Research workbench
Crystal structure analysis of the anti-testosterone Fab in complex with testosterone
Analyse Crystal structure analysis of the anti-testosterone Fab in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1VPO
- Type
- protein
- Length
- 440 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-testosterone (light chain); Anti-testosterone (heavy chain)
- Ligands
- TES
- Pockets
- 6 · best druggability 0.72
Structure
x-ray diffraction · 2 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Anti-testosterone (light chain) | protein | 219 | 5% helix, 54% strand | — |
| H | Anti-testosterone (heavy chain) | protein | 221 | 5% helix, 50% strand | — |
Ligands and binding sites
- TES · Testosterone · ligand · 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, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 161 | 0.72 | 0.90 | 28 | TES |
| 2 | 428 | 0.58 | 0.74 | 46 | empty |
| 3 | 245 | 0.56 | 0.78 | 39 | empty |
| 4 | 136 | 0.43 | 0.75 | 29 | empty |
| 5 | 83 | 0.35 | 0.75 | 21 | empty |
Interfaces
1 interface between chains.
- L–H · 1947 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
Compared structures
- 1VPO · Crystal Structure Analysis of the Anti-testosterone Fab in Complex with Testosterone · the same entry in another collection · chain L against L, 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 1VPO · PDBe 1VPO
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