Research workbench
Crystal structure (H) of U.V.-irradiated diels-alder antibody 13G5 Fab at pH 8.0 with a data set collected in house.
Analyse Crystal structure (H) of U.V.-irradiated diels-alder antibody 13G5 Fab at pH… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RUQ
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin 13G5 light chain; Immunoglobulin 13G5 heavy chain
- UniProt
- Q5XKG4, P01869
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Immunoglobulin 13G5 light chain | protein | 217 | 6% helix, 49% strand | Q5XKG4 |
| H | Immunoglobulin 13G5 heavy chain | protein | 218 | 10% helix, 52% strand | P01869 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains L, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 178 | 0.73 | 0.90 | 27 | empty |
| 2 | 586 | 0.63 | 0.75 | 62 | empty |
| 3 | 62 | 0.28 | 0.74 | 17 | empty |
Interfaces
1 interface between chains.
- L–H · 1911 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1RUQ · Crystal Structure (H) of u.v.-irradiated Diels-Alder antibody 13G5 Fab at pH 8.0 with a… · the same entry in another collection · chain L against L, TM-score 1.00
- P01869 · AlphaFold monomer V2.0 prediction for ig gamma-1 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 Q5XKG4
- Every structure of UniProt P01869
- Elsewhere: RCSB PDB 1RUQ · PDBe 1RUQ · UniProt Q5XKG4 · UniProt P01869
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