Research workbench
Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and light chain interfaces
Analyse Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5TDN
- Type
- protein
- Length
- 853 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-HER2 Fab light chain; Anti-HER2 Fab heavy chain
- Pockets
- 10 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Anti-HER2 Fab light chain | protein | 213 | 6% helix, 50% strand | — |
| B | Anti-HER2 Fab heavy chain | protein | 214 | 8% helix, 51% strand | — |
| D | Anti-HER2 Fab heavy chain | protein | 213 | 12% helix, 54% strand | — |
Ligands and binding sites
- GOL · Glycerol · additive · 3 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 493 | 0.59 | 0.74 | 45 | empty |
| 2 | 260 | 0.56 | 0.77 | 35 | GOL |
| 3 | 191 | 0.52 | 0.78 | 26 | empty |
| 4 | 207 | 0.45 | 0.73 | 29 | empty |
| 5 | 189 | 0.44 | 0.74 | 35 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1793 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1757 Ų buried · 12 hydrogen bonds · protein-protein
- B–D · 712 Ų buried · 16 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5TDN · Crystal structure of the Fab fragment of anti-HER2 antibody 4D5 with redesigned heavy and… · 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 5TDN · PDBe 5TDN
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