Research workbench
Structure of trastuzumab Fab mutant in complex with HER2 extracellular domain
Analyse Structure of trastuzumab Fab mutant in complex with HER2 extracellular domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BGT
- Type
- protein
- Length
- 1,010 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; Herceptin light chain mutant; Herceptin heavy…
- EC
- 2.7.10.1
- UniProt
- P04626, Q7Z3Y4, P0DOX5
- Ligands
- NAG
- Pockets
- 11 · best druggability 0.65
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 589 | 12% helix, 27% strand | P04626 |
| A | Herceptin light chain mutant | protein | 211 | 6% helix, 53% strand | Q7Z3Y4 |
| B | Herceptin heavy chain Fab fragment mutant | protein | 210 | 6% helix, 52% strand | P0DOX5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 450 | 0.65 | 0.78 | 52 | empty |
| 2 | 542 | 0.61 | 0.74 | 62 | empty |
| 3 | 114 | 0.57 | 0.84 | 29 | empty |
| 4 | 153 | 0.53 | 0.79 | 27 | empty |
| 5 | 80 | 0.41 | 0.79 | 24 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1744 Ų buried · 13 hydrogen bonds · protein-protein
- C–B · 605 Ų buried · 7 hydrogen bonds · protein-protein
- C–A · 491 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6BGT · Structure of Trastuzumab Fab mutant in complex with Her2 extracellular domain · the same entry in another collection · chain C against C, TM-score 1.00
- P04626 · AlphaFold monomer V2.0 prediction for receptor tyrosine-protein kinase erbb-2 (P04626) · a predicted model of the same protein · chain C against A, TM-score 0.95
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 P04626
- Every structure of UniProt Q7Z3Y4
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 6BGT · PDBe 6BGT · UniProt P04626 · UniProt Q7Z3Y4 · UniProt P0DOX5
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