MolNFT v1 · #138040 · protein
Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic peptide CP141099 (P6)
5W6R: “Crystal structure of the A/PUERTO RICO/8/1934 (H1N1) influenza virus hemagglutinin in complex with cyclic…”. X-ray diffraction, 3 ligands (ACE, 9WV, NAG), 20 pockets (best druggability 0.81). MolNFT v1 #138040 on GenesisL1: 3D…
- PDB
- 5W6R
- Type
- protein
- Length
- 2,012 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; ACE-PH8-orn-leu-glu-tyr-phe-glu-TRP-leu-ser-9WV
- UniProt
- P03452
- Ligands
- ACE, 9WV, NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Hemagglutinin | protein | 322 | 8% helix, 42% strand | P03452 |
| B, D, F, H | Hemagglutinin | protein | 171 | 56% helix, 15% strand | P03452 |
| M, O, N, Q | ACE-PH8-orn-leu-glu-tyr-phe-glu-TRP-leu-ser-9WV | protein | 10 | 0% helix, 0% strand | — |
Ligands and binding sites
- ACE · Acetyl group · ligand · 4 copies · chains B, M, D, O, F, N, H, Q
- 9WV · Beta-alanyl-3-amino-L-alanine · ligand · 4 copies · chains M, O, N, Q
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 28 copies · chains A, B, C, D, E, F, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1095 | 0.81 | 0.82 | 130 | empty |
| 2 | 125 | 0.79 | 0.97 | 16 | empty |
| 3 | 88 | 0.75 | 0.97 | 32 | empty |
| 4 | 672 | 0.72 | 0.79 | 66 | empty |
| 5 | 603 | 0.72 | 0.80 | 63 | empty |
Interfaces
26 interfaces between chains.
- A–B · 2827 Ų buried · 41 hydrogen bonds · protein-protein
- E–F · 2823 Ų buried · 43 hydrogen bonds · protein-protein
- G–H · 2822 Ų buried · 45 hydrogen bonds · protein-protein
- C–D · 2818 Ų buried · 43 hydrogen bonds · protein-protein
- D–F · 1155 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 20 glycan, 12 covalent, 8 modified (disulfide, N-glycosylation, covalent ligand, nonstandard).
Compared structures
- 5W6R · 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 5W6R · PDBe 5W6R · UniProt P03452
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