MolNFT v1 · #61914 · protein + DNA
Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with BVT.13, 9-cis retinoic acid and NCOA2 peptide
3DZU · Retinoic acid receptor rxr-alpha: “Intact ppar gamma - rxr alpha nuclear receptor complex on DNA bound with BVT.13, 9-cis retinoic acid and…”. X-ray diffraction, 3 ligands (9CR, PLB, ZN), 16 pockets (best druggability 0.85). MolNFT…
- PDB
- 3DZU
- Type
- protein + DNA
- Length
- 705 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, PLB, ZN
- Pockets
- 16 · best druggability 0.85
Structure
x-ray diffraction · 6 distinct chains · 55% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinoic acid receptor rxr-alpha | protein | 289 | 59% helix, 3% strand | P19793 |
| D | Peroxisome proliferator-activated receptor gamma | protein | 359 | 53% helix, 5% 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 | 56% helix, 0% strand | Q15596 |
| E | NCOA2 peptide | protein | 8 | 50% helix, 0% strand | Q15596 |
Ligands and binding sites
- 9CR · (9cis)-retinoic acid · ligand · chains A
- PLB · 2-[(2,4-dichlorobenzoyl)amino]-5-(pyrimidin-2-yloxy)benzoic acid · 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
16 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 957 | 0.85 | 0.86 | 104 | PLB |
| 2 | 266 | 0.85 | 0.95 | 36 | 9CR |
| 3 | 687 | 0.70 | 0.78 | 66 | empty |
| 4 | 63 | 0.66 | 0.94 | 15 | empty |
| 5 | 104 | 0.57 | 0.85 | 15 | empty |
Interfaces
8 interfaces between chains.
- A–D · 2011 Ų buried · 11 hydrogen bonds · protein-protein
- C–F · 888 Ų buried · 73 hydrogen bonds · nucleic-nucleic
- D–F · 621 Ų buried · 9 hydrogen bonds · protein-nucleic
- D–C · 588 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–G · 498 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 3DZU · Intact PPAR gamma - RXR alpha Nuclear Receptor Complex on DNA bound with BVT.13, 9-cis… · 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 3DZU · PDBe 3DZU · UniProt P19793 · UniProt P37231 · UniProt Q15596
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