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Human protocadherin 10 ectodomain

Analyse Human protocadherin 10 ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6VG4
Type
protein
Length
646 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.298
Source
Homo sapiens
Molecule
Protocadherin-10
UniProt
Q9P2E7
Ligands
TAM, NAG, MAN, BMA, CA, NA, CL
Pockets
1 · best druggability 0.26

Structure

x-ray diffraction · resolution 3.298 · 1 distinct chain · 6% helix, 45% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProtocadherin-10protein6466% helix, 45% strandQ9P2E7

Ligands and binding sites

  • TAM · Tris(hydroxyethyl)aminomethane · ligand · chains A
  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
  • MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
  • BMA · beta-D-mannopyranose · sugar
  • CA · Calcium ion · metal · 15 copies · chains A
  • NA · Sodium ion · metal · chains A
  • CL · Chloride ion · ion · chains A

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

Pockets

1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
1540.260.7417empty

Modifications

Observed in the structure: 5 glycan, 1 disulfide (O-glycosylation, N-glycosylation, disulfide).

Compared structures

  • 6VG4 · Human protocadherin 10 ectodomain · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9P2E7 · AlphaFold monomer V2.0 prediction for protocadherin-10 (Q9P2E7) · a predicted model of the same protein · chain A against A, TM-score 0.78

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