Research workbench
HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342
Analyse HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3MZW
- Type
- protein
- Length
- 622 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Tyrosine kinase-type cell surface receptor HER2; Immunoglobulin G-binding protein a
- EC
- 2.7.10.1
- UniProt
- P04626, P38507
- Ligands
- NAG
- Pockets
- 5 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 18% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Tyrosine kinase-type cell surface receptor HER2 (EC 2.7.10.1) | protein | 569 | 12% helix, 26% strand | P04626 |
| B | Immunoglobulin G-binding protein a | protein | 53 | 79% helix, 0% strand | P38507 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 700 | 0.72 | 0.78 | 88 | empty |
| 2 | 72 | 0.35 | 0.77 | 19 | empty |
| 3 | 61 | 0.33 | 0.76 | 11 | empty |
| 4 | 54 | 0.30 | 0.76 | 17 | empty |
| 5 | 59 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 971 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 22 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3MZW · HER2 extracelluar region with affinity matured 3-helix affibody ZHER2:342 · 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 A against A, TM-score 0.95
- P38507 · AlphaFold monomer V2.0 prediction for immunoglobulin G-binding protein a (P38507) · a predicted model of the same protein · chain B against A, TM-score 0.93
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 P38507
- Elsewhere: RCSB PDB 3MZW · PDBe 3MZW · UniProt P04626 · UniProt P38507
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.