MolNFT v1 · #157411 · protein
Crystal structure of INVBP.18715.A.KN11: influenza hemagglutinin from strain A/ALMATY/32/1998
6MYA: “Crystal structure of INVBP.18715.A.KN11: influenza hemagglutinin from strain A/ALMATY/32/1998”. X-ray diffraction, 1 ligand (NAG), 20 pockets (best druggability 0.81). MolNFT v1 #157411 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6MYA
- Type
- protein
- Length
- 2,907 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 6 distinct chains · 25% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 488 | 25% helix, 32% strand | — |
| B | Hemagglutinin | protein | 482 | 25% helix, 32% strand | — |
| C | Hemagglutinin | protein | 486 | 24% helix, 34% strand | — |
| D | Hemagglutinin | protein | 478 | 24% helix, 31% strand | — |
| E | Hemagglutinin | protein | 489 | 25% helix, 32% strand | — |
| F | Hemagglutinin | protein | 484 | 24% helix, 32% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 22 copies · chains B, D, E, A, C, F
- EDO · 1,2-ethanediol · additive · 22 copies · chains A, B, C, D, E, F
- PEG · Di(hydroxyethyl)ether · additive · chains 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 135 | 0.81 | 0.98 | 15 | EDO |
| 2 | 123 | 0.80 | 0.98 | 15 | empty |
| 3 | 1108 | 0.78 | 0.80 | 124 | empty |
| 4 | 1200 | 0.76 | 0.78 | 114 | empty |
| 5 | 642 | 0.73 | 0.80 | 58 | EDO |
Interfaces
7 interfaces between chains.
- B–C · 2051 Ų buried · 27 hydrogen bonds · protein-protein
- E–F · 2018 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2017 Ų buried · 26 hydrogen bonds · protein-protein
- D–E · 1989 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 1960 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 36 disulfide, 19 glycan (disulfide, N-glycosylation).
Compared structures
- 6MYA · Crystal structure of InvbP.18715.a.KN11: Influenza hemagglutinin from strain… · 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
- Elsewhere: RCSB PDB 6MYA · PDBe 6MYA
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