Research workbench
Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex
Analyse Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab'… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1DBB
- Type
- protein
- Length
- 435 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- IGG1-kappa DB3 Fab (light chain); IGG1-kappa DB3 Fab (heavy chain)
- UniProt
- P01868
- Ligands
- STR
- Pockets
- 4 · best druggability 0.52
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | IGG1-kappa DB3 Fab (light chain) | protein | 216 | 5% helix, 41% strand | — |
| H | IGG1-kappa DB3 Fab (heavy chain) | protein | 219 | 6% helix, 50% strand | P01868 |
Ligands and binding sites
- STR · Progesterone · ligand · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 137 | 0.52 | 0.80 | 20 | STR |
| 2 | 139 | 0.48 | 0.78 | 30 | empty |
| 3 | 77 | 0.34 | 0.75 | 15 | empty |
| 4 | 80 | 0.31 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- L–H · 1846 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1DBB · Three-dimensional structure of an anti-steroid Fab' and progesterone-Fab' complex · the same entry in another collection · chain L against L, TM-score 1.00
- P01868 · AlphaFold monomer V2.0 prediction for ig gamma-1 chain C region secreted form (P01868) · a predicted model of the same protein · chain H against A, TM-score 0.49
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 P01868
- Elsewhere: RCSB PDB 1DBB · PDBe 1DBB · UniProt P01868
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