Research workbench
Crystal structure of Fab CR6261 in complex with the 1918 H1N1 influenza virus hemagglutinin
Analyse Crystal structure of Fab CR6261 in complex with the 1918 H1N1 influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GBN
- Type
- protein
- Length
- 812 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Fab heavy chain; Fab lambda light chain
- UniProt
- Q9WFX3
- Ligands
- ETX, UNL, NAG, BMA, MAN, CL
- Pockets
- 9 · best druggability 0.42
Structure
x-ray diffraction · 4 distinct chains · 17% helix, 37% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 328 | 8% helix, 39% strand | Q9WFX3 |
| B | Hemagglutinin | protein | 173 | 57% helix, 14% strand | Q9WFX3 |
| H | Fab heavy chain | protein | 160 | 4% helix, 45% strand | — |
| L | Fab lambda light chain | protein | 151 | 4% helix, 52% strand | — |
Ligands and binding sites
- ETX · 2-ethoxyethanol · ligand · chains A, B
- UNL · Unknown ligand · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- MAN · alpha-D-mannopyranose · sugar
- CL · Chloride ion · ion · chains B
- EDO · 1,2-ethanediol · additive · 5 copies · chains A, B, H
- GOL · Glycerol · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 146 | 0.42 | 0.74 | 22 | empty |
| 2 | 135 | 0.41 | 0.75 | 20 | empty |
| 3 | 99 | 0.41 | 0.77 | 14 | empty |
| 4 | 64 | 0.40 | 0.80 | 15 | empty |
| 5 | 80 | 0.37 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 2982 Ų buried · 61 hydrogen bonds · protein-protein
- H–L · 1418 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 599 Ų buried · 9 hydrogen bonds · protein-protein
- A–H · 287 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 3GBN · Crystal Structure of Fab CR6261 in Complex with the 1918 H1N1 influenza virus… · the same entry in another collection · chain A against A, 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 3GBN · PDBe 3GBN · UniProt Q9WFX3
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