MolNFT v1 · #168298 · protein

Cryo-EM structure of human pannexin 1 channel N255A mutant

6WBM · Pannexin-1: “Cryo-EM structure of human pannexin 1 channel N255A mutant”. Electron microscopy, 4 ligands (PTY, CLR, 3PE), 20 pockets (best druggability 0.85). MolNFT v1 #168298 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6WBM
Type: protein
Length: 2,387 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pannexin-1
UniProt: Q96RD7
Ligands: PTY, CLR, 3PE, DGA
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 1 distinct chain · 65% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Pannexin-1	protein	341	65% helix, 4% strand	Q96RD7

Ligands and binding sites

PTY · Phosphatidylethanolamine · ligand · 14 copies · chains A, B, G, C, D, E, F
CLR · Cholesterol · ligand · 14 copies · chains A, B, C, D, E, F, G
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 7 copies · chains A, G, B, C, D, E, F
DGA · Diacyl glycerol · ligand · 7 copies · chains A, G, B, C, D, E, F

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

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	1040	0.85	0.86	118	DGA
2	1154	0.84	0.85	119	DGA
3	588	0.78	0.84	73	DGA
4	470	0.76	0.84	64	DGA
5	184	0.73	0.90	32	empty

Interfaces

7 interfaces between chains.

E–F · 2285 Å² buried · 12 hydrogen bonds · protein-protein
F–G · 2280 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 2278 Å² buried · 12 hydrogen bonds · protein-protein
B–C · 2274 Å² buried · 12 hydrogen bonds · protein-protein
D–E · 2270 Å² buried · 12 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6WBM · Cryo-EM structure of human Pannexin 1 channel N255A mutant · 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 0.98

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 6WBM · PDBe 6WBM · UniProt Q96RD7

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