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Cryo-EM structure of human KCNQ4 with retigabine

Analyse Cryo-EM structure of human KCNQ4 with retigabine in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7BYM
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, FBX, K
Pockets: 20 · best druggability 0.85

Structure

electron microscopy · 2 distinct chains · 72% 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	78% 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
FBX · Ethyl N-[2-azanyl-4-[(4-fluorophenyl) methylamino]phenyl]carbamate · ligand · 4 copies · chains A, E, G, C
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, 18 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	677	0.85	0.89	84	FBX, K
2	883	0.80	0.82	100	empty
3	117	0.79	0.97	21	empty
4	268	0.71	0.84	29	empty
5	246	0.70	0.85	32	PT5

Interfaces

10 interfaces between chains.

C–D · 2486 Å² buried · 33 hydrogen bonds · protein-protein
G–H · 2481 Å² buried · 34 hydrogen bonds · protein-protein
E–F · 2467 Å² buried · 34 hydrogen bonds · protein-protein
A–B · 2455 Å² buried · 33 hydrogen bonds · protein-protein
C–E · 2390 Å² buried · 12 hydrogen bonds · protein-protein

Compared structures

7BYM · Cryo-EM structure of human KCNQ4 with retigabine · 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 E 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 7BYM · PDBe 7BYM · UniProt P56696 · UniProt P0DP25

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