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cryo-EM structure of human Pannexin 1 channel

Analyse cryo-EM structure of human Pannexin 1 channel in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M02
Type: protein
Length: 2,345 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 3.2
Source: Homo sapiens
Molecule: Pannexin-1
UniProt: Q96RD7
Pockets: 20 · best druggability 0.77

Structure

electron microscopy · resolution 3.2 · 1 distinct chain · 51% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Pannexin-1	protein	335	51% helix, 4% strand	Q96RD7

Pockets

20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	85	0.77	0.98	19	empty
2	762	0.77	0.81	82	empty
3	89	0.77	0.98	19	empty
4	175	0.77	0.93	25	empty
5	756	0.77	0.81	76	empty

Interfaces

7 interfaces between chains.

A–G · 2880 Å² buried · 13 hydrogen bonds · protein-protein
A–B · 2878 Å² buried · 13 hydrogen bonds · protein-protein
B–C · 2876 Å² buried · 14 hydrogen bonds · protein-protein
D–E · 2874 Å² buried · 13 hydrogen bonds · protein-protein
E–F · 2872 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6M02 · Cryo-EM structure of human pannexin 1 channel · the same entry in another collection · chain G against G, TM-score 1.00
Q96RD7 · AlphaFold monomer V2.0 prediction for pannexin-1 (Q96RD7) · a predicted model of the same protein · chain A against A, TM-score 0.86

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt Q96RD7
Elsewhere: RCSB PDB 6M02 · PDBe 6M02 · UniProt Q96RD7

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