Research workbench
Crystal structure of E-cadherin EC1-2 P5A P6A
Analyse Crystal structure of E-cadherin EC1-2 P5A P6A in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3QRB
- Type
- protein
- Length
- 426 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-1
- UniProt
- P09803
- Ligands
- CA
- Pockets
- 3 · best druggability 0.59
Structure
x-ray diffraction · 1 distinct chain · 3% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Cadherin-1 | protein | 213 | 3% helix, 45% strand | P09803 |
Ligands and binding sites
- CA · Calcium ion · metal · 6 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 4 copies · chains A, B
- PGE · Triethylene glycol · additive · 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 | 257 | 0.59 | 0.79 | 39 | empty |
| 2 | 147 | 0.42 | 0.75 | 22 | empty |
| 3 | 50 | 0.39 | 0.81 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 367 Ų buried · 3 hydrogen bonds · protein-protein
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 3QRB · PDBe 3QRB · UniProt P09803
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