Research workbench
Crystal structure of the orphan nuclear receptor rev-ERB(ALPHA) DNA- binding domain bound to its cognate response element
Analyse Crystal structure of the orphan nuclear receptor rev-ERB(ALPHA) DNA- binding… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1GA5
- Type
- protein + DNA
- Length
- 400 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP *AP*G)-3'…
- UniProt
- P20393
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.60
Structure
x-ray diffraction · 6 distinct chains · 32% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, G | 5'-D(*CP*AP*AP*CP*TP*AP*GP*GP*TP*CP*AP*CP*TP*AP*GP*GP*TP*CP *AP*G)-3' | dna | 20 | — | — |
| D, H | 5'-D(*CP*TP*GP*AP*CP*CP*TP*AP*GP*TP*GP*AP*CP*CP*TP*AP*GP*TP *(5IT)P*G)-3' | dna | 20 | — | — |
| A | Orphan nuclear receptor NR1D1 | protein | 82 | 33% helix, 10% strand | P20393 |
| B | Orphan nuclear receptor NR1D1 | protein | 79 | 30% helix, 8% strand | P20393 |
| E | Orphan nuclear receptor NR1D1 | protein | 81 | 30% helix, 10% strand | P20393 |
| F | Orphan nuclear receptor NR1D1 | protein | 78 | 36% helix, 8% strand | P20393 |
Ligands and binding sites
- ZN · Zinc ion · metal · 8 copies · chains A, B, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 364 | 0.60 | 0.77 | 34 | empty |
| 2 | 368 | 0.59 | 0.77 | 33 | empty |
| 3 | 404 | 0.57 | 0.75 | 26 | empty |
| 4 | 71 | 0.34 | 0.76 | 11 | empty |
Interfaces
14 interfaces between chains.
- C–D · 902 Ų buried · 91 hydrogen bonds · nucleic-nucleic
- G–H · 900 Ų buried · 95 hydrogen bonds · nucleic-nucleic
- D–A · 627 Ų buried · 13 hydrogen bonds · protein-nucleic
- H–E · 612 Ų buried · 16 hydrogen bonds · protein-nucleic
- G–E · 587 Ų buried · 11 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 1GA5 · Crystal structure of the orphan nuclear receptor rev-ERB(ALPHA) DNA-binding domain bound… · the same entry in another collection · chain F against F, TM-score 1.00
- P20393 · AlphaFold monomer V2.0 prediction for nuclear receptor subfamily 1 group D member 1… · a predicted model of the same protein · chain F against A, TM-score 0.91
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 P20393
- Elsewhere: RCSB PDB 1GA5 · PDBe 1GA5 · UniProt P20393
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