTY.10: 7 residues within 4Å: Chain B: L.87, Y.95, A.141, I.145, H.146, L.149, L.153 5 PLIP interactions: 5 interactions with chain B Hydrophobic interactions: B:L.87, B:H.146, B:L.149, B:L.153 Hydrogen bonds: B:Y.95 PTY.15: 6 residues within 4Å: Chain C: L.87, Y.95, A.141, I.145, H.146, L.149 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.87, C:H.146, C:L.149 Hydrogen bonds: C:Y.95 PTY.19: 7 residues within 4Å: Chain D: L.87, Y.95, A.141, I.145, H.146, L.149, L.153 5 PLIP interactions: 5 interactions with chain D Hydrophobic interactions: D:L.87, D:H.146, D:L.149, D:L.153 Hydrogen bonds: D:Y.95 PTY.25: 8 residues within 4Å: Chain E: L.87, P.88, Y.95, A.141, I.145, H.146, L.149, L.153 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.87, E:H.146, E:L.149, E:L.153 Hydrogen bonds: E:Y.95 PTY.27: 7 residues within 4Å: Chain F: L.87, Y.95, A.141, I.145, H.146, L.149, L.153 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.87, F:H.146, F:L.149, F:L.153 PTY.35: 7 residues within 4Å: Chain G: L.87, Y.95, A.141, I.145, H.146, L.149 Chain H: L.24 4 PLIP interactions: 3 interactions with chain G, 1 interactions with chain H Hydrophobic interactions: G:L.87, G:H.146, G:L.149, H:L.24 PTY.39: 8 residues within 4Å: Chain H: L.87, Y.95, A.141, I.145, H.146, L.149, L.153 Chain I: L.24 5 PLIP interactions: 1 interactions with chain I, 4 interactions with chain H Hydrophobic interactions: I:L.24, H:L.87, H:H.146, H:L.149, H:L.153 PTY.45: 8 residues within 4Å: Chain I: L.87, P.88, Y.95, A.141, I.145, H.146, L.149, L.153 5 PLIP interactions: 5 interactions with chain I Hydrophobic interactions: I:L.87, I:H.146, I:L.149, I:L.153 Hydrogen bonds: I:Y.95 PTY.50: 7 residues within 4Å: Chain F: L.24 Chain J: L.87, Y.95, A.141, I.145, H.146, L.149 4 PLIP interactions: 1 interactions with chain F, 3 interactions with chain J Hydrophobic interactions: F:L.24, J:L.87, J:H.146, J:L.149

10 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-functional Binders)

3PE.4: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.6: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.11: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.16: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.21: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.28: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.31: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.36: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.41: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP) 3PE.46: 0 residues within 4Å: (No contacts) No protein-ligand interaction detected (PLIP)

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Zhang, H. et al., structure of human connexin 40.1 intercellular gap junction channel by cryoEM. To Be Published

Release Date

2023-08-30

Peptides

Gap junction delta-4 protein: ABCDEFGHIJ

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
B

C
G

D
J

E
M

F
P

G
S

H
V

I
Y

J
b

Membrane

We predict this structure to be a membrane protein.
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Gap junction delta-4 protein

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