Research workbench
Crystal structure (a) of U.V.-irradiated cationic cyclization antibody 4C6 Fab at pH 4.6 with a data set collected in-house.
Analyse Crystal structure (a) of U.V.-irradiated cationic cyclization antibody 4C6 Fab… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RU9
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin IGG2A, light chain; Immunoglobulin IGG2A, heavy chain
- UniProt
- Q8K0F8, P01865
- Ligands
- BEZ
- Pockets
- 6 · best druggability 0.65
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin IGG2A, light chain | protein | 219 | 5% helix, 52% strand | Q8K0F8 |
| H | Immunoglobulin IGG2A, heavy chain | protein | 222 | 10% helix, 51% strand | P01865 |
Ligands and binding sites
- BEZ · Benzoic acid · ligand · chains L, H
- GOL · Glycerol · additive · 5 copies · chains L, H
- ACT · Acetate ion · additive · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 133 | 0.65 | 0.87 | 26 | ACT, BEZ |
| 2 | 509 | 0.60 | 0.74 | 63 | empty |
| 3 | 64 | 0.48 | 0.85 | 23 | GOL |
| 4 | 125 | 0.42 | 0.76 | 22 | empty |
| 5 | 74 | 0.34 | 0.76 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 2091 Ų buried · 28 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 modified (disulfide, nonstandard).
Compared structures
- 1RU9 · Crystal Structure (A) of u.v.-irradiated cationic cyclization antibody 4C6 Fab at pH 4.6… · the same entry in another collection · chain L against L, TM-score 1.00
- P01865 · AlphaFold monomer V2.0 prediction for ig gamma-2A chain C region, membrane-bound form… · a predicted model of the same protein · chain H against A, TM-score 0.52
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 Q8K0F8
- Every structure of UniProt P01865
- Elsewhere: RCSB PDB 1RU9 · PDBe 1RU9 · UniProt Q8K0F8 · UniProt P01865
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