Research workbench
Cryoem MAP of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 ha
Analyse Cryoem MAP of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 ha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7T3D
- Type
- protein
- Length
- 2,796 residues
- Chains
- 18
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Hemagglutinin HA2 chain; 2B05 mab light chain; 2B05 mab heavy…
- UniProt
- C3W5S1
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.83
Structure
electron microscopy · 6 distinct chains · 14% helix, 40% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E, F | Hemagglutinin HA1 chain | protein | 324 | 6% helix, 40% strand | C3W5S1 |
| B, G, I | Hemagglutinin HA2 chain | protein | 163 | 57% helix, 15% strand | C3W5S1 |
| D, M, N | 2B05 mab light chain | protein | 107 | 3% helix, 50% strand | — |
| C, J, K | 2B05 mab heavy chain | protein | 120 | 5% helix, 54% strand | — |
| H, O, P | 222-1C06 mab heavy chain | protein | 110 | 8% helix, 42% strand | — |
| L, Q, R | 222-1C06 mab light chain | protein | 108 | 0% helix, 45% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, E, F, B, G, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 200 | 0.83 | 0.97 | 29 | empty |
| 2 | 185 | 0.78 | 0.93 | 25 | empty |
| 3 | 231 | 0.74 | 0.88 | 34 | empty |
| 4 | 238 | 0.73 | 0.88 | 35 | empty |
| 5 | 596 | 0.70 | 0.78 | 61 | empty |
Interfaces
36 interfaces between chains.
- A–B · 2714 Ų buried · 37 hydrogen bonds · protein-protein
- F–I · 2713 Ų buried · 37 hydrogen bonds · protein-protein
- E–G · 2707 Ų buried · 37 hydrogen bonds · protein-protein
- G–I · 1083 Ų buried · 9 hydrogen bonds · protein-protein
- B–G · 1079 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 disulfide, 18 glycan (disulfide, N-glycosylation).
Compared structures
- 7T3D · CryoEM map of anchor 222-1C06 Fab and lateral patch 2B05 Fab binding H1 HA · 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 C3W5S1
- Elsewhere: RCSB PDB 7T3D · PDBe 7T3D · UniProt C3W5S1
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