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Crystal structure of mouse E-cadherin ectodomain
Analyse Crystal structure of mouse E-cadherin ectodomain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3Q2V
- Type
- protein
- Length
- 972 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-1
- UniProt
- P09803
- Ligands
- MAN, CA, MN
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cadherin-1 | protein | 532 | 2% helix, 42% strand | P09803 |
| B | Cadherin-1 | protein | 440 | 2% helix, 43% strand | P09803 |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains A, B
- CA · Calcium ion · metal · 24 copies · chains A, B
- MN · Manganese (II) ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.55 | 0.80 | 26 | empty |
| 2 | 105 | 0.38 | 0.75 | 24 | empty |
| 3 | 54 | 0.28 | 0.74 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 810 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 glycan, 1 disulfide (O-glycosylation, disulfide).
Compared structures
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 P09803
- Elsewhere: RCSB PDB 3Q2V · PDBe 3Q2V · UniProt P09803
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