SMTL ID : 7f8j.1

Cryo-EM structure of human pannexin-1 in a nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

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

LBN.1: 15 residues within 4Å: Chain A: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Chain G: L.122, L.125, F.126, F.129 Ligands: LBN.37 10 PLIP interactions: 8 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:V.11, A:L.17, A:A.33, A:I.41, A:L.45, A:L.287, A:V.290, A:Y.293, G:L.122, G:L.125 LBN.2: 11 residues within 4Å: Chain A: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.38, LBN.40 9 PLIP interactions: 9 interactions with chain A Hydrophobic interactions: A:F.235, A:F.235, A:V.278, A:L.281, A:V.282, A:V.282, A:V.285 Hydrogen bonds: A:F.235, A:S.239 LBN.3: 7 residues within 4Å: Chain A: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.7 5 PLIP interactions: 5 interactions with chain A Hydrophobic interactions: A:L.122, A:L.122, A:F.126, A:F.126, A:I.211 LBN.4: 3 residues within 4Å: Ligands: LBN.5, LBN.6, LBN.8 No protein-ligand interaction detected (PLIP) LBN.5: 11 residues within 4Å: Chain A: N.100, L.101, W.104, F.108, Y.111, I.112, L.115 Chain B: L.52, I.279 Ligands: LBN.4, LBN.6 11 PLIP interactions: 2 interactions with chain B, 9 interactions with chain A Hydrophobic interactions: B:L.52, B:I.279, A:L.101, A:W.104, A:W.104, A:F.108, A:Y.111, A:I.112, A:L.115 Hydrogen bonds: A:N.100, A:L.101 LBN.6: 8 residues within 4Å: Chain A: K.91, W.104, L.115 Chain B: L.275, V.278 Ligands: LBN.4, LBN.5, LBN.8 4 PLIP interactions: 3 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.104, A:W.104, A:L.115, B:L.275 LBN.7: 14 residues within 4Å: Chain A: L.122, L.125, F.129 Chain B: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Ligands: LBN.3 10 PLIP interactions: 8 interactions with chain B, 2 interactions with chain A Hydrophobic interactions: B:V.11, B:L.17, B:A.33, B:I.41, B:L.45, B:L.287, B:V.290, B:Y.293, A:L.122, A:L.125 LBN.8: 11 residues within 4Å: Chain B: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.4, LBN.6 10 PLIP interactions: 9 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.235, B:F.235, B:V.278, B:L.281, B:V.282, B:V.282, B:V.285 Hydrogen bonds: B:F.235, B:S.239 Salt bridges: A:K.91 LBN.9: 6 residues within 4Å: Chain B: L.122, F.126, K.212, S.215, L.219 Ligands: LBN.23 3 PLIP interactions: 3 interactions with chain B Hydrophobic interactions: B:L.122, B:F.126, B:L.219 LBN.10: 3 residues within 4Å: Ligands: LBN.11, LBN.12, LBN.24 No protein-ligand interaction detected (PLIP) LBN.11: 10 residues within 4Å: Chain B: N.100, L.101, W.104, Y.111, I.112, L.115 Chain D: L.52, I.279 Ligands: LBN.10, LBN.12 9 PLIP interactions: 2 interactions with chain D, 7 interactions with chain B Hydrophobic interactions: D:L.52, D:I.279, B:L.101, B:W.104, B:Y.111, B:I.112, B:L.115 Hydrogen bonds: B:N.100, B:L.101 LBN.12: 7 residues within 4Å: Chain B: K.91, L.115 Chain D: L.275, V.278 Ligands: LBN.10, LBN.11, LBN.24 2 PLIP interactions: 1 interactions with chain B, 1 interactions with chain D Hydrophobic interactions: B:L.115, D:L.275 LBN.13: 14 residues within 4Å: Chain C: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Chain D: L.122, L.125, F.129 Ligands: LBN.19 10 PLIP interactions: 8 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:V.11, C:L.17, C:A.33, C:I.41, C:L.45, C:L.287, C:V.290, C:Y.293, D:L.122, D:L.125 LBN.14: 11 residues within 4Å: Chain C: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.20, LBN.22 9 PLIP interactions: 9 interactions with chain C Hydrophobic interactions: C:F.235, C:F.235, C:V.278, C:L.281, C:V.282, C:V.282, C:V.285 Hydrogen bonds: C:F.235, C:S.239 LBN.15: 7 residues within 4Å: Chain C: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.25 4 PLIP interactions: 4 interactions with chain C Hydrophobic interactions: C:L.122, C:F.126, C:F.126, C:I.211 LBN.16: 3 residues within 4Å: Ligands: LBN.17, LBN.18, LBN.26 No protein-ligand interaction detected (PLIP) LBN.17: 10 residues within 4Å: Chain C: N.100, L.101, W.104, Y.111, I.112, L.115 Chain E: L.52, I.279 Ligands: LBN.16, LBN.18 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain C Hydrophobic interactions: E:L.52, E:I.279, C:W.104, C:Y.111, C:I.112, C:L.115 Hydrogen bonds: C:N.100, C:L.101 LBN.18: 7 residues within 4Å: Chain C: K.91, L.115 Chain E: L.275, V.278 Ligands: LBN.16, LBN.17, LBN.26 2 PLIP interactions: 1 interactions with chain C, 1 interactions with chain E Hydrophobic interactions: C:L.115, E:L.275 LBN.19: 6 residues within 4Å: Chain D: L.122, F.126, K.212, S.215, L.219 Ligands: LBN.13 4 PLIP interactions: 4 interactions with chain D Hydrophobic interactions: D:L.122, D:F.126, D:F.126, D:L.219 LBN.20: 3 residues within 4Å: Ligands: LBN.14, LBN.21, LBN.22 No protein-ligand interaction detected (PLIP) LBN.21: 10 residues within 4Å: Chain C: L.52, I.279 Chain D: N.100, L.101, W.104, Y.111, I.112, L.115 Ligands: LBN.20, LBN.22 8 PLIP interactions: 6 interactions with chain D, 2 interactions with chain C Hydrophobic interactions: D:W.104, D:Y.111, D:I.112, D:L.115, C:L.52, C:I.279 Hydrogen bonds: D:N.100, D:L.101 LBN.22: 7 residues within 4Å: Chain C: L.275, V.278 Chain D: K.91, L.115 Ligands: LBN.14, LBN.20, LBN.21 2 PLIP interactions: 1 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:L.115, C:L.275 LBN.23: 14 residues within 4Å: Chain B: L.122, L.125, F.129 Chain D: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Ligands: LBN.9 10 PLIP interactions: 8 interactions with chain D, 2 interactions with chain B Hydrophobic interactions: D:V.11, D:L.17, D:A.33, D:I.41, D:L.45, D:L.287, D:V.290, D:Y.293, B:L.122, B:L.125 LBN.24: 11 residues within 4Å: Chain D: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.10, LBN.12 9 PLIP interactions: 9 interactions with chain D Hydrophobic interactions: D:F.235, D:F.235, D:V.278, D:L.281, D:V.282, D:V.282, D:V.285 Hydrogen bonds: D:F.235, D:S.239 LBN.25: 15 residues within 4Å: Chain C: L.122, L.125, F.126, F.129 Chain E: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Ligands: LBN.15 10 PLIP interactions: 8 interactions with chain E, 2 interactions with chain C Hydrophobic interactions: E:V.11, E:L.17, E:A.33, E:I.41, E:L.45, E:L.287, E:V.290, E:Y.293, C:L.122, C:L.125 LBN.26: 11 residues within 4Å: Chain E: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.16, LBN.18 9 PLIP interactions: 9 interactions with chain E Hydrophobic interactions: E:F.235, E:F.235, E:V.278, E:L.281, E:V.282, E:V.282, E:V.285 Hydrogen bonds: E:F.235, E:S.239 LBN.27: 7 residues within 4Å: Chain E: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.31 5 PLIP interactions: 5 interactions with chain E Hydrophobic interactions: E:L.122, E:F.126, E:F.126, E:I.211, E:L.219 LBN.28: 3 residues within 4Å: Ligands: LBN.29, LBN.30, LBN.32 No protein-ligand interaction detected (PLIP) LBN.29: 10 residues within 4Å: Chain E: N.100, L.101, W.104, Y.111, I.112, L.115 Chain F: L.52, I.279 Ligands: LBN.28, LBN.30 9 PLIP interactions: 7 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:L.101, E:W.104, E:Y.111, E:I.112, E:L.115, F:L.52, F:I.279 Hydrogen bonds: E:N.100, E:L.101 LBN.30: 7 residues within 4Å: Chain E: K.91, L.115 Chain F: L.275, V.278 Ligands: LBN.28, LBN.29, LBN.32 2 PLIP interactions: 1 interactions with chain F, 1 interactions with chain E Hydrophobic interactions: F:L.275, E:L.115 LBN.31: 15 residues within 4Å: Chain E: L.122, L.125, F.126, F.129 Chain F: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Ligands: LBN.27 10 PLIP interactions: 8 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:V.11, F:L.17, F:A.33, F:I.41, F:L.45, F:L.287, F:V.290, F:Y.293, E:L.122, E:L.125 LBN.32: 11 residues within 4Å: Chain F: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.28, LBN.30 9 PLIP interactions: 9 interactions with chain F Hydrophobic interactions: F:F.235, F:F.235, F:V.278, F:L.281, F:V.282, F:V.282, F:V.285 Hydrogen bonds: F:F.235, F:S.239 LBN.33: 7 residues within 4Å: Chain F: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.41 4 PLIP interactions: 4 interactions with chain F Hydrophobic interactions: F:L.122, F:F.126, F:F.126, F:I.211 LBN.34: 3 residues within 4Å: Ligands: LBN.35, LBN.36, LBN.42 No protein-ligand interaction detected (PLIP) LBN.35: 10 residues within 4Å: Chain F: N.100, L.101, W.104, Y.111, I.112, L.115 Chain G: L.52, I.279 Ligands: LBN.34, LBN.36 9 PLIP interactions: 7 interactions with chain F, 2 interactions with chain G Hydrophobic interactions: F:L.101, F:W.104, F:Y.111, F:I.112, F:L.115, G:L.52, G:I.279 Hydrogen bonds: F:N.100, F:L.101 LBN.36: 7 residues within 4Å: Chain F: K.91, L.115 Chain G: L.275, V.278 Ligands: LBN.34, LBN.35, LBN.42 2 PLIP interactions: 1 interactions with chain G, 1 interactions with chain F Hydrophobic interactions: G:L.275, F:L.115 LBN.37: 7 residues within 4Å: Chain G: L.122, F.126, I.211, K.212, S.215, L.219 Ligands: LBN.1 3 PLIP interactions: 3 interactions with chain G Hydrophobic interactions: G:L.122, G:F.126, G:I.211 LBN.38: 3 residues within 4Å: Ligands: LBN.2, LBN.39, LBN.40 No protein-ligand interaction detected (PLIP) LBN.39: 10 residues within 4Å: Chain A: L.52, I.279 Chain G: N.100, L.101, W.104, Y.111, I.112, L.115 Ligands: LBN.38, LBN.40 10 PLIP interactions: 2 interactions with chain A, 8 interactions with chain G Hydrophobic interactions: A:L.52, A:I.279, G:L.101, G:W.104, G:Y.111, G:I.112, G:L.115, G:L.115 Hydrogen bonds: G:N.100, G:L.101 LBN.40: 8 residues within 4Å: Chain A: L.275, V.278 Chain G: K.91, W.104, L.115 Ligands: LBN.2, LBN.38, LBN.39 3 PLIP interactions: 1 interactions with chain A, 2 interactions with chain G Hydrophobic interactions: A:L.275, G:W.104, G:L.115 LBN.41: 15 residues within 4Å: Chain F: L.122, L.125, F.126, F.129 Chain G: V.11, L.17, A.33, M.37, C.40, I.41, L.45, L.287, V.290, Y.293 Ligands: LBN.33 10 PLIP interactions: 8 interactions with chain G, 2 interactions with chain F Hydrophobic interactions: G:V.11, G:L.17, G:A.33, G:I.41, G:L.45, G:L.287, G:V.290, G:Y.293, F:L.122, F:L.125 LBN.42: 11 residues within 4Å: Chain G: F.235, L.237, S.239, Q.274, V.278, L.281, V.282, V.285, L.286 Ligands: LBN.34, LBN.36 9 PLIP interactions: 9 interactions with chain G Hydrophobic interactions: G:F.235, G:F.235, G:V.278, G:L.281, G:V.282, G:V.282, G:V.285 Hydrogen bonds: G:F.235, 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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