MolNFT v2 · #222427 · protein
CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody 09-1B12
8UT4 · Hemagglutinin HA1 chain: “CryoEM structure of A/Michigan/45/2015 H1 in complex with flu HA central stem VH1-18 antibody 09-1B12”. Electron microscopy at 3.3, 1 ligand (NAG), 20 pockets (best druggability 0.84). MolNFT v2 #222427 on…
- PDB
- 8UT4
- Type
- protein
- Length
- 1,694 residues
- Chains
- 8
- Method
- electron microscopy
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 3.3
- Source
- Homo sapiens; Influenza A virus
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; 09-1B12 HC Fv; 09-1B12 LC Fv
- UniProt
- A0A6J3XHU5, A0A6G7M316
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.84
Structure
electron microscopy · resolution 3.3 · 4 distinct chains · 17% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 323 | 7% helix, 40% strand | A0A6J3XHU5 |
| B, D, F | Hemagglutinin HA2 chain | protein | 164 | 52% helix, 13% strand | A0A6G7M316 |
| I | 09-1B12 HC Fv | protein | 126 | 5% helix, 24% strand | — |
| H | 09-1B12 LC Fv | protein | 107 | 6% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 18 copies · chains A, B, C, D, E, H, F
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 | 213 | 0.84 | 0.97 | 30 | empty |
| 2 | 332 | 0.76 | 0.87 | 59 | empty |
| 3 | 319 | 0.76 | 0.87 | 55 | empty |
| 4 | 977 | 0.73 | 0.77 | 90 | empty |
| 5 | 236 | 0.73 | 0.88 | 43 | empty |
Interfaces
20 interfaces between chains.
- A–B · 2838 Ų buried · 41 hydrogen bonds · protein-protein
- C–D · 2810 Ų buried · 31 hydrogen bonds · protein-protein
- E–F · 2772 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 1214 Ų buried · 8 hydrogen bonds · protein-protein
- B–F · 1198 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 17 glycan, 15 disulfide (N-glycosylation, disulfide).
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 A0A6J3XHU5
- Every structure of UniProt A0A6G7M316
- Elsewhere: RCSB PDB 8UT4 · PDBe 8UT4 · UniProt A0A6J3XHU5 · UniProt A0A6G7M316
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.