MolNFT v1 · #159829 · protein
Tethered pxr-LBD/SRC-1P bound to garcinoic acid
6P2B · Nuclear receptor subfamily 1 group I member 2: “Tethered pxr-LBD/SRC-1P bound to garcinoic acid”. X-ray diffraction, 1 ligand (NQD), 6 pockets (best druggability 0.86). MolNFT v1 #159829 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6P2B
- Type
- protein
- Length
- 569 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor subfamily 1 group I member 2
- UniProt
- O75469
- Ligands
- NQD
- Pockets
- 6 · best druggability 0.86
Structure
x-ray diffraction · 2 distinct chains · 60% helix, 8% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor subfamily 1 group I member 2 | protein | 289 | 59% helix, 8% strand | O75469 |
| B | Nuclear receptor subfamily 1 group I member 2 | protein | 280 | 62% helix, 8% strand | O75469 |
Ligands and binding sites
- NQD · (2Z,6E,10E)-13-[(2R)-6-hydroxy-2,8-dimethyl-3,4-dihydro-2H-1-benzopyran-2-yl]-2,6,10-trimethyltrideca-2,6,10-trienoic acid · ligand · 2 copies · chains A, B
- DMS · Dimethyl sulfoxide · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 328 | 0.86 | 0.95 | 36 | NQD |
| 2 | 352 | 0.86 | 0.94 | 36 | NQD |
| 3 | 80 | 0.36 | 0.76 | 20 | empty |
| 4 | 77 | 0.35 | 0.76 | 14 | empty |
| 5 | 61 | 0.35 | 0.77 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 790 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
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 O75469
- Elsewhere: RCSB PDB 6P2B · PDBe 6P2B · UniProt O75469
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