Research workbench

KCC3 bound with DIOA

Analyse KCC3 bound with DIOA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6M22
Type: protein
Length: 1,770 residues
Chains: 2
Method: electron microscopy
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 2.7
Source: Homo sapiens
Molecule: Solute carrier family 12 member 6
UniProt: Q9UHW9
Ligands: EZC, NAG, K, CL
Pockets: 20 · best druggability 0.82

Structure

electron microscopy · resolution 2.7 · 1 distinct chain · 49% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Solute carrier family 12 member 6	protein	885	49% helix, 10% strand	Q9UHW9

Ligands and binding sites

EZC · 2-[[(2~{R})-2-butyl-6,7-bis(chloranyl)-2-cyclopentyl-1-oxidanylidene-3~{H}-inden-5-yl]oxy]ethanoic acid · ligand · 2 copies · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 16 copies · chains A, B
K · Potassium ion · metal · 2 copies · chains A, B
CL · Chloride ion · ion · 4 copies · chains A, B

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

Pockets

20 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	173	0.82	0.97	42	empty
2	144	0.79	0.96	36	CL
3	1066	0.77	0.79	88	empty
4	1092	0.77	0.79	91	empty
5	562	0.77	0.83	51	empty

Interfaces

1 interface between chains.

A–B · 3230 Å² buried · 15 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 glycan, 2 disulfide (N-glycosylation, disulfide).

Compared structures

6M22 · KCC3 bound with dioa · the same entry in another collection · chain A against A, TM-score 1.00
Q9UHW9 · AlphaFold monomer V2.0 prediction for solute carrier family 12 member 6 (Q9UHW9) · a predicted model of the same protein · chain A against A, TM-score 0.97

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 Q9UHW9
Elsewhere: RCSB PDB 6M22 · PDBe 6M22 · UniProt Q9UHW9

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