Research workbench
Crystal structure of broadly neutralizing antibody 5J8 bound to 2009 pandemic influenza hemagglutinin, HA1 subunit
Analyse Crystal structure of broadly neutralizing antibody 5J8 bound to 2009 pandemic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4M5Z
- Type
- protein
- Length
- 642 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Hemagglutinin HA1 chain; Fab 5J8 heavy chain; Fab 5J8 light chain
- UniProt
- G8XMJ2
- Pockets
- 7 · best druggability 0.60
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Hemagglutinin HA1 chain | protein | 210 | 11% helix, 40% strand | G8XMJ2 |
| H | Fab 5J8 heavy chain | protein | 220 | 10% helix, 52% strand | — |
| L | Fab 5J8 light chain | protein | 212 | 8% helix, 49% strand | — |
Pockets
7 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 111 | 0.60 | 0.86 | 33 | empty |
| 2 | 432 | 0.57 | 0.74 | 51 | empty |
| 3 | 118 | 0.44 | 0.77 | 23 | empty |
| 4 | 147 | 0.43 | 0.75 | 21 | empty |
| 5 | 62 | 0.43 | 0.82 | 23 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1892 Ų buried · 13 hydrogen bonds · protein-protein
- A–H · 525 Ų buried · 8 hydrogen bonds · protein-protein
- A–L · 417 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide (disulfide).
Compared structures
- 4M5Z · Crystal structure of broadly neutralizing antibody 5J8 bound to 2009 pandemic influenza… · 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 G8XMJ2
- Elsewhere: RCSB PDB 4M5Z · PDBe 4M5Z · UniProt G8XMJ2
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