Research workbench
Crystal structure of retinoic acid receptor-related orphan receptor (ror) gamma ligand binding domain complex with ML209
Analyse Crystal structure of retinoic acid receptor-related orphan receptor (ror) gamma… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5K3N
- Type
- protein
- Length
- 910 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 6Q6
- Pockets
- 19 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 64% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Nuclear receptor ror-gamma | protein | 228 | 67% helix, 4% strand | P51449 |
| B | Nuclear receptor ror-gamma | protein | 226 | 61% helix, 4% strand | P51449 |
Ligands and binding sites
- 6Q6 · (3S)-3-(2H-1,3-benzodioxol-5-yl)-1-[(3R,5S)-3,5-dimethylpiperidin-1-yl]-3-(2-hydroxy-4,6-dimethoxyphenyl)propan-1-one · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 492 | 0.85 | 0.91 | 44 | 6Q6 |
| 2 | 453 | 0.84 | 0.90 | 34 | 6Q6 |
| 3 | 407 | 0.84 | 0.91 | 35 | 6Q6 |
| 4 | 402 | 0.83 | 0.91 | 34 | 6Q6 |
| 5 | 614 | 0.72 | 0.79 | 50 | empty |
Interfaces
5 interfaces between chains.
- A–B · 867 Ų buried · 4 hydrogen bonds · protein-protein
- C–D · 863 Ų buried · 6 hydrogen bonds · protein-protein
- B–D · 662 Ų buried · 2 hydrogen bonds · protein-protein
- B–C · 191 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 183 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 5K3N · Crystal structure of Retinoic acid receptor-related orphan receptor (ROR) gamma ligand… · 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 P51449
- Elsewhere: RCSB PDB 5K3N · PDBe 5K3N · UniProt P51449
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