Research workbench
Cryo-EM structure of HER2 extracellular domain-trastuzumab Fab- pertuzumab Fab complex
Analyse Cryo-EM structure of HER2 extracellular domain-trastuzumab Fab- pertuzumab Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OGE
- Type
- protein
- Length
- 1,489 residues
- Chains
- 5
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; Pertuzumab Fab light chain; Pertuzumab Fab heavy…
- EC
- 2.7.10.1
- UniProt
- P04626, P01834, P0DOX5, Q6GMX6
- Ligands
- NAG, BMA, MAN
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 5 distinct chains · 5% helix, 26% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 619 | 7% helix, 19% strand | P04626 |
| B | Pertuzumab Fab light chain | protein | 214 | 5% helix, 40% strand | P01834 |
| C | Pertuzumab Fab heavy chain | protein | 222 | 3% helix, 40% strand | P0DOX5 |
| D | Trastuzumab Fab light chain | protein | 214 | 1% helix, 20% strand | P01834 |
| E | Trastuzumab Fab heavy chain | protein | 220 | 3% helix, 23% strand | Q6GMX6 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 814 | 0.78 | 0.81 | 73 | empty |
| 2 | 113 | 0.75 | 0.95 | 39 | empty |
| 3 | 325 | 0.72 | 0.85 | 49 | empty |
| 4 | 55 | 0.71 | 0.98 | 21 | empty |
| 5 | 287 | 0.64 | 0.81 | 44 | empty |
Interfaces
6 interfaces between chains.
- D–E · 1951 Ų buried · 16 hydrogen bonds · protein-protein
- B–C · 1736 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 930 Ų buried · 13 hydrogen bonds · protein-protein
- A–E · 541 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 447 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 34 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6OGE · Cryo-EM structure of Her2 extracellular domain-Trastuzumab Fab-Pertuzumab Fab complex · the same entry in another collection · chain E against E, 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 A against A, TM-score 0.92
- P01834 · AlphaFold monomer V2.0 prediction for immunoglobulin kappa constant (P01834) · a predicted model of the same protein · chain B against A, TM-score 0.48
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 P01834
- Every structure of UniProt P0DOX5
- Every structure of UniProt Q6GMX6
- Elsewhere: RCSB PDB 6OGE · PDBe 6OGE · UniProt P04626 · UniProt P01834 · UniProt P0DOX5 · UniProt Q6GMX6
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