SMTL ID : 7f8n.1

Human pannexin-1 showing a conformational change in the N-terminal domain and blocked pore

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

49 x LBN: 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine(Non-covalent)

LBN.1: 14 residues within 4Å: Chain A: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Chain B: F.126 Ligands: LBN.2, LBN.7 11 PLIP interactions: 11 interactions with chain A Hydrophobic interactions: A:L.225, A:L.225, A:P.289, A:V.292, A:Y.293, A:Y.293 Hydrogen bonds: A:Y.293, A:Y.293 Salt bridges: A:R.300, A:E.336, A:E.337 LBN.2: 10 residues within 4Å: Chain A: M.37, Y.293, F.299, Q.301 Chain B: F.126, I.211, K.212, S.215, L.219 Ligands: LBN.1 7 PLIP interactions: 3 interactions with chain A, 4 interactions with chain B Hydrogen bonds: A:Y.293, A:Y.293 Salt bridges: A:K.302 Hydrophobic interactions: B:F.126, B:F.126, B:I.211, B:L.219 LBN.3: 7 residues within 4Å: Chain A: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.7 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:T.39, A:L.47, A:Y.121 LBN.4: 7 residues within 4Å: Chain A: L.275, V.278, I.279, V.282 Chain B: Q.89 Ligands: LBN.5, LBN.8 3 PLIP interactions: 3 interactions with chain A Hydrophobic interactions: A:L.275, A:I.279, A:V.282 LBN.5: 6 residues within 4Å: Chain A: F.235, S.239 Chain B: Q.89, K.91 Ligands: LBN.4, LBN.8 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:F.235 Hydrogen bonds: A:S.239 LBN.6: 3 residues within 4Å: Chain A: K.91 Ligands: LBN.48, LBN.49 No protein-ligand interaction detected (PLIP) LBN.7: 16 residues within 4Å: Chain A: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Chain B: L.115, I.118, L.119, L.122, L.125 Ligands: LBN.1, LBN.3 8 PLIP interactions: 5 interactions with chain A, 3 interactions with chain B Hydrophobic interactions: A:I.41, A:L.45, A:L.286, A:L.287, A:P.289, B:I.118, B:L.122, B:L.125 LBN.8: 3 residues within 4Å: Chain B: K.91 Ligands: LBN.4, LBN.5 No protein-ligand interaction detected (PLIP) LBN.9: 14 residues within 4Å: Chain B: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Chain C: F.126 Ligands: LBN.10, LBN.14 11 PLIP interactions: 11 interactions with chain B Hydrophobic interactions: B:L.225, B:L.225, B:P.289, B:V.292, B:Y.293, B:Y.293 Hydrogen bonds: B:Y.293, B:Y.293 Salt bridges: B:R.300, B:E.336, B:E.337 LBN.10: 10 residues within 4Å: Chain B: M.37, Y.293, F.299, Q.301 Chain C: L.122, F.126, K.212, S.215, L.219 Ligands: LBN.9 8 PLIP interactions: 3 interactions with chain B, 5 interactions with chain C Hydrogen bonds: B:Y.293, B:Y.293 Salt bridges: B:K.302 Hydrophobic interactions: C:L.122, C:F.126, C:F.126, C:F.126, C:L.219 LBN.11: 7 residues within 4Å: Chain B: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.14 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:T.39, B:L.47, B:Y.121 LBN.12: 7 residues within 4Å: Chain B: L.275, V.278, I.279, V.282 Chain C: Q.89 Ligands: LBN.13, LBN.15 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.275, B:I.279, B:V.282 LBN.13: 6 residues within 4Å: Chain B: F.235, S.239 Chain C: Q.89, K.91 Ligands: LBN.12, LBN.15 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:F.235 Hydrogen bonds: B:S.239 LBN.14: 15 residues within 4Å: Chain B: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Chain C: L.115, I.118, L.119, L.122 Ligands: LBN.9, LBN.11 7 PLIP interactions: 5 interactions with chain B, 2 interactions with chain C Hydrophobic interactions: B:I.41, B:L.45, B:L.286, B:L.287, B:P.289, C:I.118, C:L.122 LBN.15: 3 residues within 4Å: Chain C: K.91 Ligands: LBN.12, LBN.13 No protein-ligand interaction detected (PLIP) LBN.16: 14 residues within 4Å: Chain C: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Chain D: F.126 Ligands: LBN.17, LBN.20 12 PLIP interactions: 11 interactions with chain C, 1 interactions with chain D Hydrophobic interactions: C:L.225, C:L.225, C:P.289, C:V.292, C:Y.293, C:Y.293, D:F.126 Hydrogen bonds: C:Y.293, C:Y.293 Salt bridges: C:R.300, C:E.336, C:E.337 LBN.17: 11 residues within 4Å: Chain C: M.37, Y.293, F.299, Q.301 Chain D: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.16 11 PLIP interactions: 3 interactions with chain C, 8 interactions with chain D Hydrogen bonds: C:Y.293, C:Y.293 Salt bridges: C:K.302, D:K.212 Hydrophobic interactions: D:L.122, D:F.126, D:F.126, D:F.126, D:I.211, D:K.212, D:L.219 LBN.18: 7 residues within 4Å: Chain C: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.20 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:T.39, C:L.47, C:Y.121 LBN.19: 5 residues within 4Å: Chain C: F.235, S.239 Chain D: Q.89 Ligands: LBN.21, LBN.22 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:F.235 Hydrogen bonds: C:S.239 LBN.20: 16 residues within 4Å: Chain C: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Chain D: L.115, I.118, L.119, Y.121, L.122 Ligands: LBN.16, LBN.18 9 PLIP interactions: 4 interactions with chain D, 5 interactions with chain C Hydrophobic interactions: D:I.118, D:Y.121, D:L.122, D:L.122, C:I.41, C:L.45, C:L.286, C:L.287, C:P.289 LBN.21: 3 residues within 4Å: Chain D: K.91 Ligands: LBN.19, LBN.22 No protein-ligand interaction detected (PLIP) LBN.22: 7 residues within 4Å: Chain C: L.275, V.278, I.279, V.282 Chain D: Q.89 Ligands: LBN.19, LBN.21 3 PLIP interactions: 3 interactions with chain C Hydrophobic interactions: C:L.275, C:I.279, C:V.282 LBN.23: 14 residues within 4Å: Chain D: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Chain E: F.126 Ligands: LBN.26, LBN.27 12 PLIP interactions: 11 interactions with chain D, 1 interactions with chain E Hydrophobic interactions: D:L.225, D:L.225, D:P.289, D:V.292, D:Y.293, D:Y.293, E:F.126 Hydrogen bonds: D:Y.293, D:Y.293 Salt bridges: D:R.300, D:E.336, D:E.337 LBN.24: 7 residues within 4Å: Chain D: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.27 3 PLIP interactions: 3 interactions with chain D Hydrophobic interactions: D:T.39, D:L.47, D:Y.121 LBN.25: 6 residues within 4Å: Chain D: F.235, S.239 Chain E: Q.89, K.91 Ligands: LBN.28, LBN.29 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:F.235 Hydrogen bonds: D:S.239 LBN.26: 11 residues within 4Å: Chain D: M.37, Y.293, F.299, Q.301 Chain E: L.122, P.123, F.126, K.212, S.215, L.219 Ligands: LBN.23 11 PLIP interactions: 8 interactions with chain E, 3 interactions with chain D Hydrophobic interactions: E:L.122, E:F.126, E:F.126, E:F.126, E:F.126, E:K.212, E:L.219 Salt bridges: E:K.212, D:K.302 Hydrogen bonds: D:Y.293, D:Y.293 LBN.27: 15 residues within 4Å: Chain D: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Chain E: L.115, I.118, L.119, L.122 Ligands: LBN.23, LBN.24 7 PLIP interactions: 5 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:I.41, D:L.45, D:L.286, D:L.287, D:P.289, E:I.118, E:L.122 LBN.28: 3 residues within 4Å: Chain E: K.91 Ligands: LBN.25, LBN.29 No protein-ligand interaction detected (PLIP) LBN.29: 9 residues within 4Å: Chain D: L.275, V.278, I.279, V.282 Chain E: Q.89, W.104, L.115 Ligands: LBN.25, LBN.28 5 PLIP interactions: 3 interactions with chain D, 2 interactions with chain E Hydrophobic interactions: D:L.275, D:I.279, D:V.282, E:W.104, E:L.115 LBN.30: 14 residues within 4Å: Chain E: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Chain F: F.126 Ligands: LBN.31, LBN.35 11 PLIP interactions: 11 interactions with chain E Hydrophobic interactions: E:L.225, E:L.225, E:P.289, E:V.292, E:Y.293, E:Y.293 Hydrogen bonds: E:Y.293, E:Y.293 Salt bridges: E:R.300, E:E.336, E:E.337 LBN.31: 11 residues within 4Å: Chain E: M.37, Y.293, F.299, Q.301 Chain F: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.30 9 PLIP interactions: 6 interactions with chain F, 3 interactions with chain E Hydrophobic interactions: F:L.122, F:F.126, F:F.126, F:F.126, F:I.211, F:L.219 Hydrogen bonds: E:Y.293, E:Y.293 Salt bridges: E:K.302 LBN.32: 7 residues within 4Å: Chain E: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.35 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:T.39, E:L.47, E:Y.121 LBN.33: 7 residues within 4Å: Chain E: L.275, V.278, I.279, V.282 Chain F: Q.89 Ligands: LBN.34, LBN.36 3 PLIP interactions: 3 interactions with chain E Hydrophobic interactions: E:L.275, E:I.279, E:V.282 LBN.34: 6 residues within 4Å: Chain E: F.235, S.239 Chain F: Q.89, K.91 Ligands: LBN.33, LBN.36 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:F.235 Hydrogen bonds: E:S.239 LBN.35: 15 residues within 4Å: Chain E: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Chain F: L.115, I.118, L.119, L.122 Ligands: LBN.30, LBN.32 7 PLIP interactions: 5 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:I.41, E:L.45, E:L.286, E:L.287, E:P.289, F:I.118, F:L.122 LBN.36: 3 residues within 4Å: Chain F: K.91 Ligands: LBN.33, LBN.34 No protein-ligand interaction detected (PLIP) LBN.37: 14 residues within 4Å: Chain F: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Chain G: F.126 Ligands: LBN.38, LBN.42 11 PLIP interactions: 11 interactions with chain F Hydrophobic interactions: F:L.225, F:L.225, F:P.289, F:V.292, F:Y.293, F:Y.293 Hydrogen bonds: F:Y.293, F:Y.293 Salt bridges: F:R.300, F:E.336, F:E.337 LBN.38: 10 residues within 4Å: Chain F: M.37, Y.293, F.299, Q.301 Chain G: F.126, I.211, K.212, S.215, L.219 Ligands: LBN.37 7 PLIP interactions: 3 interactions with chain F, 4 interactions with chain G Hydrogen bonds: F:Y.293, F:Y.293 Salt bridges: F:K.302 Hydrophobic interactions: G:F.126, G:F.126, G:I.211, G:L.219 LBN.39: 7 residues within 4Å: Chain F: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.42 3 PLIP interactions: 3 interactions with chain F Hydrophobic interactions: F:T.39, F:L.47, F:Y.121 LBN.40: 8 residues within 4Å: Chain F: L.275, V.278, I.279, V.282 Chain G: Q.89, W.104 Ligands: LBN.41, LBN.43 4 PLIP interactions: 3 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:L.275, F:I.279, F:V.282, G:W.104 LBN.41: 6 residues within 4Å: Chain F: F.235, S.239 Chain G: Q.89, K.91 Ligands: LBN.40, LBN.43 3 PLIP interactions: 2 interactions with chain F, 1 interactions with chain G Hydrophobic interactions: F:F.235, G:K.91 Hydrogen bonds: F:S.239 LBN.42: 16 residues within 4Å: Chain F: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Chain G: L.115, I.118, L.119, L.122, L.125 Ligands: LBN.37, LBN.39 8 PLIP interactions: 5 interactions with chain F, 3 interactions with chain G Hydrophobic interactions: F:I.41, F:L.45, F:L.286, F:L.287, F:P.289, G:I.118, G:L.122, G:L.125 LBN.43: 3 residues within 4Å: Chain G: K.91 Ligands: LBN.40, LBN.41 No protein-ligand interaction detected (PLIP) LBN.44: 14 residues within 4Å: Chain A: F.126 Chain G: V.34, M.37, L.225, P.289, V.290, V.292, Y.293, R.300, K.302, E.336, E.337 Ligands: LBN.45, LBN.46 11 PLIP interactions: 11 interactions with chain G Hydrophobic interactions: G:L.225, G:L.225, G:P.289, G:V.292, G:Y.293, G:Y.293 Hydrogen bonds: G:Y.293, G:Y.293 Salt bridges: G:R.300, G:E.336, G:E.337 LBN.45: 9 residues within 4Å: Chain A: F.126, I.211, K.212, L.219 Chain G: M.37, Y.293, F.299, Q.301 Ligands: LBN.44 6 PLIP interactions: 3 interactions with chain A, 3 interactions with chain G Hydrophobic interactions: A:F.126, A:I.211, A:L.219 Hydrogen bonds: G:Y.293, G:Y.293 Salt bridges: G:K.302 LBN.46: 16 residues within 4Å: Chain A: L.115, I.118, L.119, L.122, L.125 Chain G: C.40, I.41, L.45, I.279, V.283, L.286, L.287, P.289, V.290 Ligands: LBN.44, LBN.47 8 PLIP interactions: 3 interactions with chain A, 5 interactions with chain G Hydrophobic interactions: A:I.118, A:L.122, A:L.125, G:I.41, G:L.45, G:L.286, G:L.287, G:P.289 LBN.47: 7 residues within 4Å: Chain G: E.31, T.39, G.44, L.47, L.48, Y.121 Ligands: LBN.46 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:T.39, G:L.47, G:Y.121 LBN.48: 7 residues within 4Å: Chain A: Q.89 Chain G: L.275, V.278, I.279, V.282 Ligands: LBN.6, LBN.49 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:L.275, G:I.279, G:V.282 LBN.49: 5 residues within 4Å: Chain A: K.91 Chain G: F.235, S.239 Ligands: LBN.6, LBN.48 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:F.235 Hydrogen bonds: G:S.239

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Kuzuya, M. et al., Structures of human pannexin-1 in nanodiscs reveal gating mediated by dynamic movement of the N terminus and phospholipids. Sci.Signal. (2022)

Release Date

2022-01-26

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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