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The overall structure of KCC3

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

PDB
6M1Y
Type
protein
Length
1,876 residues
Chains
2
Method
electron microscopy
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Solute carrier family 12 member 6
UniProt
Q9UHW9
Ligands
NAG, K, CL
Pockets
20 · best druggability 0.80

Structure

electron microscopy · 1 distinct chain · 46% helix, 9% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BSolute carrier family 12 member 6protein93846% helix, 9% strandQ9UHW9

Ligands and binding sites

  • 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, 13 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
110810.800.81106empty
211220.800.81107empty
31240.770.9632CL
41140.760.9627CL
55170.740.8352empty

Interfaces

1 interface between chains.

  • A–B · 3505 Ų buried · 19 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 10 glycan, 4 disulfide, 4 modified (N-glycosylation, disulfide, phosphorylation).

Compared structures

  • 6M1Y · The overall structure of KCC3 · the same entry in another collection · chain B against B, 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 0.99

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