Research workbench
Crystal structure of flua-20 Fab in complex with the head domain of H1 (A/SOLOMON ISLANDS/3/2006)
Analyse Crystal structure of flua-20 Fab in complex with the head domain of H1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6OC3
- Type
- protein
- Length
- 1,295 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Heavy chain of flua-20 Fab; Light chain of flua-20 Fab; Hemagglutinin
- UniProt
- A7Y8I1
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Heavy chain of flua-20 Fab | protein | 224 | 5% helix, 50% strand | — |
| B, D | Light chain of flua-20 Fab | protein | 213 | 6% helix, 52% strand | — |
| C | Heavy chain of flua-20 Fab | protein | 221 | 5% helix, 50% strand | — |
| E, F | Hemagglutinin | protein | 212 | 12% helix, 38% strand | A7Y8I1 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · chains E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1134 | 0.79 | 0.81 | 109 | empty |
| 2 | 440 | 0.71 | 0.81 | 37 | empty |
| 3 | 448 | 0.65 | 0.78 | 36 | empty |
| 4 | 681 | 0.63 | 0.74 | 62 | empty |
| 5 | 526 | 0.58 | 0.73 | 51 | empty |
Interfaces
9 interfaces between chains.
- A–B · 1829 Ų buried · 11 hydrogen bonds · protein-protein
- C–D · 1819 Ų buried · 15 hydrogen bonds · protein-protein
- A–F · 541 Ų buried · 7 hydrogen bonds · protein-protein
- C–E · 530 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 470 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 1 glycan (disulfide, N-glycosylation).
Compared structures
- 6OC3 · Crystal structure of FluA-20 Fab in complex with the head domain of H1 (A/Solomon… · 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 A7Y8I1
- Elsewhere: RCSB PDB 6OC3 · PDBe 6OC3 · UniProt A7Y8I1
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