MolNFT v1 · #117160 · protein

Protocadherin alpha 4 extracellular cadherin domains 1-4

5DZW · Protocadherin alpha-4: “Protocadherin alpha 4 extracellular cadherin domains 1-4”. X-ray diffraction, 3 ligands (MAN, NAG, CA). MolNFT v1 #117160 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5DZW
Type: protein
Length: 417 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Protocadherin alpha-4
UniProt: O88689
Ligands: MAN, NAG, CA

Structure

x-ray diffraction · 1 distinct chain · 7% helix, 43% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Protocadherin alpha-4	protein	417	7% helix, 43% strand	O88689

Ligands and binding sites

MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
CA · Calcium ion · metal · 9 copies · chains A

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

Modifications

Observed in the structure: 4 glycan, 1 disulfide (O-glycosylation, disulfide, N-glycosylation).

Compared structures

5DZW · Protocadherin alpha 4 extracellular cadherin domains 1-4 · the same entry in another collection · chain A against A, TM-score 1.00
O88689 · AlphaFold monomer V2.0 prediction for protocadherin alpha-4 (O88689) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 O88689
Elsewhere: RCSB PDB 5DZW · PDBe 5DZW · UniProt O88689

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