Research workbench
Crystal structure of cortisol complexed with its nanobody at pH 3.5
Analyse Crystal structure of cortisol complexed with its nanobody at pH 3.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ITP
- Type
- protein
- Length
- 250 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-cortisol camelid antibody
- Ligands
- HCY
- Pockets
- 3 · best druggability 0.55
Structure
x-ray diffraction · 1 distinct chain · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Anti-cortisol camelid antibody | protein | 125 | 5% helix, 52% strand | — |
Ligands and binding sites
- HCY · (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione · ligand · 2 copies · chains A, B
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 | 166 | 0.55 | 0.81 | 27 | HCY |
| 2 | 167 | 0.53 | 0.80 | 27 | HCY |
| 3 | 62 | 0.30 | 0.75 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 725 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 6ITP · Crystal structure of cortisol complexed with its nanobody at pH 3.5 · 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 6ITP · PDBe 6ITP
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