Research workbench
Crystal structure of the Fab fragment of the anti-EGFR antibody 7A7
Analyse Crystal structure of the Fab fragment of the anti-EGFR antibody 7A7 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XKN
- Type
- protein
- Length
- 846 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-EGFR antibody 7A7
- Pockets
- 9 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Anti-EGFR antibody 7A7 | protein | 213 | 7% helix, 51% strand | — |
| B | Anti-EGFR antibody 7A7 | protein | 209 | 6% helix, 52% strand | — |
| D | Anti-EGFR antibody 7A7 | protein | 211 | 6% helix, 53% strand | — |
Ligands and binding sites
- PE4 · 2-{2-[2-(2-{2-[2-(2-ethoxy-ethoxy)-ethoxy]-ethoxy}-ethoxy)-ethoxy]-ethoxy}-ethanol · additive · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 977 | 0.68 | 0.73 | 76 | empty |
| 2 | 540 | 0.62 | 0.75 | 64 | PE4 |
| 3 | 425 | 0.59 | 0.75 | 56 | empty |
| 4 | 87 | 0.39 | 0.77 | 19 | PE4 |
| 5 | 101 | 0.39 | 0.76 | 24 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1631 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1630 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 308 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 47 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 2XKN · Crystal structure of the Fab fragment of the anti-EGFR antibody 7A7 · the same entry in another collection · chain A against A, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Elsewhere: RCSB PDB 2XKN · PDBe 2XKN
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