Research workbench
Trastuzumab Fab complexed with Protein L and Protein A fragments
Analyse Trastuzumab Fab complexed with Protein L and Protein A fragments in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4HKZ
- Type
- protein
- Length
- 551 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.08
- Source
- FINEGOLDIA MAGNA; Homo sapiens; Staphylococcus aureus
- Molecule
- Trastuzumab light chain; Trastuzumab heavy chain; Immunoglobulin G-binding protein A…
- UniProt
- P0A015
- Ligands
- CL
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · resolution 2.08 · 4 distinct chains · 17% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Trastuzumab light chain | protein | 213 | 6% helix, 52% strand | — |
| B | Trastuzumab heavy chain | protein | 221 | 8% helix, 52% strand | — |
| H | Immunoglobulin G-binding protein A | protein | 54 | 76% helix, 0% strand | P0A015 |
| E | Protein L fragment | protein | 63 | 35% helix, 44% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 725 | 0.65 | 0.74 | 79 | empty |
| 2 | 68 | 0.52 | 0.87 | 23 | empty |
| 3 | 79 | 0.45 | 0.81 | 21 | empty |
| 4 | 147 | 0.43 | 0.75 | 26 | empty |
| 5 | 105 | 0.35 | 0.73 | 26 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1887 Ų buried · 19 hydrogen bonds · protein-protein
- A–E · 724 Ų buried · 11 hydrogen bonds · protein-protein
- B–H · 586 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4HKZ · Trastuzumab Fab complexed with protein L and protein a fragments · the same entry in another collection · chain A against A, TM-score 1.00
- P0A015 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P0A015) · a predicted model of the same protein · chain H against A, TM-score 0.88
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 P0A015
- Elsewhere: RCSB PDB 4HKZ · PDBe 4HKZ · UniProt P0A015
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