Research workbench
Crystal structure of epcam in complex with scfv
Analyse Crystal structure of epcam in complex with scfv in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6I07
- Type
- protein
- Length
- 906 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Single chain fv; Epithelial cell adhesion molecule
- UniProt
- P16422
- Pockets
- 16 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Single chain fv | protein | 228 | 4% helix, 51% strand | — |
| B | Single chain fv | protein | 226 | 4% helix, 47% strand | — |
| C | Epithelial cell adhesion molecule | protein | 225 | 19% helix, 25% strand | P16422 |
| D | Epithelial cell adhesion molecule | protein | 227 | 18% helix, 25% strand | P16422 |
Ligands and binding sites
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1074 | 0.79 | 0.80 | 88 | empty |
| 2 | 200 | 0.53 | 0.78 | 32 | empty |
| 3 | 106 | 0.50 | 0.81 | 18 | empty |
| 4 | 171 | 0.50 | 0.77 | 22 | empty |
| 5 | 148 | 0.47 | 0.77 | 20 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1339 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 943 Ų buried · 21 hydrogen bonds · protein-protein
- B–D · 880 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 2 modified (disulfide, cyclization).
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 P16422
- Elsewhere: RCSB PDB 6I07 · PDBe 6I07 · UniProt P16422
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