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Crystal structure of H7-specific antibody M826 in complex with the HA1 domain of hemagglutinin from H7N9 influenza virus
Analyse Crystal structure of H7-specific antibody M826 in complex with the HA1 domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VAG
- Type
- protein
- Length
- 644 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Light chain of antibody M826; Heavy chain of antibody M826
- UniProt
- R4NN21
- Pockets
- 6 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 209 | 13% helix, 38% strand | R4NN21 |
| B | Light chain of antibody M826 | protein | 214 | 6% helix, 50% strand | — |
| C | Heavy chain of antibody M826 | protein | 221 | 10% helix, 50% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 10 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 126 | 0.60 | 0.85 | 25 | empty |
| 2 | 335 | 0.54 | 0.74 | 43 | EDO |
| 3 | 181 | 0.49 | 0.77 | 26 | empty |
| 4 | 53 | 0.36 | 0.80 | 18 | empty |
| 5 | 61 | 0.32 | 0.76 | 14 | empty |
Interfaces
3 interfaces between chains.
- B–C · 1862 Ų buried · 19 hydrogen bonds · protein-protein
- A–C · 637 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 546 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 5VAG · Crystal structure of H7-specific antibody m826 in complex with the HA1 domain of… · 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 R4NN21
- Elsewhere: RCSB PDB 5VAG · PDBe 5VAG · UniProt R4NN21
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