MolNFT v1 · #64524 · protein
Antibodies specifically targeting a locally misfolded region of tumor associated EGFR
3G5V · 806 light chain: “Antibodies specifically targeting a locally misfolded region of tumor associated EGFR”. X-ray diffraction, 4 pockets (best druggability 0.63). MolNFT v1 #64524 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 3G5V
- Type
- protein
- Length
- 428 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 806 light chain; 808 heavy chain; Epidermal growth factor receptor peptide
- Pockets
- 4 · best druggability 0.63
Structure
x-ray diffraction · 3 distinct chains · 5% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | 806 light chain | protein | 212 | 6% helix, 51% strand | — |
| B | 808 heavy chain | protein | 200 | 5% helix, 49% strand | — |
| C | Epidermal growth factor receptor peptide | protein | 16 | 0% helix, 38% strand | — |
Ligands and binding sites
- FMT · Formic acid · additive · 3 copies · chains B, C
- ACT · Acetate ion · additive · 2 copies · chains A, C
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 95 | 0.63 | 0.89 | 26 | empty |
| 2 | 409 | 0.59 | 0.75 | 49 | GOL |
| 3 | 125 | 0.41 | 0.75 | 29 | ACT |
| 4 | 60 | 0.27 | 0.73 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1864 Ų buried · 18 hydrogen bonds · protein-protein
- B–C · 375 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 338 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 3G5V · Antibodies Specifically Targeting a Locally Misfolded Region of Tumor Associated EGFR · 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 3G5V · PDBe 3G5V
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