MolNFT v1 · #168299 · protein

Cryo-EM structure of human pannexin 1 channel N255A mutant, gap junction

6WBN · Pannexin-1: “Cryo-EM structure of human pannexin 1 channel N255A mutant, gap junction”. Electron microscopy, 4 ligands (PTY, CLR, 3PE), 20 pockets (best druggability 0.83). MolNFT v1 #168299 on GenesisL1: 3D structure, binding sites…

PDB: 6WBN
Type: protein
Length: 4,774 residues
Chains: 14
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 0.83

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, H, I, J, K, L, M, N	Pannexin-1	protein	341	65% helix, 4% strand	Q96RD7

Ligands and binding sites

PTY · Phosphatidylethanolamine · ligand · 28 copies · chains A, B, G, C, D, E, F, H, I, N, J, K, L, M
CLR · Cholesterol · ligand · 28 copies · chains A, B, C, D, E, F, G, H, I, J, K, L, M, N
3PE · 1,2-diacyl-sn-glycero-3-phosphoethanolamine · ligand · 14 copies · chains A, G, B, C, D, E, F, H, N, I, J, K, L, M
DGA · Diacyl glycerol · ligand · 14 copies · chains A, G, B, C, D, E, F, H, I, J, K, L, M, N

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	711	0.83	0.86	85	DGA
2	727	0.82	0.85	82	DGA
3	206	0.76	0.91	35	empty
4	193	0.74	0.90	29	empty
5	199	0.74	0.89	33	empty

Interfaces

21 interfaces between chains.

M–N · 2338 Å² buried · 13 hydrogen bonds · protein-protein
L–M · 2335 Å² buried · 13 hydrogen bonds · protein-protein
J–K · 2332 Å² buried · 13 hydrogen bonds · protein-protein
H–N · 2330 Å² buried · 13 hydrogen bonds · protein-protein
H–I · 2327 Å² buried · 13 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 28 disulfide (disulfide).

Compared structures

6WBN · Cryo-EM structure of human Pannexin 1 channel N255A mutant, gap junction · the same entry in another collection · chain N against N, TM-score 1.00

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 6WBN · PDBe 6WBN · UniProt Q96RD7

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