MolNFT v1 · #128194 · protein + DNA
Structural basis for aryl hydrocarbon receptor mediated gene activation
5NJ8: “Structural basis for aryl hydrocarbon receptor mediated gene activation”. X-ray diffraction, 1 ligand (ER3), 12 pockets (best druggability 0.84). MolNFT v1 #128194 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5NJ8
- Type
- protein + DNA
- Length
- 708 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Aryl hydrocarbon receptor; Aryl hydrocarbon receptor nuclear translocator; DNA…
- UniProt
- P35869, P53762
- Ligands
- ER3
- Pockets
- 12 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 43% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Aryl hydrocarbon receptor | protein | 176 | 43% helix, 23% strand | P35869 |
| B | Aryl hydrocarbon receptor nuclear translocator | protein | 174 | 39% helix, 24% strand | P53762 |
| C | Aryl hydrocarbon receptor | protein | 176 | 44% helix, 16% strand | P35869 |
| D | Aryl hydrocarbon receptor nuclear translocator | protein | 134 | 47% helix, 7% strand | P53762 |
| E, G | DNA (5'-D(*GP*GP*TP*CP*AP*CP*GP*CP*AP*AP*CP*C)-3') | dna | 12 | — | — |
| F, H | DNA (5'-D(*GP*GP*TP*TP*GP*CP*GP*TP*GP*AP*CP*C)-3') | dna | 12 | — | — |
Ligands and binding sites
- ER3 · Erbium (III) ion · metal · 12 copies · chains A, B, E, C, D, G, H
- ACT · Acetate ion · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 291 | 0.84 | 0.95 | 27 | empty |
| 2 | 316 | 0.83 | 0.94 | 28 | empty |
| 3 | 1001 | 0.81 | 0.82 | 116 | empty |
| 4 | 409 | 0.76 | 0.86 | 49 | empty |
| 5 | 363 | 0.62 | 0.78 | 46 | ER3 |
Interfaces
20 interfaces between chains.
- A–B · 2673 Ų buried · 19 hydrogen bonds · protein-protein
- C–D · 2176 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 609 Ų buried · 11 hydrogen bonds · protein-protein
- E–F · 542 Ų buried · 40 hydrogen bonds · nucleic-nucleic
- G–H · 538 Ų buried · 41 hydrogen bonds · nucleic-nucleic
Compared structures
- 5NJ8 · Structural basis for aryl hydrocarbon receptor mediated gene activation · the same entry in another collection · chain H against H, TM-score 1.00
- P35869 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor (P35869) · a predicted model of the same protein · chain A against A, TM-score 0.96
- P53762 · AlphaFold monomer V2.0 prediction for aryl hydrocarbon receptor nuclear translocator… · a predicted model of the same protein · chain B against A, TM-score 0.83
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 P35869
- Every structure of UniProt P53762
- Elsewhere: RCSB PDB 5NJ8 · PDBe 5NJ8 · UniProt P35869 · UniProt P53762
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