MolNFT v1 · #167188 · protein

Cryo-EM structure of xenopus tropicalis pannexin 1 channel

6VD7: “Cryo-EM structure of xenopus tropicalis pannexin 1 channel”. Electron microscopy, 20 pockets (best druggability 0.81). MolNFT v1 #167188 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6VD7
Type: protein
Length: 2,079 residues
Chains: 7
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pannexin
UniProt: B3DLA5
Pockets: 20 · best druggability 0.81

Structure

electron microscopy · 1 distinct chain · 62% helix, 4% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D, E, F, G	Pannexin	protein	297	62% helix, 4% strand	B3DLA5

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	857	0.81	0.83	87	empty
2	859	0.78	0.81	86	empty
3	840	0.78	0.81	93	empty
4	926	0.76	0.79	85	empty
5	1005	0.76	0.78	81	empty

Interfaces

7 interfaces between chains.

A–B · 2271 Å² buried · 8 hydrogen bonds · protein-protein
C–D · 2269 Å² buried · 8 hydrogen bonds · protein-protein
A–G · 2266 Å² buried · 8 hydrogen bonds · protein-protein
B–C · 2265 Å² buried · 8 hydrogen bonds · protein-protein
F–G · 2265 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 14 disulfide (disulfide).

Compared structures

6VD7 · Cryo-EM structure of Xenopus tropicalis pannexin 1 channel · the same entry in another collection · chain A against A, 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 B3DLA5
Elsewhere: RCSB PDB 6VD7 · PDBe 6VD7 · UniProt B3DLA5

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