Research workbench
Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with rosiglitazone, 9-cis retinoic acid and NCOA2 peptide
Analyse Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3DZY
- Type
- protein + DNA
- Length
- 715 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinoic acid receptor rxr-alpha; Peroxisome proliferator-activated receptor gamma; DNA…
- UniProt
- P19793, P37231, Q15596
- Ligands
- 9CR, BRL, ZN
- Pockets
- 17 · best druggability 0.83
Structure
x-ray diffraction · 6 distinct chains · 54% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 302 | 51% helix, 3% strand | P19793 |
| D | Peroxisome proliferator-activated receptor gamma | protein | 354 | 56% helix, 4% strand | P37231 |
| C | DNA (5'- D(*DCP*DAP*DAP*DAP*DCP*DTP*DAP*DGP*DGP*DTP*DCP*DAP*DAP*DAP*DGP*DGP*DT P*DCP*DAP*DG)-3') | dna | 20 | — | — |
| F | DNA (5'- D(*DCP*DTP*DGP*DAP*DCP*DCP*DTP*DTP*DTP*DGP*DAP*DCP*DCP*DTP*DAP*DGP*DT P*DTP*DTP*DG)-3') | dna | 20 | — | — |
| G | NCOA2 peptide | protein | 9 | 78% helix, 0% strand | Q15596 |
| E | NCOA2 peptide | protein | 10 | 50% helix, 0% strand | Q15596 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · chains A
- BRL · 2,4-thiazolidiinedione, 5-[[4-[2-(methyl-2-pyridinylamino)ethoxy]phenyl]methyl]-(9CL) · ligand · chains D
- ZN · Zinc ion · metal · 4 copies · chains A, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 306 | 0.83 | 0.92 | 34 | 9CR |
| 2 | 642 | 0.80 | 0.84 | 81 | BRL |
| 3 | 797 | 0.69 | 0.76 | 53 | empty |
| 4 | 56 | 0.61 | 0.92 | 18 | empty |
| 5 | 294 | 0.55 | 0.76 | 29 | empty |
Interfaces
8 interfaces between chains.
- A–D · 2072 Ų buried · 20 hydrogen bonds · protein-protein
- C–F · 895 Ų buried · 71 hydrogen bonds · nucleic-nucleic
- D–F · 640 Ų buried · 16 hydrogen bonds · protein-nucleic
- D–C · 578 Ų buried · 14 hydrogen bonds · protein-nucleic
- D–E · 561 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3DZY · Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with Rosiglitazone… · the same entry in another collection · chain A against A, 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 P19793
- Every structure of UniProt P37231
- Every structure of UniProt Q15596
- Elsewhere: RCSB PDB 3DZY · PDBe 3DZY · UniProt P19793 · UniProt P37231 · UniProt Q15596
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