MolNFT v1 · #64716 · protein
Crystal structure of Fab CR6261 in complex with the 1918 H1N1 influenza virus hemagglutinin
3GBN: “Crystal structure of Fab CR6261 in complex with the 1918 H1N1 influenza virus hemagglutinin”. X-ray diffraction, 6 ligands (ETX, UNL, NAG), 9 pockets (best druggability 0.42). MolNFT v1 #64716 on GenesisL1: 3D structure, binding…
- 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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