Research workbench
Cryoem structure of influenza hemagglutinin A/MICHIGAN/45/2015 in complex with cyno antibody 1C4
Analyse Cryoem structure of influenza hemagglutinin A/MICHIGAN/45/2015 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6XGC
- Type
- protein
- Length
- 2,157 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; 1C4 Fab heavy chain; 1C4 Fab light chain
- UniProt
- A0A3Q8LWJ2, A0A482NTT4
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.74
Structure
electron microscopy · 4 distinct chains · 17% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E | Hemagglutinin HA1 chain | protein | 323 | 7% helix, 37% strand | A0A3Q8LWJ2 |
| B, D, F | Hemagglutinin HA2 chain | protein | 164 | 57% helix, 14% strand | A0A482NTT4 |
| M, H, I | 1C4 Fab heavy chain | protein | 125 | 2% helix, 54% strand | — |
| N, L, J | 1C4 Fab light chain | protein | 107 | 4% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, C, E, B, D, 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 86 | 0.74 | 0.96 | 16 | empty |
| 2 | 107 | 0.74 | 0.95 | 23 | empty |
| 3 | 106 | 0.74 | 0.95 | 24 | empty |
| 4 | 758 | 0.73 | 0.78 | 76 | empty |
| 5 | 116 | 0.73 | 0.93 | 29 | empty |
Interfaces
24 interfaces between chains.
- C–D · 2705 Ų buried · 33 hydrogen bonds · protein-protein
- A–B · 2702 Ų buried · 33 hydrogen bonds · protein-protein
- E–F · 2692 Ų buried · 30 hydrogen bonds · protein-protein
- D–F · 1234 Ų buried · 16 hydrogen bonds · protein-protein
- B–D · 1197 Ų buried · 15 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 6XGC · CryoEM structure of influenza hemagglutinin A/Michigan/45/2015 in complex with cyno… · the same entry in another collection · chain M against M, 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 A0A3Q8LWJ2
- Every structure of UniProt A0A482NTT4
- Elsewhere: RCSB PDB 6XGC · PDBe 6XGC · UniProt A0A3Q8LWJ2 · UniProt A0A482NTT4
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