Research workbench
Cryo-EM structure of SRR2899884.46167H+MEDI8852L Fab in complex with victoria ha
Analyse Cryo-EM structure of SRR2899884.46167H+MEDI8852L Fab in complex with victoria ha in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7KC1
- Type
- protein
- Length
- 2,106 residues
- Chains
- 12
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Fusion protein of hemagglutinin and envelope glycoprotein; Fab heavy…
- UniProt
- L0HR89, A0A2P1E3C0
- Ligands
- NAG, MAN, BMA
- Pockets
- 20 · best druggability 0.80
Structure
electron microscopy · 4 distinct chains · 17% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, G | Hemagglutinin | protein | 314 | 9% helix, 36% strand | L0HR89 |
| B, D, I | Fusion protein of hemagglutinin and envelope glycoprotein | protein | 164 | 51% helix, 10% strand | A0A2P1E3C0 |
| H, E, J | Fab heavy chain | protein | 125 | 2% helix, 50% strand | — |
| L, F, K | Fab light chain | protein | 99 | 3% helix, 46% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 39 copies · chains A, H, C, E, G, J, B, D, I
- MAN · alpha-D-mannopyranose · sugar · 18 copies · chains H, C, E, G, J, A
- BMA · beta-D-mannopyranose · sugar · 12 copies · chains C, G, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 933 | 0.80 | 0.82 | 56 | empty |
| 2 | 693 | 0.73 | 0.79 | 63 | empty |
| 3 | 823 | 0.73 | 0.78 | 78 | empty |
| 4 | 71 | 0.72 | 0.97 | 19 | empty |
| 5 | 70 | 0.72 | 0.97 | 18 | empty |
Interfaces
27 interfaces between chains.
- G–I · 2825 Ų buried · 27 hydrogen bonds · protein-protein
- A–B · 2825 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2811 Ų buried · 29 hydrogen bonds · protein-protein
- B–I · 1190 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 1187 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 27 glycan, 24 disulfide (N-glycosylation, disulfide).
Compared structures
- 7KC1 · Cryo-EM structure of SRR2899884.46167H+MEDI8852L fab in complex with Victoria 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 L0HR89
- Every structure of UniProt A0A2P1E3C0
- Elsewhere: RCSB PDB 7KC1 · PDBe 7KC1 · UniProt L0HR89 · UniProt A0A2P1E3C0
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