Research workbench
Inferred intermediate I-7 (I-7-1) of the human antibody lineage 652 in complex with influenza hemagglutinin head domain of A/BEIJING/262/95(H1N1)
Analyse Inferred intermediate I-7 (I-7-1) of the human antibody lineage 652 in complex… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Q0L
- Type
- protein
- Length
- 658 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin; Fab heavy chain; Fab lambda chain
- UniProt
- B4UPF7
- Ligands
- NAG
- Pockets
- 9 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 212 | 13% helix, 36% strand | B4UPF7 |
| H | Fab heavy chain | protein | 233 | 8% helix, 48% strand | — |
| L | Fab lambda chain | protein | 213 | 7% helix, 51% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 2 copies · chains A
- GOL · Glycerol · additive · 7 copies · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 581 | 0.62 | 0.74 | 57 | GOL |
| 2 | 217 | 0.55 | 0.78 | 29 | empty |
| 3 | 126 | 0.51 | 0.80 | 19 | empty |
| 4 | 166 | 0.50 | 0.78 | 31 | empty |
| 5 | 109 | 0.45 | 0.79 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2068 Ų buried · 17 hydrogen bonds · protein-protein
- A–H · 926 Ų buried · 24 hydrogen bonds · protein-protein
- A–L · 34 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q0L · Inferred intermediate I-7 (I-7-1) of the human antibody lineage 652 in complex with… · 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 B4UPF7
- Elsewhere: RCSB PDB 6Q0L · PDBe 6Q0L · UniProt B4UPF7
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