Research workbench
Crystal structure of the ahr-arnt heterodimer in complex with the dre
Analyse Crystal structure of the ahr-arnt heterodimer in complex with the dre in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5V0L
- Type
- protein + DNA
- Length
- 373 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryl hydrocarbon receptor nuclear translocator; Aryl hydrocarbon receptor; DNA (5'…
- UniProt
- P27540, P30561
- Pockets
- 8 · best druggability 0.84
Structure
x-ray diffraction · 4 distinct chains · 31% helix, 13% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryl hydrocarbon receptor nuclear translocator | protein | 176 | 32% helix, 10% strand | P27540 |
| B | Aryl hydrocarbon receptor | protein | 166 | 30% helix, 17% strand | P30561 |
| C | DNA (5'- D(P*GP*GP*AP*TP*TP*GP*CP*GP*TP*GP*AP*GP*AP*AP*CP*TP*G)-3') | dna | 17 | — | — |
| D | DNA (5'-D(P*AP*GP*TP*TP*CP*TP*CP*AP*CP*GP*CP*AP*AP*T)-3') | dna | 14 | — | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.84 | 0.96 | 40 | empty |
| 2 | 957 | 0.80 | 0.82 | 78 | empty |
| 3 | 58 | 0.51 | 0.86 | 16 | empty |
| 4 | 166 | 0.50 | 0.78 | 26 | empty |
| 5 | 123 | 0.43 | 0.76 | 21 | empty |
Interfaces
6 interfaces between chains.
- A–B · 2407 Ų buried · 18 hydrogen bonds · protein-protein
- C–D · 626 Ų buried · 42 hydrogen bonds · nucleic-nucleic
- A–C · 392 Ų buried · 5 hydrogen bonds · protein-nucleic
- B–C · 219 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–D · 187 Ų buried · 4 hydrogen bonds · protein-nucleic
Compared structures
- 5V0L · Crystal structure of the AHR-ARNT heterodimer in complex with the DRE · the same entry in another collection · chain A against A, TM-score 1.00
- P30561 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor (P30561) · a predicted model of the same protein · chain B against A, TM-score 0.90
- P27540 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor nuclear translocator… · a predicted model of the same protein · chain A against A, TM-score 0.76
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 P27540
- Every structure of UniProt P30561
- Elsewhere: RCSB PDB 5V0L · PDBe 5V0L · UniProt P27540 · UniProt P30561
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