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Crystal structure of monomeric human protocadherin 10 EC1-EC4

Analyse Crystal structure of monomeric human protocadherin 10 EC1-EC4 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6VFQ
Type
protein
Length
424 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Protocadherin-10
UniProt
Q9P2E7
Ligands
NAG, MAN, FUC, CA
Pockets
1 · best druggability 0.27

Structure

x-ray diffraction · 1 distinct chain · 8% helix, 46% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
AProtocadherin-10protein4248% helix, 46% strandQ9P2E7

Ligands and binding sites

  • NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
  • MAN · alpha-D-mannopyranose · sugar · 2 copies · chains A
  • FUC · alpha-L-fucopyranose · sugar · chains A
  • CA · Calcium ion · metal · 9 copies · chains A
  • EDO · 1,2-ethanediol · additive · 4 copies · chains A
  • ACT · Acetate ion · additive · 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
1580.270.7421empty

Modifications

Observed in the structure: 3 glycan, 1 disulfide (O-glycosylation, disulfide, N-glycosylation).

Compared structures

  • 6VFQ · Crystal structure of monomeric human protocadherin 10 EC1-EC4 · 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 0.95

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