Research workbench
Crystal structure (I) of native diels-alder antibody 13G5 Fab at pH 8.0 with a data set collected at ssrl beamline 9-1.
Analyse Crystal structure (I) of native diels-alder antibody 13G5 Fab at pH 8.0 with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1RUR
- 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
- 4 · best druggability 0.73
Structure
x-ray diffraction · 2 distinct chains · 7% 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 | 8% 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
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 156 | 0.73 | 0.91 | 26 | empty |
| 2 | 585 | 0.63 | 0.74 | 63 | empty |
| 3 | 62 | 0.29 | 0.74 | 16 | empty |
| 4 | 52 | 0.27 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- L–H · 1885 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1RUR · Crystal Structure (I) of native Diels-Alder antibody 13G5 Fab at pH 8.0 with a data set… · the same entry in another collection · chain H against H, 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 1RUR · PDBe 1RUR · UniProt Q5XKG4 · UniProt P01869
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