MolNFT v1 · #136734 · protein
Crystal structure of Fab H7.167 in complex with influenza virus hemagglutinin from A/SHANGHAI/02/2013 (H7N9)
5V2A: “Crystal structure of Fab H7.167 in complex with influenza virus hemagglutinin from A/SHANGHAI/02/2013 (H7N9)”. X-ray diffraction, 2 ligands (NAG, BMA), 14 pockets (best druggability 0.78). MolNFT v1 #136734 on GenesisL1: 3D…
- PDB
- 5V2A
- Type
- protein
- Length
- 922 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Light chain (kappa) of H7.167 antibody; Heavy chain of H7.167 antibody
- UniProt
- A0A0R5TXT5, A0A097PHH8
- Ligands
- NAG, BMA
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 13% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 317 | 6% helix, 33% strand | A0A0R5TXT5 |
| B | Hemagglutinin | protein | 170 | 48% helix, 9% strand | A0A097PHH8 |
| L | Light chain (kappa) of H7.167 antibody | protein | 221 | 4% helix, 45% strand | — |
| H | Heavy chain of H7.167 antibody | protein | 214 | 6% helix, 44% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 4 copies · chains H, A, B
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 223 | 0.78 | 0.92 | 38 | empty |
| 2 | 50 | 0.61 | 0.93 | 19 | empty |
| 3 | 209 | 0.58 | 0.80 | 24 | empty |
| 4 | 90 | 0.57 | 0.85 | 15 | empty |
| 5 | 207 | 0.48 | 0.75 | 33 | empty |
Interfaces
4 interfaces between chains.
- A–B · 3401 Ų buried · 37 hydrogen bonds · protein-protein
- L–H · 1761 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 384 Ų buried · 6 hydrogen bonds · protein-protein
- A–L · 367 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 3 glycan (disulfide, N-glycosylation).
Compared structures
- 5V2A · Crystal structure of Fab H7.167 in complex with influenza virus hemagglutinin from… · 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 A0A0R5TXT5
- Every structure of UniProt A0A097PHH8
- Elsewhere: RCSB PDB 5V2A · PDBe 5V2A · UniProt A0A0R5TXT5 · UniProt A0A097PHH8
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