Research workbench
Crystal structure of human E-cadherin EC1-5 bound by mouse monoclonal antibody Fab mab-1_19A11
Analyse Crystal structure of human E-cadherin EC1-5 bound by mouse monoclonal antibody… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7STZ
- Type
- protein
- Length
- 1,837 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-1; Mab-1_19A11 heavy chain; Mab-1_19A11 light chain
- UniProt
- P12830
- Ligands
- BMA, MAN, NAG, CA
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 5 distinct chains · 4% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cadherin-1 | protein | 540 | 1% helix, 46% strand | P12830 |
| H | Mab-1_19A11 heavy chain | protein | 219 | 7% helix, 49% strand | — |
| L, M | Mab-1_19A11 light chain | protein | 220 | 6% helix, 55% strand | — |
| D | Cadherin-1 | protein | 422 | 2% helix, 43% strand | P12830 |
| I | Mab-1_19A11 heavy chain | protein | 216 | 7% helix, 51% strand | — |
Ligands and binding sites
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains C, D
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains C
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
- CA · Calcium ion · metal · 24 copies · chains C, D, I, M
- EDO · 1,2-ethanediol · additive · 5 copies · chains C, H, I
- PG4 · Tetraethylene glycol · additive · 5 copies · chains C, H, L, D, I, M
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 812 | 0.78 | 0.82 | 70 | empty |
| 2 | 436 | 0.66 | 0.79 | 41 | empty |
| 3 | 566 | 0.63 | 0.75 | 55 | EDO |
| 4 | 582 | 0.62 | 0.74 | 47 | empty |
| 5 | 230 | 0.48 | 0.74 | 34 | empty |
Interfaces
9 interfaces between chains.
- I–M · 1879 Ų buried · 22 hydrogen bonds · protein-protein
- H–L · 1822 Ų buried · 17 hydrogen bonds · protein-protein
- C–D · 871 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 499 Ų buried · 7 hydrogen bonds · protein-protein
- D–I · 488 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 glycan, 9 disulfide, 1 covalent (O-glycosylation, disulfide, additive adduct, N-glycosylation).
Compared structures
- 7STZ · Crystal Structure of Human E-cadherin EC1-5 bound by mouse monoclonal antibody Fab… · the same entry in another collection · chain M against M, TM-score 1.00
- P12830 · AlphaFold monomer V2.0 prediction for cadherin-1 (P12830) · a predicted model of the same protein · chain C against A, TM-score 0.86
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 P12830
- Elsewhere: RCSB PDB 7STZ · PDBe 7STZ · UniProt P12830
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