Research workbench
Crystal structure of the de novo designed binding protein HB36.3 in complex the the 1918 influenza virus hemagglutinin
Analyse Crystal structure of the de novo designed binding protein HB36.3 in complex the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3R2X
- Type
- protein
- Length
- 575 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; HB36.3, designed hemagglutinin binding protein
- UniProt
- Q9WFX3
- Ligands
- NAG, BMA, MAN
- Pockets
- 2 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 33% helix, 27% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 9% helix, 41% strand | Q9WFX3 |
| B | Hemagglutinin | protein | 171 | 56% helix, 13% strand | Q9WFX3 |
| C | HB36.3, designed hemagglutinin binding protein | protein | 82 | 78% helix, 0% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 395 | 0.60 | 0.76 | 42 | empty |
| 2 | 193 | 0.49 | 0.76 | 28 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2715 Ų buried · 48 hydrogen bonds · protein-protein
- B–C · 597 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 295 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 3R2X · Crystal structure of the de novo designed binding protein HB36.3 in complex the the 1918… · the same entry in another collection · chain B against B, TM-score 1.00
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 Q9WFX3
- Elsewhere: RCSB PDB 3R2X · PDBe 3R2X · UniProt Q9WFX3
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