Research workbench
Structure of rorgt in complex with a novel agonist.
Analyse Structure of rorgt in complex with a novel agonist. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6E3G
- Type
- protein
- Length
- 506 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma; Co-activator peptide
- UniProt
- P51449
- Ligands
- HOJ
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 73% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Nuclear receptor ror-gamma | protein | 245 | 73% helix, 4% strand | P51449 |
| C, D | Co-activator peptide | protein | 8 | 75% helix, 0% strand | — |
Ligands and binding sites
- HOJ · (5R)-6-acetyl-2-methoxy-N-{4-[(2-methoxyphenyl) methoxy]phenyl}-5,6,7,8-tetrahydro-1,6-naphthyridine-5-carboxamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 339 | 0.81 | 0.91 | 38 | HOJ |
| 2 | 320 | 0.81 | 0.91 | 38 | HOJ |
| 3 | 1175 | 0.78 | 0.80 | 84 | empty |
| 4 | 212 | 0.53 | 0.78 | 20 | empty |
| 5 | 86 | 0.40 | 0.78 | 15 | empty |
Interfaces
3 interfaces between chains.
- B–D · 503 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 486 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 438 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 6E3G · Structure of RORgt in complex with a novel agonist. · 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 6E3G · PDBe 6E3G · UniProt P51449
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