Research workbench
Human antibody 641 I-9 in complex with influenza hemagglutinin H1 solomon ISLANDS/03/2006
Analyse Human antibody 641 I-9 in complex with influenza hemagglutinin H1 solomon… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4YK4
- Type
- protein
- Length
- 1,277 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 641 I-9 vlcl antibody; 641 I-9 vhch antibody; Hemagglutinin
- UniProt
- A7UPX0
- Ligands
- NAG
- Pockets
- 16 · best druggability 0.69
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| Y, B | 641 I-9 vlcl antibody | protein | 211 | 6% helix, 52% strand | — |
| Z | 641 I-9 vhch antibody | protein | 223 | 7% helix, 53% strand | — |
| E, A | Hemagglutinin | protein | 206 | 12% helix, 33% strand | A7UPX0 |
| C | 641 I-9 vhch antibody | protein | 220 | 7% helix, 55% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains E, A, Z
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 937 | 0.69 | 0.75 | 92 | empty |
| 2 | 641 | 0.65 | 0.75 | 69 | empty |
| 3 | 660 | 0.63 | 0.74 | 62 | empty |
| 4 | 535 | 0.59 | 0.73 | 57 | empty |
| 5 | 74 | 0.55 | 0.87 | 19 | empty |
Interfaces
8 interfaces between chains.
- Y–Z · 1819 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 1767 Ų buried · 9 hydrogen bonds · protein-protein
- Z–E · 660 Ų buried · 8 hydrogen bonds · protein-protein
- C–A · 658 Ų buried · 7 hydrogen bonds · protein-protein
- E–C · 555 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide, 6 glycan (disulfide, N-glycosylation).
Compared structures
- 4YK4 · Human antibody 641 I-9 in complex with influenza hemagglutinin H1 Solomon Islands/03/2006 · the same entry in another collection · chain Y against Y, 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 A7UPX0
- Elsewhere: RCSB PDB 4YK4 · PDBe 4YK4 · UniProt A7UPX0
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