Research workbench
Structural evidence for induced fit as a mechanism for antibody- antigen recognition
Analyse Structural evidence for induced fit as a mechanism for antibody- antigen… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1HIM
- Type
- protein
- Length
- 879 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG2A-kappa 17/9 Fab (light chain); IGG2A-kappa 17/9 Fab (heavy chain); Influenza…
- Ligands
- NH2
- Pockets
- 5 · best druggability 0.50
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H, J | IGG2A-kappa 17/9 Fab (light chain) | protein | 217 | 6% helix, 53% strand | — |
| L, M | IGG2A-kappa 17/9 Fab (heavy chain) | protein | 214 | 6% helix, 50% strand | — |
| P | Influenza hemagglutinin HA1 (strain X47) (residues 100- 108) | protein | 8 | 0% helix, 0% strand | — |
| R | Influenza hemagglutinin HA1 (strain X47) (residues 100- 108) | protein | 9 | 0% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains P, R
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 269 | 0.50 | 0.74 | 41 | empty |
| 2 | 250 | 0.49 | 0.74 | 39 | empty |
| 3 | 91 | 0.38 | 0.76 | 16 | empty |
| 4 | 83 | 0.33 | 0.74 | 20 | empty |
| 5 | 50 | 0.24 | 0.73 | 14 | empty |
Interfaces
6 interfaces between chains.
- J–M · 1820 Ų buried · 15 hydrogen bonds · protein-protein
- H–L · 1805 Ų buried · 19 hydrogen bonds · protein-protein
- M–R · 491 Ų buried · 15 hydrogen bonds · protein-protein
- L–P · 482 Ų buried · 12 hydrogen bonds · protein-protein
- J–R · 234 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 1HIM · Structural evidence for induced fit as a mechanism for antibody-antigen recognition · the same entry in another collection · chain H against H, 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
- Elsewhere: RCSB PDB 1HIM · PDBe 1HIM
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