MolNFT v1 · #97642 · protein

HCN4 cnbd in complex with cgmp

4KL1 · POTASSIUM/SODIUM hyperpolarization-activated cyclic…: “HCN4 cnbd in complex with cgmp”. X-ray diffraction, 1 ligand (PCG), 11 pockets (best druggability 0.73). MolNFT v1 #97642 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 4KL1
Type: protein
Length: 772 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 4
UniProt: Q9Y3Q4
Ligands: PCG
Pockets: 11 · best druggability 0.73

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 19% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B, C, D	POTASSIUM/SODIUM hyperpolarization-activated cyclic nucleotide-gated channel 4	protein	193	51% helix, 19% strand	Q9Y3Q4

Ligands and binding sites

PCG · Cyclic guanosine monophosphate · ligand · 8 copies · chains A, C, B, D
ACT · Acetate ion · additive · 4 copies · chains A, C
GOL · Glycerol · additive · 2 copies · chains A, C, D

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

Pockets

11 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	889	0.73	0.77	73	PCG, ACT
2	466	0.66	0.78	34	PCG
3	329	0.66	0.81	36	GOL
4	400	0.65	0.79	34	PCG
5	436	0.64	0.78	45	empty

Interfaces

4 interfaces between chains.

A–C · 1193 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1152 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 1151 Å² buried · 16 hydrogen bonds · protein-protein
C–D · 1140 Å² buried · 14 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 modified (oxidation).

Compared structures

4KL1 · HCN4 CNBD in complex with cGMP · the same entry in another collection · chain A against A, TM-score 1.00
Q9Y3Q4 · AlphaFold monomer V2.0 prediction for POTASSIUM/SODIUM hyperpolarization-activated cyclic… · 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 Q9Y3Q4
Elsewhere: RCSB PDB 4KL1 · PDBe 4KL1 · UniProt Q9Y3Q4

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