Research workbench
Inferred intermediate I-7 (I-7-6) 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-7-6) 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
- 6Q0I
- Type
- protein
- Length
- 650 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
- 5 · best druggability 0.59
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin | protein | 207 | 10% helix, 39% strand | B4UPF7 |
| H | Fab heavy chain | protein | 231 | 5% helix, 48% strand | — |
| L | Fab lambda chain | protein | 212 | 6% helix, 50% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains A
- GOL · Glycerol · additive · chains H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 548 | 0.59 | 0.73 | 59 | empty |
| 2 | 304 | 0.57 | 0.77 | 52 | empty |
| 3 | 108 | 0.44 | 0.79 | 24 | empty |
| 4 | 97 | 0.44 | 0.79 | 22 | empty |
| 5 | 54 | 0.25 | 0.73 | 19 | empty |
Interfaces
2 interfaces between chains.
- H–L · 2023 Ų buried · 21 hydrogen bonds · protein-protein
- A–H · 894 Ų buried · 24 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6Q0I · Inferred intermediate I-7 (I-7-6) 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 6Q0I · PDBe 6Q0I · UniProt B4UPF7
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