MolNFT v1 · #182696 · protein

Structure of tax-4_R421W apo closed state

7N16 · Cyclic nucleotide-gated cation channel: “Structure of tax-4_R421W apo closed state”. Electron microscopy, 2 ligands (CPL, NA), 20 pockets (best druggability 0.74). MolNFT v1 #182696 on GenesisL1: 3D structure, binding sites and…

PDB: 7N16
Type: protein
Length: 2,056 residues
Chains: 4
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Cyclic nucleotide-gated cation channel
UniProt: Q03611
Ligands: CPL, NA
Pockets: 20 · best druggability 0.74

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
D, A, B, C	Cyclic nucleotide-gated cation channel	protein	514	53% helix, 12% strand	Q03611

Ligands and binding sites

CPL · 1-palmitoyl-2-linoleoyl-sn-glycero-3-phosphocholine · ligand · 16 copies · chains D, C, A, B
NA · Sodium ion · metal · chains D, A, 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	819	0.74	0.78	82	CPL
2	740	0.73	0.79	86	CPL
3	765	0.72	0.78	80	empty
4	66	0.71	0.97	20	empty
5	530	0.70	0.80	40	empty

Interfaces

6 interfaces between chains.

D–A · 2767 Å² buried · 17 hydrogen bonds · protein-protein
D–C · 2763 Å² buried · 18 hydrogen bonds · protein-protein
B–C · 2761 Å² buried · 17 hydrogen bonds · protein-protein
A–B · 2753 Å² buried · 15 hydrogen bonds · protein-protein
A–C · 43 Å² buried · 0 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

7N16 · Structure of TAX-4_R421W apo closed state · the same entry in another collection · chain C against C, 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 A against A, TM-score 0.96

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 7N16 · PDBe 7N16 · UniProt Q03611

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