Research workbench
Molecular architecture of the ERBB2 extracellular domain homodimer
Analyse Molecular architecture of the ERBB2 extracellular domain homodimer in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3WLW
- Type
- protein
- Length
- 1,978 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Receptor tyrosine-protein kinase erbb-2; Antibody H chain; Antibody L chain
- EC
- 2.7.10.1
- UniProt
- P04626
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 555 | 11% helix, 23% strand | P04626 |
| H, C | Antibody H chain | protein | 217 | 3% helix, 41% strand | — |
| L, D | Antibody L chain | protein | 217 | 2% helix, 33% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
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 | 1023 | 0.81 | 0.82 | 105 | empty |
| 2 | 670 | 0.73 | 0.79 | 82 | empty |
| 3 | 54 | 0.67 | 0.96 | 26 | empty |
| 4 | 476 | 0.65 | 0.78 | 63 | empty |
| 5 | 446 | 0.59 | 0.75 | 48 | empty |
Interfaces
7 interfaces between chains.
- C–D · 1964 Ų buried · 14 hydrogen bonds · protein-protein
- H–L · 1899 Ų buried · 15 hydrogen bonds · protein-protein
- A–B · 635 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 527 Ų buried · 7 hydrogen bonds · protein-protein
- B–H · 527 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 50 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 3WLW · Molecular Architecture of the ErbB2 Extracellular Domain Homodimer · the same entry in another collection · chain D against D, 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 0.97
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 P04626
- Elsewhere: RCSB PDB 3WLW · PDBe 3WLW · UniProt P04626
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