Research workbench
Crystal structure of retinoic acid receptor-related orphan receptor (ror) gamma ligand binding domain complex with SBI0654919
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
- 5K6E
- Type
- protein
- Length
- 460 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 6QP
- Pockets
- 8 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 226 | 68% helix, 4% strand | P51449 |
| B | Nuclear receptor ror-gamma | protein | 234 | 66% helix, 4% strand | P51449 |
Ligands and binding sites
- 6QP · 2-chloranyl-6-fluoranyl-~{N}-[(2~{R})-4-(4-fluorophenyl)sulfonyl-2-(hydroxymethyl)-2,3-dihydro-1, 4-benzoxazin-6-yl]benzamide · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 892 | 0.82 | 0.84 | 80 | 6QP |
| 2 | 482 | 0.80 | 0.87 | 41 | 6QP |
| 3 | 69 | 0.43 | 0.81 | 12 | empty |
| 4 | 106 | 0.43 | 0.77 | 17 | empty |
| 5 | 66 | 0.41 | 0.81 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 900 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 5K6E · 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 5K6E · PDBe 5K6E · UniProt P51449
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