Research workbench
Crystal structure of extracellular domain of HER2 in complex with fcab STAB19
Analyse Crystal structure of extracellular domain of HER2 in complex with fcab STAB19 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K33
- Type
- protein
- Length
- 776 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; Receptor tyrosine-protein kinase erbb-2
- EC
- 2.7.10.1
- UniProt
- P01857, P04626
- Ligands
- NAG, MAN, BMA
- Pockets
- 6 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 11% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ig gamma-1 chain C region | protein | 213 | 12% helix, 46% strand | P01857 |
| C | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 563 | 11% helix, 25% strand | P04626 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, C
- MAN · alpha-D-mannopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, C
- GOL · Glycerol · additive · chains A
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 | 584 | 0.68 | 0.77 | 63 | empty |
| 2 | 135 | 0.52 | 0.80 | 24 | empty |
| 3 | 148 | 0.45 | 0.76 | 26 | NAG |
| 4 | 75 | 0.42 | 0.80 | 18 | empty |
| 5 | 50 | 0.30 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–C · 663 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 5K33 · Crystal structure of extracellular domain of HER2 in complex with Fcab STAB19 · the same entry in another collection · chain A against A, 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 0.97
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 P01857
- Every structure of UniProt P04626
- Elsewhere: RCSB PDB 5K33 · PDBe 5K33 · UniProt P01857 · UniProt P04626
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