MolNFT v1 · #169878 · protein
Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain of A/TEXAS/50/2012(H3N2)
6XPR: “Human antibody D2 H1-1/H3-1 H3 in complex with the influenza hemagglutinin head domain of…”. X-ray diffraction, 2 ligands (NAG, BMA), 11 pockets (best druggability 0.63). MolNFT v1 #169878 on GenesisL1: 3D structure, binding sites…
- PDB
- 6XPR
- Type
- protein
- Length
- 1,407 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Antibody D2 H1-1/H3-1 H3 heavy chain; Antibody D2 H1-1/H3-1 H3 light chain
- UniProt
- R4L1D1
- Ligands
- NAG, BMA
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 43% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Hemagglutinin | protein | 269 | 12% helix, 36% strand | R4L1D1 |
| B | Antibody D2 H1-1/H3-1 H3 heavy chain | protein | 226 | 7% helix, 46% strand | — |
| C, F | Antibody D2 H1-1/H3-1 H3 light chain | protein | 211 | 6% helix, 45% strand | — |
| E | Antibody D2 H1-1/H3-1 H3 heavy chain | protein | 221 | 7% helix, 48% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 9 copies · chains A, D
- BMA · beta-D-mannopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 545 | 0.63 | 0.75 | 45 | empty |
| 2 | 352 | 0.62 | 0.78 | 40 | empty |
| 3 | 388 | 0.62 | 0.77 | 48 | empty |
| 4 | 281 | 0.56 | 0.76 | 28 | empty |
| 5 | 242 | 0.52 | 0.76 | 28 | empty |
Interfaces
7 interfaces between chains.
- B–C · 2058 Ų buried · 17 hydrogen bonds · protein-protein
- E–F · 1963 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 517 Ų buried · 0 hydrogen bonds · protein-protein
- D–E · 498 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 478 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 6XPR · Human antibody D2 H1-1/H3-1 H3 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 6XPR · PDBe 6XPR · UniProt R4L1D1
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