SMTL ID : 6wbf.1

Cryo-EM structure of wild type human Pannexin 1 channel

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

14 x PTY: PHOSPHATIDYLETHANOLAMINE(Non-covalent)

PTY.1: 13 residues within 4Å: Chain A: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Chain B: L.52, L.275, I.279 Ligands: CLR.5, PTY.9 12 PLIP interactions: 9 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:L.101, A:W.104, A:W.104, A:I.112, A:I.112, A:L.114, A:L.115, B:L.52, B:L.275, B:I.279 Hydrogen bonds: A:N.100, A:L.101 PTY.2: 9 residues within 4Å: Chain A: F.235, L.237, S.239, Q.274, L.275, V.278, V.282 Chain G: L.115 Ligands: PTY.43 6 PLIP interactions: 5 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:F.235, A:V.278, A:V.282, G:L.115 Hydrogen bonds: A:L.237, A:Q.274 PTY.8: 13 residues within 4Å: Chain B: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Chain C: L.52, L.275, I.279 Ligands: CLR.12, PTY.16 12 PLIP interactions: 9 interactions with chain B, 3 interactions with chain C Hydrophobic interactions: B:L.101, B:W.104, B:W.104, B:I.112, B:I.112, B:L.114, B:L.115, C:L.52, C:L.275, C:I.279 Hydrogen bonds: B:N.100, B:L.101 PTY.9: 9 residues within 4Å: Chain A: L.115 Chain B: F.235, L.237, S.239, Q.274, L.275, V.278, V.282 Ligands: PTY.1 6 PLIP interactions: 5 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.235, B:V.278, B:V.282, A:L.115 Hydrogen bonds: B:L.237, B:Q.274 PTY.15: 13 residues within 4Å: Chain C: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Chain D: L.52, L.275, I.279 Ligands: CLR.19, PTY.23 12 PLIP interactions: 9 interactions with chain C, 3 interactions with chain D Hydrophobic interactions: C:L.101, C:W.104, C:W.104, C:I.112, C:I.112, C:L.114, C:L.115, D:L.52, D:L.275, D:I.279 Hydrogen bonds: C:N.100, C:L.101 PTY.16: 9 residues within 4Å: Chain B: L.115 Chain C: F.235, L.237, S.239, Q.274, L.275, V.278, V.282 Ligands: PTY.8 6 PLIP interactions: 1 interactions with chain B, 5 interactions with chain C Hydrophobic interactions: B:L.115, C:F.235, C:V.278, C:V.282 Hydrogen bonds: C:L.237, C:Q.274 PTY.22: 13 residues within 4Å: Chain D: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Chain E: L.52, L.275, I.279 Ligands: CLR.26, PTY.30 12 PLIP interactions: 9 interactions with chain D, 3 interactions with chain E Hydrophobic interactions: D:L.101, D:W.104, D:W.104, D:I.112, D:I.112, D:L.114, D:L.115, E:L.52, E:L.275, E:I.279 Hydrogen bonds: D:N.100, D:L.101 PTY.23: 9 residues within 4Å: Chain C: L.115 Chain D: F.235, L.237, S.239, Q.274, L.275, V.278, V.282 Ligands: PTY.15 6 PLIP interactions: 5 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.235, D:V.278, D:V.282, C:L.115 Hydrogen bonds: D:L.237, D:Q.274 PTY.29: 13 residues within 4Å: Chain E: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Chain F: L.52, L.275, I.279 Ligands: CLR.33, PTY.37 12 PLIP interactions: 9 interactions with chain E, 3 interactions with chain F Hydrophobic interactions: E:L.101, E:W.104, E:W.104, E:I.112, E:I.112, E:L.114, E:L.115, F:L.52, F:L.275, F:I.279 Hydrogen bonds: E:N.100, E:L.101 PTY.30: 9 residues within 4Å: Chain D: L.115 Chain E: F.235, L.237, S.239, Q.274, L.275, V.278, V.282 Ligands: PTY.22 6 PLIP interactions: 5 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.235, E:V.278, E:V.282, D:L.115 Hydrogen bonds: E:L.237, E:Q.274 PTY.36: 12 residues within 4Å: Chain F: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Chain G: L.52, L.275, I.279 Ligands: CLR.40 12 PLIP interactions: 9 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:L.101, F:W.104, F:W.104, F:I.112, F:I.112, F:L.114, F:L.115, G:L.52, G:L.275, G:I.279 Hydrogen bonds: F:N.100, F:L.101 PTY.37: 9 residues within 4Å: Chain E: L.115 Chain F: F.235, L.237, S.239, Q.274, L.275, V.278, V.282 Ligands: PTY.29 6 PLIP interactions: 5 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:F.235, F:V.278, F:V.282, E:L.115 Hydrogen bonds: F:L.237, F:Q.274 PTY.43: 13 residues within 4Å: Chain A: L.52, L.275, I.279 Chain G: G.99, N.100, L.101, W.104, Y.111, I.112, L.114, L.115 Ligands: PTY.2, CLR.47 12 PLIP interactions: 3 interactions with chain A, 9 interactions with chain G Hydrophobic interactions: A:L.52, A:L.275, A:I.279, G:L.101, G:W.104, G:W.104, G:I.112, G:I.112, G:L.114, G:L.115 Hydrogen bonds: G:N.100, G:L.101 PTY.44: 8 residues within 4Å: Chain F: W.104, L.115 Chain G: F.235, L.237, S.239, Q.274, L.275, V.278 7 PLIP interactions: 6 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:F.235, G:L.275, G:V.278, G:V.278, F:L.115 Hydrogen bonds: G:L.237, G:Q.274

7 x 3PE: 1,2-Distearoyl-sn-glycerophosphoethanolamine(Non-covalent)

3PE.3: 10 residues within 4Å: Chain A: V.34, M.37, Y.293, R.300, L.333, E.336 Chain G: F.126, S.215, L.219 Ligands: DGA.4 11 PLIP interactions: 4 interactions with chain G, 7 interactions with chain A Hydrophobic interactions: G:F.126, G:F.126, G:F.126, G:L.219, A:V.34, A:Y.293, A:Y.293, A:Y.293 Hydrogen bonds: A:Y.293, A:E.336 Salt bridges: A:R.300 3PE.10: 10 residues within 4Å: Chain A: F.126, S.215, L.219 Chain B: V.34, M.37, Y.293, R.300, L.333, E.336 Ligands: DGA.11 11 PLIP interactions: 7 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:V.34, B:Y.293, B:Y.293, B:Y.293, A:F.126, A:F.126, A:F.126, A:L.219 Hydrogen bonds: B:Y.293, B:E.336 Salt bridges: B:R.300 3PE.17: 10 residues within 4Å: Chain B: F.126, S.215, L.219 Chain C: V.34, M.37, Y.293, R.300, L.333, E.336 Ligands: DGA.18 11 PLIP interactions: 7 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:V.34, C:Y.293, C:Y.293, C:Y.293, B:F.126, B:F.126, B:F.126, B:L.219 Hydrogen bonds: C:Y.293, C:E.336 Salt bridges: C:R.300 3PE.24: 10 residues within 4Å: Chain C: F.126, S.215, L.219 Chain D: V.34, M.37, Y.293, R.300, L.333, E.336 Ligands: DGA.25 11 PLIP interactions: 7 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:V.34, D:Y.293, D:Y.293, D:Y.293, C:F.126, C:F.126, C:F.126, C:L.219 Hydrogen bonds: D:Y.293, D:E.336 Salt bridges: D:R.300 3PE.31: 10 residues within 4Å: Chain D: F.126, S.215, L.219 Chain E: V.34, M.37, Y.293, R.300, L.333, E.336 Ligands: DGA.32 11 PLIP interactions: 4 interactions with chain D, 7 interactions with chain E Hydrophobic interactions: D:F.126, D:F.126, D:F.126, D:L.219, E:V.34, E:Y.293, E:Y.293, E:Y.293 Hydrogen bonds: E:Y.293, E:E.336 Salt bridges: E:R.300 3PE.38: 10 residues within 4Å: Chain E: F.126, S.215, L.219 Chain F: V.34, M.37, Y.293, R.300, L.333, E.336 Ligands: DGA.39 11 PLIP interactions: 7 interactions with chain F, 4 interactions with chain E Hydrophobic interactions: F:V.34, F:Y.293, F:Y.293, F:Y.293, E:F.126, E:F.126, E:F.126, E:L.219 Hydrogen bonds: F:Y.293, F:E.336 Salt bridges: F:R.300 3PE.45: 10 residues within 4Å: Chain F: F.126, S.215, L.219 Chain G: V.34, M.37, Y.293, R.300, L.333, E.336 Ligands: DGA.46 11 PLIP interactions: 4 interactions with chain F, 7 interactions with chain G Hydrophobic interactions: F:F.126, F:F.126, F:F.126, F:L.219, G:V.34, G:Y.293, G:Y.293, G:Y.293 Hydrogen bonds: G:Y.293, G:E.336 Salt bridges: G:R.300

7 x DGA: DIACYL GLYCEROL(Non-covalent)

DGA.4: 14 residues within 4Å: Chain A: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Chain G: I.118, L.122, L.125, F.129 Ligands: 3PE.3 10 PLIP interactions: 6 interactions with chain A, 4 interactions with chain G Hydrophobic interactions: A:L.17, A:M.37, A:I.41, A:I.41, A:L.287, A:V.290, G:L.125, G:F.129, G:F.129, G:F.129 DGA.11: 14 residues within 4Å: Chain A: I.118, L.122, L.125, F.129 Chain B: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Ligands: 3PE.10 10 PLIP interactions: 6 interactions with chain B, 4 interactions with chain A Hydrophobic interactions: B:L.17, B:M.37, B:I.41, B:I.41, B:L.287, B:V.290, A:L.125, A:F.129, A:F.129, A:F.129 DGA.18: 14 residues within 4Å: Chain B: I.118, L.122, L.125, F.129 Chain C: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Ligands: 3PE.17 10 PLIP interactions: 6 interactions with chain C, 4 interactions with chain B Hydrophobic interactions: C:L.17, C:M.37, C:I.41, C:I.41, C:L.287, C:V.290, B:L.125, B:F.129, B:F.129, B:F.129 DGA.25: 14 residues within 4Å: Chain C: I.118, L.122, L.125, F.129 Chain D: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Ligands: 3PE.24 10 PLIP interactions: 6 interactions with chain D, 4 interactions with chain C Hydrophobic interactions: D:L.17, D:M.37, D:I.41, D:I.41, D:L.287, D:V.290, C:L.125, C:F.129, C:F.129, C:F.129 DGA.32: 14 residues within 4Å: Chain D: I.118, L.122, L.125, F.129 Chain E: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Ligands: 3PE.31 10 PLIP interactions: 6 interactions with chain E, 4 interactions with chain D Hydrophobic interactions: E:L.17, E:M.37, E:I.41, E:I.41, E:L.287, E:V.290, D:L.125, D:F.129, D:F.129, D:F.129 DGA.39: 14 residues within 4Å: Chain E: I.118, L.122, L.125, F.129 Chain F: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Ligands: 3PE.38 10 PLIP interactions: 4 interactions with chain E, 6 interactions with chain F Hydrophobic interactions: E:L.125, E:F.129, E:F.129, E:F.129, F:L.17, F:M.37, F:I.41, F:I.41, F:L.287, F:V.290 DGA.46: 14 residues within 4Å: Chain F: I.118, L.122, L.125, F.129 Chain G: Y.10, V.11, L.17, M.37, I.41, L.45, L.286, L.287, V.290 Ligands: 3PE.45 10 PLIP interactions: 6 interactions with chain G, 4 interactions with chain F Hydrophobic interactions: G:L.17, G:M.37, G:I.41, G:I.41, G:L.287, G:V.290, F:L.125, F:F.129, F:F.129, F:F.129

14 x CLR: CHOLESTEROL(Non-covalent)

CLR.5: 7 residues within 4Å: Chain A: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.1, CLR.6 4 PLIP interactions: 4 interactions with chain A Hydrophobic interactions: A:F.116, A:I.229, A:Y.230, A:Y.233 CLR.6: 5 residues within 4Å: Chain A: C.228, I.229, Y.233, S.236 Ligands: CLR.5 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:I.229, A:Y.233 CLR.12: 7 residues within 4Å: Chain B: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.8, CLR.13 4 PLIP interactions: 4 interactions with chain B Hydrophobic interactions: B:F.116, B:I.229, B:Y.230, B:Y.233 CLR.13: 5 residues within 4Å: Chain B: C.228, I.229, Y.233, S.236 Ligands: CLR.12 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:I.229, B:Y.233 CLR.19: 7 residues within 4Å: Chain C: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.15, CLR.20 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:F.116, C:I.229, C:Y.230, C:Y.233 CLR.20: 5 residues within 4Å: Chain C: C.228, I.229, Y.233, S.236 Ligands: CLR.19 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:I.229, C:Y.233 CLR.26: 7 residues within 4Å: Chain D: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.22, CLR.27 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:F.116, D:I.229, D:Y.230, D:Y.233 CLR.27: 5 residues within 4Å: Chain D: C.228, I.229, Y.233, S.236 Ligands: CLR.26 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:I.229, D:Y.233 CLR.33: 7 residues within 4Å: Chain E: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.29, CLR.34 4 PLIP interactions: 4 interactions with chain E Hydrophobic interactions: E:F.116, E:I.229, E:Y.230, E:Y.233 CLR.34: 5 residues within 4Å: Chain E: C.228, I.229, Y.233, S.236 Ligands: CLR.33 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:I.229, E:Y.233 CLR.40: 7 residues within 4Å: Chain F: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.36, CLR.41 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:F.116, F:I.229, F:Y.230, F:Y.233 CLR.41: 5 residues within 4Å: Chain F: C.228, I.229, Y.233, S.236 Ligands: CLR.40 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:I.229, F:Y.233 CLR.47: 7 residues within 4Å: Chain G: L.101, F.116, I.229, Y.230, Y.233 Ligands: PTY.43, CLR.48 4 PLIP interactions: 4 interactions with chain G Hydrophobic interactions: G:F.116, G:I.229, G:Y.230, G:Y.233 CLR.48: 5 residues within 4Å: Chain G: C.228, I.229, Y.233, S.236 Ligands: CLR.47 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:I.229, G:Y.233

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

NAG.7: 1 residues within 4Å: Chain A: N.255 1 PLIP interactions: 1 interactions with chain A Hydrogen bonds: A:N.255 NAG.14: 1 residues within 4Å: Chain B: N.255 1 PLIP interactions: 1 interactions with chain B Hydrogen bonds: B:N.255 NAG.21: 1 residues within 4Å: Chain C: N.255 1 PLIP interactions: 1 interactions with chain C Hydrogen bonds: C:N.255 NAG.28: 1 residues within 4Å: Chain D: N.255 1 PLIP interactions: 1 interactions with chain D Hydrogen bonds: D:N.255 NAG.35: 1 residues within 4Å: Chain E: N.255 1 PLIP interactions: 1 interactions with chain E Hydrogen bonds: E:N.255 NAG.42: 1 residues within 4Å: Chain F: N.255 1 PLIP interactions: 1 interactions with chain F Hydrogen bonds: F:N.255 NAG.49: 1 residues within 4Å: Chain G: N.255 1 PLIP interactions: 1 interactions with chain G Hydrogen bonds: G:N.255

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Ruan, Z. et al., Structures of human pannexin 1 reveal ion pathways and mechanism of gating. Nature (2020)

Release Date

2020-06-03

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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