Research workbench
Crystal structure of the reactive loop cleaved corticosteroid binding globulin complexed with cortisol
Analyse Crystal structure of the reactive loop cleaved corticosteroid binding globulin… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VDY
- Type
- protein
- Length
- 722 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Corticosteroid-binding globulin
- UniProt
- P08185
- Ligands
- HCY
- Pockets
- 5 · best druggability 0.49
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Corticosteroid-binding globulin | protein | 361 | 29% helix, 38% strand | P08185 |
| B | Corticosteroid-binding globulin | protein | 361 | 30% helix, 38% strand | P08185 |
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
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 243 | 0.49 | 0.74 | 33 | empty |
| 2 | 125 | 0.46 | 0.78 | 15 | HCY |
| 3 | 118 | 0.46 | 0.78 | 15 | HCY |
| 4 | 116 | 0.44 | 0.77 | 17 | empty |
| 5 | 80 | 0.35 | 0.76 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 150 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 2VDY · Crystal structure of the reactive loop cleaved Corticosteroid Binding Globulin complexed… · the same entry in another collection · chain A against A, TM-score 1.00
- P08185 · AlphaFold monomer V2.0 prediction for corticosteroid-binding globulin (P08185) · a predicted model of the same protein · chain A against A, TM-score 0.92
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 P08185
- Elsewhere: RCSB PDB 2VDY · PDBe 2VDY · UniProt P08185
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