SMTL ID : 7f8o.1

Cryo-EM structure of the C-terminal deletion mutant of human PANX1 in a nanodisc

Coordinates

PDB Format Compare

Method

ELECTRON MICROSCOPY

Oligo State

homo-heptamer

Ligands

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

LBN.1: 4 residues within 4Å: Chain A: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain A Hydrophobic interactions: A:Y.293 Salt bridges: A:R.300 LBN.2: 8 residues within 4Å: Chain A: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 Chain B: I.279 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain B Hydrophobic interactions: A:W.104, A:W.104, A:Y.111, A:I.112, B:I.279 Hydrogen bonds: A:G.99 Salt bridges: A:K.91 LBN.3: 7 residues within 4Å: Chain A: F.235, L.237, S.239, Q.274, L.275, V.282 Chain G: K.91 7 PLIP interactions: 6 interactions with chain A, 1 interactions with chain G Hydrophobic interactions: A:F.235, A:L.275, A:V.282 Hydrogen bonds: A:F.235, A:F.235, A:Q.274 Salt bridges: G:K.91 LBN.4: 4 residues within 4Å: Chain B: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain B Hydrophobic interactions: B:Y.293 Salt bridges: B:R.300 LBN.5: 9 residues within 4Å: Chain B: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 Chain C: L.275, I.279 7 PLIP interactions: 1 interactions with chain C, 6 interactions with chain B Hydrophobic interactions: C:L.275, B:W.104, B:W.104, B:Y.111, B:I.112 Hydrogen bonds: B:G.99 Salt bridges: B:K.91 LBN.6: 7 residues within 4Å: Chain A: K.91 Chain B: F.235, L.237, S.239, Q.274, L.275, V.282 7 PLIP interactions: 6 interactions with chain B, 1 interactions with chain A Hydrophobic interactions: B:F.235, B:L.275, B:V.282 Hydrogen bonds: B:F.235, B:F.235, B:Q.274 Salt bridges: A:K.91 LBN.7: 4 residues within 4Å: Chain C: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain C Hydrophobic interactions: C:Y.293 Salt bridges: C:R.300 LBN.8: 10 residues within 4Å: Chain C: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 Chain D: L.275, I.279 Ligands: LBN.12 8 PLIP interactions: 6 interactions with chain C, 2 interactions with chain D Hydrophobic interactions: C:W.104, C:W.104, C:Y.111, C:I.112, D:L.275, D:I.279 Hydrogen bonds: C:G.99 Salt bridges: C:K.91 LBN.9: 7 residues within 4Å: Chain B: K.91 Chain C: F.235, L.237, S.239, Q.274, L.275, V.282 7 PLIP interactions: 6 interactions with chain C, 1 interactions with chain B Hydrophobic interactions: C:F.235, C:L.275, C:V.282 Hydrogen bonds: C:F.235, C:F.235, C:Q.274 Salt bridges: B:K.91 LBN.10: 4 residues within 4Å: Chain D: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain D Hydrophobic interactions: D:Y.293 Salt bridges: D:R.300 LBN.11: 10 residues within 4Å: Chain D: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 Chain E: L.275, I.279 Ligands: LBN.15 8 PLIP interactions: 2 interactions with chain E, 6 interactions with chain D Hydrophobic interactions: E:L.275, E:I.279, D:W.104, D:W.104, D:Y.111, D:I.112 Hydrogen bonds: D:G.99 Salt bridges: D:K.91 LBN.12: 8 residues within 4Å: Chain C: K.91 Chain D: F.235, L.237, S.239, Q.274, L.275, V.282 Ligands: LBN.8 7 PLIP interactions: 6 interactions with chain D, 1 interactions with chain C Hydrophobic interactions: D:F.235, D:L.275, D:V.282 Hydrogen bonds: D:F.235, D:F.235, D:Q.274 Salt bridges: C:K.91 LBN.13: 4 residues within 4Å: Chain E: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain E Hydrophobic interactions: E:Y.293 Salt bridges: E:R.300 LBN.14: 10 residues within 4Å: Chain E: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 Chain F: L.275, I.279 Ligands: LBN.18 8 PLIP interactions: 6 interactions with chain E, 2 interactions with chain F Hydrophobic interactions: E:W.104, E:W.104, E:Y.111, E:I.112, F:L.275, F:I.279 Hydrogen bonds: E:G.99 Salt bridges: E:K.91 LBN.15: 8 residues within 4Å: Chain D: K.91 Chain E: F.235, L.237, S.239, Q.274, L.275, V.282 Ligands: LBN.11 7 PLIP interactions: 6 interactions with chain E, 1 interactions with chain D Hydrophobic interactions: E:F.235, E:L.275, E:V.282 Hydrogen bonds: E:F.235, E:F.235, E:Q.274 Salt bridges: D:K.91 LBN.16: 4 residues within 4Å: Chain F: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain F Hydrophobic interactions: F:Y.293 Salt bridges: F:R.300 LBN.17: 10 residues within 4Å: Chain F: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 Chain G: L.275, I.279 Ligands: LBN.21 8 PLIP interactions: 2 interactions with chain G, 6 interactions with chain F Hydrophobic interactions: G:L.275, G:I.279, F:W.104, F:W.104, F:Y.111, F:I.112 Hydrogen bonds: F:G.99 Salt bridges: F:K.91 LBN.18: 9 residues within 4Å: Chain E: K.91, W.104 Chain F: F.235, L.237, S.239, Q.274, L.275, V.282 Ligands: LBN.14 8 PLIP interactions: 6 interactions with chain F, 2 interactions with chain E Hydrophobic interactions: F:F.235, F:L.275, F:V.282, E:W.104 Hydrogen bonds: F:F.235, F:F.235, F:Q.274 Salt bridges: E:K.91 LBN.19: 4 residues within 4Å: Chain G: V.34, P.289, Y.293, R.300 2 PLIP interactions: 2 interactions with chain G Hydrophobic interactions: G:Y.293 Salt bridges: G:R.300 LBN.20: 9 residues within 4Å: Chain A: L.275, I.279 Chain G: K.91, G.99, L.101, W.104, Y.111, I.112, L.115 8 PLIP interactions: 2 interactions with chain A, 6 interactions with chain G Hydrophobic interactions: A:L.275, A:I.279, G:W.104, G:W.104, G:Y.111, G:I.112 Hydrogen bonds: G:G.99 Salt bridges: G:K.91 LBN.21: 9 residues within 4Å: Chain F: K.91, W.104 Chain G: F.235, L.237, S.239, Q.274, L.275, V.282 Ligands: LBN.17 8 PLIP interactions: 2 interactions with chain F, 6 interactions with chain G Hydrophobic interactions: F:W.104, G:F.235, G:L.275, G:V.282 Salt bridges: F:K.91 Hydrogen bonds: G:F.235, G:F.235, G:Q.274

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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