MolNFT v1 · #167236 · protein
Crystal structure of human E-cadherin bound by mouse monoclonal antibody 66E8FAB
6VEL · 66E8 Fab heavy chain: “Crystal structure of human E-cadherin bound by mouse monoclonal antibody 66E8FAB”. X-ray diffraction, 2 ligands (CA, SO4), 8 pockets (best druggability 0.61). MolNFT v1 #167236 on GenesisL1: 3D structure…
- PDB
- 6VEL
- Type
- protein
- Length
- 630 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 66E8 Fab heavy chain; 66E8 Fab light chain; Ubiquitin-like protein SMT3,CADHERIN-1
- UniProt
- Q12306, P12830
- Ligands
- CA, SO4
- Pockets
- 8 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 66E8 Fab heavy chain | protein | 211 | 9% helix, 52% strand | — |
| L | 66E8 Fab light chain | protein | 210 | 6% helix, 50% strand | — |
| C | Ubiquitin-like protein SMT3,CADHERIN-1 | protein | 209 | 3% helix, 41% strand | Q12306, P12830 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 317 | 0.61 | 0.78 | 36 | SO4 |
| 2 | 94 | 0.51 | 0.83 | 20 | empty |
| 3 | 240 | 0.46 | 0.73 | 41 | empty |
| 4 | 122 | 0.42 | 0.76 | 27 | SO4 |
| 5 | 53 | 0.36 | 0.79 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1730 Ų buried · 15 hydrogen bonds · protein-protein
- H–C · 479 Ų buried · 10 hydrogen bonds · protein-protein
- L–C · 327 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 6VEL · Crystal Structure of Human E-cadherin bound by mouse monoclonal antibody 66E8Fab · the same entry in another collection · chain H against H, 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 0.98
- Q12306 · AlphaFold monomer V2.0 prediction for ubiquitin-like protein SMT3 (Q12306) · a predicted model of the same protein · chain C against A, TM-score 0.21
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 Q12306
- Every structure of UniProt P12830
- Elsewhere: RCSB PDB 6VEL · PDBe 6VEL · UniProt Q12306 · UniProt P12830
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