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Crystal structure of HER2 domain IV and rb-H2
Analyse Crystal structure of HER2 domain IV and rb-H2 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6LBX
- Type
- protein
- Length
- 337 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Repebody (rb-H2); Receptor tyrosine-protein kinase erbb-2
- EC
- 2.7.10.1
- UniProt
- P04626
- Ligands
- NAG
- Pockets
- 1 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Repebody (rb-H2) | protein | 265 | 15% helix, 13% strand | — |
| B | Receptor tyrosine-protein kinase erbb-2 (EC 2.7.10.1) | protein | 72 | 0% helix, 33% strand | P04626 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 628 | 0.72 | 0.79 | 49 | empty |
Interfaces
1 interface between chains.
- A–B · 792 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
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 6LBX · PDBe 6LBX · UniProt P04626
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