MolNFT v1 · #74576 · protein
Anti-EGFR/HER3 Fab DL11 alone
3P0V · Fab DL11 light chain: “Anti-EGFR/HER3 Fab DL11 alone”. X-ray diffraction, 1 ligand (CA), 9 pockets (best druggability 0.61). MolNFT v1 #74576 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 3P0V
- Type
- protein
- Length
- 861 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab DL11 light chain; Fab DL11 heavy chain
- Ligands
- CA
- Pockets
- 9 · best druggability 0.61
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L, M | Fab DL11 light chain | protein | 212 | 6% helix, 52% strand | — |
| H | Fab DL11 heavy chain | protein | 218 | 3% helix, 55% strand | — |
| I | Fab DL11 heavy chain | protein | 219 | 3% helix, 52% strand | — |
Ligands and binding sites
- CA · Calcium ion · metal · 4 copies · chains L, H, M, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 596 | 0.61 | 0.74 | 67 | empty |
| 2 | 566 | 0.61 | 0.74 | 56 | empty |
| 3 | 130 | 0.38 | 0.74 | 20 | empty |
| 4 | 107 | 0.37 | 0.74 | 24 | empty |
| 5 | 91 | 0.34 | 0.74 | 24 | empty |
Interfaces
3 interfaces between chains.
- M–I · 1903 Ų buried · 18 hydrogen bonds · protein-protein
- L–H · 1843 Ų buried · 21 hydrogen bonds · protein-protein
- H–I · 275 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3P0V · anti-EGFR/HER3 Fab DL11 alone · the same entry in another collection · chain L against L, 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 3P0V · PDBe 3P0V
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