MolNFT v1 · #174538 · protein

Cryo-EM structure of human KCNQ4 with linopirdine

7BYN · Green fluorescent PROTEIN,POTASSIUM voltage-gated channel…: “Cryo-EM structure of human KCNQ4 with linopirdine”. Electron microscopy, 3 ligands (PT5, FCC, K), 20 pockets (best druggability 0.86). MolNFT v1 #174538 on GenesisL1: 3D…

PDB: 7BYN
Type: protein
Length: 2,000 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Green fluorescent PROTEIN,POTASSIUM voltage-gated channel subfamily kqt member 4…
UniProt: P56696, P0DP25
Ligands: PT5, FCC, K
Pockets: 20 · best druggability 0.86

Structure

electron microscopy · 2 distinct chains · 73% helix, 2% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Green fluorescent PROTEIN,POTASSIUM voltage-gated channel subfamily kqt member 4	protein	354	79% helix, 0% strand	P56696
B, D, F, H	Calmodulin-3	protein	146	58% helix, 7% strand	P0DP25

Ligands and binding sites

PT5 · (1S)-2-{[(R)-hydroxy{[(1r,2r,3s,4r,5r,6s)-2,3,6-trihydroxy-4,5-bis(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy) methyl]ethyl (8E,11E)-icosa-5,8,11,14-tetraenoate · ligand · 4 copies · chains A, C, E, G
FCC · 1-phenyl-3,3-bis(pyridin-4-ylmethyl)indol-2-one · ligand · chains C, E, G
K · Potassium ion · metal · 3 copies · chains A, C, E, G

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	564	0.86	0.91	85	K
2	116	0.80	0.98	20	empty
3	249	0.72	0.86	32	empty
4	369	0.70	0.83	59	PT5
5	178	0.70	0.87	26	empty

Interfaces

10 interfaces between chains.

E–F · 2482 Å² buried · 32 hydrogen bonds · protein-protein
G–H · 2476 Å² buried · 29 hydrogen bonds · protein-protein
C–D · 2474 Å² buried · 31 hydrogen bonds · protein-protein
A–B · 2472 Å² buried · 29 hydrogen bonds · protein-protein
E–G · 2414 Å² buried · 13 hydrogen bonds · protein-protein

Compared structures

7BYN · Cryo-EM structure of human KCNQ4 with linopirdine · the same entry in another collection · chain H against H, TM-score 1.00
P56696 · AlphaFold monomer V2.0 prediction for potassium voltage-gated channel subfamily kqt… · a predicted model of the same protein · chain A against A, TM-score 0.71

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 P56696
Every structure of UniProt P0DP25
Elsewhere: RCSB PDB 7BYN · PDBe 7BYN · UniProt P56696 · UniProt P0DP25

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