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Crystal structure of C05 V110P/A117E mutant bound to H3 influenza hemagglutinin, HA1 subunit
Analyse Crystal structure of C05 V110P/A117E mutant bound to H3 influenza… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6D0U
- Type
- protein
- Length
- 2,872 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody C05 V110P/A117E mutant, heavy chain; Antibody C05, light chain
- UniProt
- Q91MA7
- Ligands
- NAG
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B, J, G | Hemagglutinin | protein | 267 | 11% helix, 39% strand | Q91MA7 |
| E, C, K, H | Antibody C05 V110P/A117E mutant, heavy chain | protein | 238 | 5% helix, 51% strand | — |
| F, D, L, I | Antibody C05, light chain | protein | 213 | 7% helix, 52% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains J, G
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1183 | 0.76 | 0.78 | 113 | empty |
| 2 | 617 | 0.64 | 0.75 | 58 | empty |
| 3 | 647 | 0.63 | 0.74 | 65 | empty |
| 4 | 589 | 0.63 | 0.75 | 59 | empty |
| 5 | 600 | 0.62 | 0.74 | 66 | empty |
Interfaces
18 interfaces between chains.
- E–F · 1857 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 1806 Ų buried · 9 hydrogen bonds · protein-protein
- K–L · 1770 Ų buried · 7 hydrogen bonds · protein-protein
- C–D · 1765 Ų buried · 10 hydrogen bonds · protein-protein
- J–K · 778 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 32 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6D0U · Crystal structure of C05 V110P/A117E mutant bound to H3 influenza hemagglutinin, HA1… · 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 Q91MA7
- Elsewhere: RCSB PDB 6D0U · PDBe 6D0U · UniProt Q91MA7
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