Research workbench
Anti-EGFR/HER3 Fab DL11 in complex with domain III of EGFR extracellular region
Analyse Anti-EGFR/HER3 Fab DL11 in complex with domain III of EGFR extracellular region in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3P0Y
- Type
- protein
- Length
- 625 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Epidermal growth factor receptor; Fab DL11 heavy chain; Fab DL11 light chain
- EC
- 2.7.10.1
- UniProt
- P00533
- Ligands
- NAG, FUL
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 42% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Epidermal growth factor receptor (EC 2.7.10.1) | protein | 194 | 21% helix, 21% strand | P00533 |
| H | Fab DL11 heavy chain | protein | 218 | 6% helix, 52% strand | — |
| L | Fab DL11 light chain | protein | 213 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- FUL · beta-L-fucopyranose · sugar
- GOL · Glycerol · additive · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 637 | 0.64 | 0.75 | 51 | empty |
| 2 | 436 | 0.62 | 0.76 | 56 | empty |
| 3 | 101 | 0.36 | 0.74 | 26 | empty |
| 4 | 106 | 0.36 | 0.74 | 27 | empty |
| 5 | 51 | 0.30 | 0.76 | 11 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1854 Ų buried · 22 hydrogen bonds · protein-protein
- A–H · 744 Ų buried · 16 hydrogen bonds · protein-protein
- A–L · 149 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3P0Y · anti-EGFR/HER3 Fab DL11 in complex with domain III of EGFR extracellular region · the same entry in another collection · chain L against L, TM-score 1.00
- P00533 · AlphaFold monomer V2.0 prediction for epidermal growth factor receptor (P00533) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P00533
- Elsewhere: RCSB PDB 3P0Y · PDBe 3P0Y · UniProt P00533
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