MolNFT v1 · #146153 · protein
Crystal structure of ppar gamma in complex with mediator of RNA polymerase II transcription subunit 1
6D94 · Peroxisome proliferator-activated receptor gamma: “Crystal structure of ppar gamma in complex with mediator of RNA polymerase II transcription subunit 1”. X-ray diffraction, 1 ligand (EDK), 2 pockets (best druggability 0.86). MolNFT…
- PDB
- 6D94
- Type
- protein
- Length
- 286 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma; Mediator of RNA polymerase II…
- UniProt
- P37231, Q15648
- Ligands
- EDK
- Pockets
- 2 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 66% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 271 | 66% helix, 5% strand | P37231 |
| B | Mediator of RNA polymerase II transcription subunit 1 | protein | 15 | 67% helix, 0% strand | Q15648 |
Ligands and binding sites
- EDK · (2~{S})-3-[4-[2-[methyl(pyridin-2-yl) amino]ethoxy]phenyl]-2-[[2-(phenylcarbonyl) phenyl]amino]propanoic acid · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 423 | 0.86 | 0.94 | 48 | EDK |
| 2 | 56 | 0.28 | 0.74 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 692 Ų buried · 11 hydrogen bonds · protein-protein
Compared structures
- 6D94 · Crystal structure of PPAR gamma in complex with Mediator of RNA polymerase II… · the same entry in another collection · chain A against A, TM-score 1.00
- Q15648 · AlphaFold monomer V2.0 prediction for mediator of RNA polymerase II transcription subunit… · a predicted model of the same protein · chain B against A, TM-score 0.49
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 P37231
- Every structure of UniProt Q15648
- Elsewhere: RCSB PDB 6D94 · PDBe 6D94 · UniProt P37231 · UniProt Q15648
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