MolNFT v1 · #94082 · protein
Crystal structure of Fab C179 in complex with a H2N2 influenza virus hemagglutinin
4HLZ · Hemagglutinin HA1: “Crystal structure of Fab C179 in complex with a H2N2 influenza virus hemagglutinin”. X-ray diffraction, 4 ligands (NAG, BMA, MAN), 20 pockets (best druggability 0.82). MolNFT v1 #94082 on GenesisL1: 3D structure…
- PDB
- 4HLZ
- Type
- protein
- Length
- 2,754 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Fab C179 heavy chain; Fab C179 light chain
- UniProt
- C7S226
- Ligands
- NAG, BMA, MAN, SO4
- Pockets
- 20 · best druggability 0.82
Structure
x-ray diffraction · 10 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 | protein | 324 | 9% helix, 40% strand | C7S226 |
| B | Hemagglutinin HA2 | protein | 168 | 58% helix, 14% strand | C7S226 |
| D | Hemagglutinin HA2 | protein | 170 | 58% helix, 12% strand | C7S226 |
| F | Hemagglutinin HA2 | protein | 172 | 58% helix, 13% strand | C7S226 |
| G | Fab C179 heavy chain | protein | 223 | 5% helix, 47% strand | — |
| H | Fab C179 light chain | protein | 211 | 6% helix, 50% strand | — |
| I | Fab C179 heavy chain | protein | 221 | 4% helix, 45% strand | — |
| J | Fab C179 light chain | protein | 212 | 7% helix, 50% strand | — |
| K | Fab C179 heavy chain | protein | 200 | 3% helix, 45% strand | — |
| L | Fab C179 light chain | protein | 205 | 2% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains A, G, C, I, E, K, F, B, L
- BMA · beta-D-mannopyranose · sugar · 3 copies · chains G, I
- MAN · alpha-D-mannopyranose · sugar
- SO4 · Sulfate ion · ion · 7 copies · chains B, H, D, J, E, F, L
- EDO · 1,2-ethanediol · additive · chains J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 787 | 0.82 | 0.85 | 57 | empty |
| 2 | 927 | 0.80 | 0.81 | 146 | empty |
| 3 | 86 | 0.77 | 0.98 | 15 | empty |
| 4 | 728 | 0.73 | 0.79 | 84 | SO4 |
| 5 | 501 | 0.71 | 0.80 | 52 | empty |
Interfaces
27 interfaces between chains.
- C–D · 2624 Ų buried · 40 hydrogen bonds · protein-protein
- E–F · 2604 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2600 Ų buried · 42 hydrogen bonds · protein-protein
- I–J · 1883 Ų buried · 16 hydrogen bonds · protein-protein
- G–H · 1842 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 disulfide, 10 glycan (disulfide, N-glycosylation).
Compared structures
- 4HLZ · Crystal Structure of Fab C179 in Complex with a H2N2 influenza virus hemagglutinin · 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 C7S226
- Elsewhere: RCSB PDB 4HLZ · PDBe 4HLZ · UniProt C7S226
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