Research workbench
Crystal structure of homodimeric androgen receptor ligand-binding domain bound to dht and lxxll peptide
Analyse Crystal structure of homodimeric androgen receptor ligand-binding domain bound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5JJM
- Type
- protein
- Length
- 1,045 residues
- Chains
- 12
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Androgen receptor; Unknown peptide; UBA3-derived peptide
- UniProt
- P10275
- Ligands
- DHT, ZN, SO4, CL
- Pockets
- 14 · best druggability 0.84
Structure
x-ray diffraction · 7 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Androgen receptor | protein | 252 | 66% helix, 5% strand | P10275 |
| M, F, K, L | Unknown peptide | protein | 3 | 0% helix, 0% strand | — |
| B | Androgen receptor | protein | 251 | 67% helix, 5% strand | P10275 |
| C | Androgen receptor | protein | 250 | 67% helix, 5% strand | P10275 |
| D | Androgen receptor | protein | 249 | 68% helix, 5% strand | P10275 |
| G | UBA3-derived peptide | protein | 7 | 71% helix, 0% strand | — |
| H, I, J | UBA3-derived peptide | protein | 8 | 75% helix, 0% strand | — |
Ligands and binding sites
- DHT · 5-alpha-dihydrotestosterone · ligand · 4 copies · chains A, B, C, D
- ZN · Zinc ion · metal · 4 copies · chains A, M, B, F, C, K, D, L
- SO4 · Sulfate ion · ion · 5 copies · chains A, C, B, D
- CL · Chloride ion · ion · 3 copies · chains A, B, C, D
- EDO · 1,2-ethanediol · additive · 8 copies · chains A, B, C, D
- GOL · Glycerol · additive · 2 copies · chains A, B, C
- PGE · Triethylene glycol · additive · chains C
- ACT · Acetate ion · additive · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 176 | 0.84 | 0.98 | 21 | DHT |
| 2 | 179 | 0.84 | 0.98 | 22 | DHT |
| 3 | 172 | 0.84 | 0.98 | 21 | DHT |
| 4 | 164 | 0.83 | 0.98 | 21 | DHT |
| 5 | 165 | 0.81 | 0.96 | 29 | GOL |
Interfaces
11 interfaces between chains.
- B–C · 1099 Ų buried · 7 hydrogen bonds · protein-protein
- D–J · 442 Ų buried · 1 hydrogen bond · protein-protein
- A–G · 437 Ų buried · 0 hydrogen bonds · protein-protein
- B–H · 435 Ų buried · 1 hydrogen bond · protein-protein
- C–I · 417 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 5 modified (formylation, nonstandard).
Compared structures
- 5JJM · Crystal Structure of Homodimeric Androgen Receptor Ligand-Binding Domain bound to DHT and… · the same entry in another collection · chain J against J, 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
- Every structure of UniProt P10275
- Elsewhere: RCSB PDB 5JJM · PDBe 5JJM · UniProt P10275
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