Research workbench
Cryoem structure of monoclonal Fab 045-09 2B05 binding the lateral patch of influenza virus H1 ha
Analyse Cryoem structure of monoclonal Fab 045-09 2B05 binding the lateral patch of… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7MEM
- Type
- protein
- Length
- 2,124 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Light chain of monoclonal antibody 045-09 2B05; Heavy chain of…
- UniProt
- C3W5S1
- Ligands
- NAG, FUC
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 4 distinct chains · 18% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E, C, F | Hemagglutinin HA1 chain | protein | 321 | 7% helix, 41% strand | C3W5S1 |
| L, J, K | Light chain of monoclonal antibody 045-09 2B05 | protein | 107 | 3% helix, 50% strand | — |
| H, G, I | Heavy chain of monoclonal antibody 045-09 2B05 | protein | 120 | 8% helix, 49% strand | — |
| D, A, B | Hemagglutinin HA2 chain | protein | 160 | 58% helix, 16% strand | C3W5S1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 15 copies · chains E, C, F
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains E, C, 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, 18 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 227 | 0.83 | 0.96 | 30 | empty |
| 2 | 310 | 0.75 | 0.87 | 47 | empty |
| 3 | 275 | 0.74 | 0.87 | 41 | empty |
| 4 | 243 | 0.73 | 0.88 | 35 | empty |
| 5 | 734 | 0.71 | 0.77 | 90 | empty |
Interfaces
24 interfaces between chains.
- C–B · 2528 Ų buried · 35 hydrogen bonds · protein-protein
- E–A · 2528 Ų buried · 35 hydrogen bonds · protein-protein
- D–F · 2526 Ų buried · 35 hydrogen bonds · protein-protein
- D–B · 1065 Ų buried · 10 hydrogen bonds · protein-protein
- D–A · 1062 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 disulfide, 12 glycan (disulfide, N-glycosylation).
Compared structures
- 7MEM · CryoEM structure of monoclonal Fab 045-09 2B05 binding the lateral patch of influenza… · the same entry in another collection · chain B against B, 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 C3W5S1
- Elsewhere: RCSB PDB 7MEM · PDBe 7MEM · UniProt C3W5S1
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