Research workbench
Crystal structure of cortisol complexed with its nanobody at pH 10.5
Analyse Crystal structure of cortisol complexed with its nanobody at pH 10.5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ITQ
- Type
- protein
- Length
- 489 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti-cortisol camelid antibody
- Ligands
- HCY, SO4
- Pockets
- 6 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, D | Anti-cortisol camelid antibody | protein | 122 | 5% helix, 52% strand | — |
| B | Anti-cortisol camelid antibody | protein | 120 | 8% helix, 53% strand | — |
| C | Anti-cortisol camelid antibody | protein | 125 | 5% helix, 51% strand | — |
Ligands and binding sites
- HCY · (11alpha,14beta)-11,17,21-trihydroxypregn-4-ene-3,20-dione · ligand · 4 copies · chains A, B, C, D
- SO4 · Sulfate ion · ion · 2 copies · chains C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1051 | 0.81 | 0.82 | 112 | HCY |
| 2 | 208 | 0.59 | 0.81 | 41 | empty |
| 3 | 189 | 0.57 | 0.81 | 29 | HCY |
| 4 | 165 | 0.56 | 0.81 | 23 | HCY |
| 5 | 140 | 0.42 | 0.75 | 25 | empty |
Interfaces
5 interfaces between chains.
- A–C · 703 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 432 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 426 Ų buried · 8 hydrogen bonds · protein-protein
- B–D · 246 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 50 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 6ITQ · Crystal structure of cortisol complexed with its nanobody at pH 10.5 · 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 6ITQ · PDBe 6ITQ
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