MolNFT v1 · #122969 · protein
Crystal structure of a chimera of human desmocollin-2 EC1 and human desmoglein-2 EC2-EC5
5J5J · Desmocollin-2,DESMOGLEIN-2: “Crystal structure of a chimera of human desmocollin-2 EC1 and human desmoglein-2 EC2-EC5”. X-ray diffraction, 7 ligands (NAG, MAN, BMA), 1 pocket (best druggability 0.50). MolNFT v1 #122969 on GenesisL1…
- PDB
- 5J5J
- Type
- protein
- Length
- 552 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Desmocollin-2,DESMOGLEIN-2
- UniProt
- Q02487, Q14126
- Ligands
- NAG, MAN, BMA, GAL, FUC, CA, CL
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 1 distinct chain · 1% helix, 39% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Desmocollin-2,DESMOGLEIN-2 | protein | 552 | 1% helix, 39% strand | Q02487, Q14126 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 10 copies · chains A
- MAN · alpha-D-mannopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies
- GAL · beta-D-galactopyranose · sugar
- FUC · alpha-L-fucopyranose · sugar
- CA · Calcium ion · metal · 11 copies · chains A
- CL · Chloride ion · ion · 2 copies · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.50 | 0.85 | 22 | empty |
Modifications
Observed in the structure: 8 glycan, 3 disulfide (N-glycosylation, disulfide, O-glycosylation).
Compared structures
- 5J5J · Crystal structure of a chimera of human Desmocollin-2 EC1 and human Desmoglein-2 EC2-EC5 · the same entry in another collection · chain A against A, TM-score 1.00
- Q14126 · AlphaFold monomer V2.0 prediction for desmoglein-2 (Q14126) · a predicted model of the same protein · chain A against A, TM-score 0.83
- Q02487 · AlphaFold monomer V2.0 prediction for desmocollin-2 (Q02487) · a predicted model of the same protein · chain A against A, TM-score 0.75
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 Q02487
- Every structure of UniProt Q14126
- Elsewhere: RCSB PDB 5J5J · PDBe 5J5J · UniProt Q02487 · UniProt Q14126
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