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Structure of TAX-4_R421W w/cGMP open state

Analyse Structure of TAX-4_R421W w/cGMP open state in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7N15
Type: protein
Length: 2,080 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.9
Source: Caenorhabditis elegans
Molecule: Cyclic nucleotide-gated cation channel
UniProt: Q03611
Ligands: CPL, PCG, PX2
Pockets: 20 · best druggability 0.80

Structure

electron microscopy · resolution 2.9 · 1 distinct chain · 53% helix, 12% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	Cyclic nucleotide-gated cation channel	protein	520	53% helix, 12% strand	Q03611

Ligands and binding sites

CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 20 copies · chains A, B, C, D
PCG · Cyclic guanosine monophosphate · ligand · 4 copies · chains A, B, C, D
PX2 · 1,2-dilauroyl-sn-glycero-3-phosphate · ligand · 4 copies · chains A, D, B, C

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	0.80	0.82	61	empty
2	697	0.71	0.78	71	empty
3	611	0.69	0.78	60	empty
4	590	0.69	0.78	60	empty
5	471	0.69	0.80	55	empty

Interfaces

6 interfaces between chains.

A–B · 2782 Å² buried · 27 hydrogen bonds · protein-protein
A–D · 2772 Å² buried · 26 hydrogen bonds · protein-protein
C–D · 2770 Å² buried · 26 hydrogen bonds · protein-protein
B–C · 2762 Å² buried · 26 hydrogen bonds · protein-protein
B–D · 24 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7N15 · Structure of tax-4_R421W W/CGMP open state · the same entry in another collection · chain D against D, TM-score 1.00
Q03611 · AlphaFold monomer V2.0 prediction for cyclic nucleotide-gated cation channel (Q03611) · a predicted model of the same protein · chain C against A, TM-score 0.92

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 Q03611
Elsewhere: RCSB PDB 7N15 · PDBe 7N15 · UniProt Q03611

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