Research workbench
Human peroxisome proliferator-activated receptor gamma ligand binding domain complexed with 8-oxo- eicosatetraenoic acid
Analyse Human peroxisome proliferator-activated receptor gamma ligand binding domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ZK3
- Type
- protein
- Length
- 537 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peroxisome proliferator-activated receptor gamma
- UniProt
- P37231
- Ligands
- OCX
- Pockets
- 9 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peroxisome proliferator-activated receptor gamma | protein | 274 | 66% helix, 5% strand | P37231 |
| B | Peroxisome proliferator-activated receptor gamma | protein | 263 | 63% helix, 5% strand | P37231 |
Ligands and binding sites
- OCX · (5E,11E,14E)-8-oxoicosa-5,9,11,14-tetraenoic acid · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 467 | 0.86 | 0.93 | 62 | OCX |
| 2 | 592 | 0.81 | 0.86 | 59 | OCX |
| 3 | 109 | 0.57 | 0.85 | 22 | empty |
| 4 | 177 | 0.57 | 0.81 | 22 | empty |
| 5 | 233 | 0.53 | 0.76 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 972 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 covalent (covalent ligand).
Compared structures
- 2ZK3 · Human peroxisome proliferator-activated receptor gamma ligand binding domain complexed… · 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 P37231
- Elsewhere: RCSB PDB 2ZK3 · PDBe 2ZK3 · UniProt P37231
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