Research workbench
Crystal structure of a H5N1 influenza virus hemagglutinin with CBS1117
Analyse Crystal structure of a H5N1 influenza virus hemagglutinin with CBS1117 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6VMZ
- Type
- protein
- Length
- 1,454 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- UniProt
- Q1KHJ8, Q1KHK7
- Ligands
- R3P, NAG
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 4 distinct chains · 24% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 320 | 10% helix, 41% strand | Q1KHJ8 |
| C, E | Hemagglutinin | protein | 322 | 10% helix, 41% strand | Q1KHJ8 |
| B, D | Hemagglutinin | protein | 174 | 55% helix, 11% strand | Q1KHK7 |
| F | Hemagglutinin | protein | 142 | 53% helix, 13% strand | Q1KHK7 |
Ligands and binding sites
- R3P · 2,6-dichloro-N-[1-(propan-2-yl)piperidin-4-yl]benzamide · ligand · 3 copies · chains A, B, C, D, E, F
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 371 | 0.80 | 0.89 | 65 | empty |
| 2 | 73 | 0.76 | 0.99 | 16 | empty |
| 3 | 259 | 0.76 | 0.89 | 42 | empty |
| 4 | 137 | 0.66 | 0.88 | 29 | empty |
| 5 | 429 | 0.65 | 0.78 | 50 | empty |
Interfaces
15 interfaces between chains.
- C–D · 2565 Ų buried · 35 hydrogen bonds · protein-protein
- A–B · 2526 Ų buried · 30 hydrogen bonds · protein-protein
- E–F · 2503 Ų buried · 36 hydrogen bonds · protein-protein
- B–D · 1440 Ų buried · 12 hydrogen bonds · protein-protein
- B–F · 1355 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 6VMZ · Crystal Structure of a H5N1 influenza virus hemagglutinin with CBS1117 · 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 Q1KHJ8
- Every structure of UniProt Q1KHK7
- Elsewhere: RCSB PDB 6VMZ · PDBe 6VMZ · UniProt Q1KHJ8 · UniProt Q1KHK7
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