MolNFT v1 · #91881 · protein
Crystal structure of Fab CR9114 in complex with a H5N1 influenza virus hemagglutinin
4FQI · Hemagglutinin HA1: “Crystal structure of Fab CR9114 in complex with a H5N1 influenza virus hemagglutinin”. X-ray diffraction, 1 ligand (NAG), 7 pockets (best druggability 0.61). MolNFT v1 #91881 on GenesisL1: 3D structure, binding…
- PDB
- 4FQI
- Type
- protein
- Length
- 926 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1; Hemagglutinin HA2; Antibody CR9114 heavy chain; Antibody CR9114 light…
- UniProt
- Q6DQ33
- Ligands
- NAG
- Pockets
- 7 · best druggability 0.61
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 41% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 | protein | 324 | 10% helix, 41% strand | Q6DQ33 |
| B | Hemagglutinin HA2 | protein | 176 | 57% helix, 13% strand | Q6DQ33 |
| H | Antibody CR9114 heavy chain | protein | 215 | 6% helix, 52% strand | — |
| L | Antibody CR9114 light chain | protein | 211 | 9% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 11 copies · chains A, B, H
- GOL · Glycerol · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 341 | 0.61 | 0.78 | 51 | empty |
| 2 | 322 | 0.54 | 0.75 | 44 | EDO |
| 3 | 95 | 0.40 | 0.77 | 21 | empty |
| 4 | 96 | 0.39 | 0.76 | 22 | empty |
| 5 | 112 | 0.36 | 0.74 | 24 | empty |
Interfaces
5 interfaces between chains.
- A–B · 2560 Ų buried · 39 hydrogen bonds · protein-protein
- H–L · 1524 Ų buried · 10 hydrogen bonds · protein-protein
- B–H · 567 Ų buried · 6 hydrogen bonds · protein-protein
- A–H · 276 Ų buried · 3 hydrogen bonds · protein-protein
- B–L · 18 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide, 4 glycan (disulfide, N-glycosylation).
Compared structures
- 4FQI · Crystal Structure of Fab CR9114 in Complex with a H5N1 influenza virus hemagglutinin · the same entry in another collection · chain L against L, 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 Q6DQ33
- Elsewhere: RCSB PDB 4FQI · PDBe 4FQI · UniProt Q6DQ33
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