Research workbench
Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP151070 (P7)
Analyse Crystal structure of the A/PUERTO RICO/8/1934 (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
- 5W6T
- Type
- protein
- Length
- 503 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; ACE-PH8-orn-mle-glu-tyr-zcl-glu-TRP-leu-ser-9WV
- UniProt
- P03452
- Ligands
- ACE, 9WV, NAG, CL
- Pockets
- 4 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 8% helix, 43% strand | P03452 |
| B | Hemagglutinin | protein | 171 | 56% helix, 13% strand | P03452 |
| F | ACE-PH8-orn-mle-glu-tyr-zcl-glu-TRP-leu-ser-9WV | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, F
- 9WV · Beta-alanyl-3-amino-L-alanine · ligand · chains F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains A
- CL · Chloride ion · ion · chains B
- GOL · Glycerol · additive · 2 copies · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 67 | 0.54 | 0.87 | 20 | empty |
| 2 | 160 | 0.46 | 0.76 | 21 | empty |
| 3 | 63 | 0.34 | 0.77 | 15 | empty |
| 4 | 51 | 0.27 | 0.75 | 16 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2780 Ų buried · 48 hydrogen bonds · protein-protein
- B–F · 502 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 214 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 4 covalent, 4 modified, 3 glycan (disulfide, nonstandard, covalent ligand, N-glycosylation, additive adduct).
Compared structures
- 5W6T · Crystal structure of the A/Puerto Rico/8/1934 (H1N1) influenza virus hemagglutinin in… · 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 P03452
- Elsewhere: RCSB PDB 5W6T · PDBe 5W6T · UniProt P03452
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