Research workbench
Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza hemagglutinin (A/PUERTORICO/8/1934)
Analyse Computationally designed inhibitor peptide HB1.6928.2.3 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VLI
- Type
- protein
- Length
- 531 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Computationally designed peptide HB1.6928.2.3
- UniProt
- P03452
- Ligands
- PGF, NAG, BMA
- Pockets
- 4 · best druggability 0.40
Structure
x-ray diffraction · 3 distinct chains · 26% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 322 | 9% helix, 43% strand | P03452 |
| B | Hemagglutinin | protein | 170 | 56% helix, 17% strand | P03452 |
| C | Computationally designed peptide HB1.6928.2.3 | protein | 39 | 33% helix, 38% strand | — |
Ligands and binding sites
- PGF · 2,5,8,11-tetraoxatridecane · ligand · chains A
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 5 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar
- PEG · Di(hydroxyethyl)ether · additive · 3 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 142 | 0.40 | 0.74 | 19 | empty |
| 2 | 107 | 0.39 | 0.75 | 18 | empty |
| 3 | 77 | 0.38 | 0.78 | 22 | empty |
| 4 | 78 | 0.36 | 0.76 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2802 Ų buried · 53 hydrogen bonds · protein-protein
- B–C · 623 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 285 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5VLI · Computationally designed inhibitor peptide HB1.6928.2.3 in complex with influenza… · 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 5VLI · PDBe 5VLI · UniProt P03452
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