Research workbench
Crystal structure of an antigen-binding fragment of monoclonal antibody against sulfonamides in complex with sulfathiazole
Analyse Crystal structure of an antigen-binding fragment of monoclonal antibody against… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CP3
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Light chain of antigen-binding fragment of monoclonal antibody of 4C7; Heavy chain of…
- Ligands
- YTZ, CA
- Pockets
- 5 · best druggability 0.62
Structure
x-ray diffraction · 2 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Light chain of antigen-binding fragment of monoclonal antibody of 4C7 | protein | 218 | 6% helix, 52% strand | — |
| H | Heavy chain of antigen-binding fragment of monoclonal antibody of 4C7 | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- YTZ · 4-amino-N-(1,3-thiazol-2-yl)benzenesulfonamide · ligand · chains A, H
- CA · Calcium ion · metal · chains A
- GOL · Glycerol · additive · chains A, H
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 | 97 | 0.62 | 0.88 | 19 | YTZ |
| 2 | 163 | 0.46 | 0.76 | 24 | empty |
| 3 | 183 | 0.45 | 0.75 | 28 | empty |
| 4 | 133 | 0.40 | 0.74 | 23 | empty |
| 5 | 52 | 0.27 | 0.74 | 18 | empty |
Interfaces
1 interface between chains.
- A–H · 1712 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5CP3 · Crystal Structure of an Antigen-Binding Fragment of Monoclonal Antibody against… · 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
- Elsewhere: RCSB PDB 5CP3 · PDBe 5CP3
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