MolNFT v1 · #169877 · protein
Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of A/TEXAS/50/2012(H3N2)
6XPQ: “Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head domain of A/TEXAS/50/2012(H3N2)”. X-ray diffraction, 2 ligands (NAG, BMA), 7 pockets (best druggability 0.72). MolNFT v1 #169877 on GenesisL1: 3D…
- PDB
- 6XPQ
- Type
- protein
- Length
- 704 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody D1 H1-17/H3-14 light chain; Antibody D1 H1-17/H3-14 heavy chain
- UniProt
- R4L1D1
- Ligands
- NAG, BMA
- Pockets
- 7 · best druggability 0.72
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 274 | 11% helix, 37% strand | R4L1D1 |
| C | Antibody D1 H1-17/H3-14 light chain | protein | 209 | 6% helix, 49% strand | — |
| B | Antibody D1 H1-17/H3-14 heavy chain | protein | 221 | 3% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A
- BMA · beta-D-mannopyranose · sugar · 3 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 411 | 0.72 | 0.83 | 41 | empty |
| 2 | 722 | 0.67 | 0.75 | 82 | empty |
| 3 | 242 | 0.56 | 0.78 | 30 | empty |
| 4 | 160 | 0.43 | 0.74 | 22 | empty |
| 5 | 69 | 0.31 | 0.74 | 16 | empty |
Interfaces
3 interfaces between chains.
- C–B · 1837 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 457 Ų buried · 9 hydrogen bonds · protein-protein
- A–C · 317 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6XPQ · Human antibody D1 H1-17/H3-14 in complex with the influenza hemagglutinin head 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 R4L1D1
- Elsewhere: RCSB PDB 6XPQ · PDBe 6XPQ · UniProt R4L1D1
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