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Structure of human KCNQ4-ML213 complex with PIP2

Analyse Structure of human KCNQ4-ML213 complex with PIP2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 7VNP
Type: protein
Length: 1,904 residues
Chains: 8
Method: electron microscopy
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Potassium voltage-gated channel subfamily kqt member 4, maltodextrin-binding protein…
UniProt: P56696, P0DP25
Ligands: PT5, 7YV, K
Pockets: 20 · best druggability 0.79

Structure

electron microscopy · 2 distinct chains · 75% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, E, G	Potassium voltage-gated channel subfamily kqt member 4, maltodextrin-binding protein	protein	332	82% helix, 0% strand	P56696
B, D, F, H	Calmodulin-3	protein	144	57% helix, 0% 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 · 8 copies · chains A, C, E, G
7YV · (1S,2S,4R)-N-(2,4,6-trimethylphenyl) bicyclo[2.2.1]heptane-2-carboxamid · ligand · 4 copies · chains A, C, G, E
K · Potassium ion · metal · 4 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	846	0.79	0.82	88	empty
2	158	0.76	0.93	33	empty
3	210	0.76	0.90	39	empty
4	155	0.76	0.93	33	empty
5	154	0.75	0.92	32	empty

Interfaces

14 interfaces between chains.

C–E · 2035 Å² buried · 14 hydrogen bonds · protein-protein
A–C · 2033 Å² buried · 16 hydrogen bonds · protein-protein
A–G · 2025 Å² buried · 15 hydrogen bonds · protein-protein
E–G · 2022 Å² buried · 15 hydrogen bonds · protein-protein
A–B · 1449 Å² buried · 8 hydrogen bonds · protein-protein

Compared structures

7VNP · Structure of human KCNQ4-ML213 complex with PIP2 · 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 C against A, TM-score 0.78

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 7VNP · PDBe 7VNP · UniProt P56696 · UniProt P0DP25

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