MolNFT v1 · #145775 · protein
Crystal structure of human E-cadherin bound by mouse monoclonal antibody Fab mab-1_19A11
6CXY · Cadherin-1: “Crystal structure of human E-cadherin bound by mouse monoclonal antibody Fab mab-1_19A11”. X-ray diffraction, 1 ligand (CA), 3 pockets (best druggability 0.61). MolNFT v1 #145775 on GenesisL1: 3D structure, binding…
- PDB
- 6CXY
- Type
- protein
- Length
- 640 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cadherin-1; Heavy chain; Light chain
- UniProt
- P12830
- Ligands
- CA
- Pockets
- 3 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Cadherin-1 | protein | 213 | 3% helix, 44% strand | P12830 |
| H | Heavy chain | protein | 210 | 10% helix, 53% strand | — |
| L | Light chain | protein | 217 | 6% helix, 55% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 3 copies · chains C
- EDO · 1,2-ethanediol · additive · 18 copies · chains C, L, H
- PG4 · Tetraethylene glycol · additive · chains C
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 | 535 | 0.61 | 0.75 | 62 | EDO |
| 2 | 73 | 0.50 | 0.84 | 24 | empty |
| 3 | 52 | 0.26 | 0.74 | 16 | EDO |
Interfaces
3 interfaces between chains.
- H–L · 1710 Ų buried · 17 hydrogen bonds · protein-protein
- C–H · 511 Ų buried · 9 hydrogen bonds · protein-protein
- C–L · 324 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6CXY · Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody Fab mAb-1_19A11 · the same entry in another collection · chain C against C, 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 0.97
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 6CXY · PDBe 6CXY · UniProt P12830
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