MolNFT v1 · #138006 · protein
Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141019 (P5)
5W5S: “Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic…”. X-ray diffraction, 3 ligands (ACE, NAG, CL), 5 pockets (best druggability 0.55). MolNFT v1 #138006 on GenesisL1: 3D…
- PDB
- 5W5S
- Type
- protein
- Length
- 504 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; ACE-PH8-orn-leu-glu-tyr-zcl-glu-TRP-leu-ser-bal
- UniProt
- P03452
- Ligands
- ACE, NAG, CL
- Pockets
- 5 · best druggability 0.55
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, 42% strand | P03452 |
| B | Hemagglutinin | protein | 171 | 56% helix, 15% strand | P03452 |
| D | ACE-PH8-orn-leu-glu-tyr-zcl-glu-TRP-leu-ser-bal | protein | 11 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · chains B, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- CL · Chloride ion · ion · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 80 | 0.55 | 0.86 | 19 | empty |
| 2 | 162 | 0.45 | 0.75 | 20 | empty |
| 3 | 86 | 0.38 | 0.77 | 21 | empty |
| 4 | 68 | 0.36 | 0.77 | 14 | empty |
| 5 | 50 | 0.26 | 0.74 | 18 | empty |
Interfaces
3 interfaces between chains.
- A–B · 2784 Ų buried · 50 hydrogen bonds · protein-protein
- B–D · 501 Ų buried · 4 hydrogen bonds · protein-protein
- A–D · 213 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 6 disulfide, 5 glycan, 4 modified, 1 covalent (disulfide, N-glycosylation, nonstandard, covalent ligand).
Compared structures
- 5W5S · 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 5W5S · PDBe 5W5S · UniProt P03452
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