MolNFT v1 · #124035 · protein
Crystal structure of extracellular domain of HER2 in complex with fcab STAB19
5K33 · Ig gamma-1 chain C region: “Crystal structure of extracellular domain of HER2 in complex with fcab STAB19”. X-ray diffraction, 3 ligands (NAG, MAN, BMA), 6 pockets (best druggability 0.68). MolNFT v1 #124035 on GenesisL1: 3D…
- 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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