Research workbench
X-ray structures of the antigen-binding domains from three variants of humanized anti-P185-HER2 antibody 4D5 and comparison with molecular modeling
Analyse X-ray structures of the antigen-binding domains from three variants of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FVD
- Type
- protein
- Length
- 874 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa 4D5 Fab (light chain); IGG1-kappa 4D5 Fab (heavy chain)
- Pockets
- 11 · best druggability 0.57
Structure
x-ray diffraction · 2 distinct chains · 4% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | IGG1-kappa 4D5 Fab (light chain) | protein | 214 | 4% helix, 50% strand | — |
| B, D | IGG1-kappa 4D5 Fab (heavy chain) | protein | 223 | 4% helix, 51% strand | — |
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.57 | 0.76 | 40 | empty |
| 2 | 52 | 0.54 | 0.89 | 20 | empty |
| 3 | 64 | 0.54 | 0.88 | 22 | empty |
| 4 | 154 | 0.49 | 0.78 | 22 | empty |
| 5 | 230 | 0.45 | 0.73 | 34 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1873 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1844 Ų buried · 11 hydrogen bonds · protein-protein
- A–C · 377 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1FVD · X-ray structures of the antigen-binding domains from three variants of humanized… · 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 1FVD · PDBe 1FVD
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