Research workbench
Crystal structure of the A/VIET NAM/1203/2004(H5N1) influenza virus hemagglutinin in complex with small molecule N-cyclohexyltaurine
Analyse Crystal structure of the A/VIET NAM/1203/2004(H5N1) influenza virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6CF5
- Type
- protein
- Length
- 1,497 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q5EP31, Q6DQ18
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.87
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 324 | 10% helix, 41% strand | Q5EP31 |
| B, D | Hemagglutinin | protein | 176 | 57% helix, 13% strand | Q6DQ18 |
| C, E | Hemagglutinin | protein | 323 | 10% helix, 41% strand | Q5EP31 |
| F | Hemagglutinin | protein | 175 | 58% helix, 13% strand | Q6DQ18 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, E, C
- PEG · Di(hydroxyethyl)ether · additive · 9 copies · chains A, B, C, D, F, E
- GOL · Glycerol · additive · 4 copies · chains A, B, C, D, E, F
- NHE · 2-[N-cyclohexylamino]ethane sulfonic acid · additive · 3 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1187 | 0.87 | 0.88 | 144 | PEG |
| 2 | 70 | 0.75 | 0.98 | 15 | empty |
| 3 | 348 | 0.64 | 0.79 | 44 | empty |
| 4 | 390 | 0.64 | 0.78 | 43 | empty |
| 5 | 287 | 0.63 | 0.80 | 42 | empty |
Interfaces
15 interfaces between chains.
- A–B · 2529 Ų buried · 37 hydrogen bonds · protein-protein
- E–F · 2528 Ų buried · 40 hydrogen bonds · protein-protein
- C–D · 2525 Ų buried · 39 hydrogen bonds · protein-protein
- D–F · 1472 Ų buried · 16 hydrogen bonds · protein-protein
- B–F · 1453 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 18 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6CF5 · Crystal structure of the A/Viet Nam/1203/2004(H5N1) influenza virus hemagglutinin in… · the same entry in another collection · chain C against C, 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 Q5EP31
- Every structure of UniProt Q6DQ18
- Elsewhere: RCSB PDB 6CF5 · PDBe 6CF5 · UniProt Q5EP31 · UniProt Q6DQ18
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