Research workbench
Rorgamma in complex with inverse agonist 48
Analyse Rorgamma in complex with inverse agonist 48 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZJR
- Type
- protein
- Length
- 876 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 4P3
- Pockets
- 13 · best druggability 0.81
Structure
x-ray diffraction · 4 distinct chains · 70% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 217 | 70% helix, 5% strand | P51449 |
| B | Nuclear receptor ror-gamma | protein | 220 | 70% helix, 5% strand | P51449 |
| C | Nuclear receptor ror-gamma | protein | 220 | 69% helix, 5% strand | P51449 |
| D | Nuclear receptor ror-gamma | protein | 219 | 71% helix, 5% strand | P51449 |
Ligands and binding sites
- 4P3 · 6-chloro-4'-[(2-chloro-6-fluorobenzoyl)(methyl)amino]-3'-(2,2,2-trifluoroethoxy)biphenyl-3-carboxamide · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
13 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 591 | 0.81 | 0.86 | 55 | 4P3 |
| 2 | 446 | 0.79 | 0.86 | 35 | 4P3 |
| 3 | 451 | 0.79 | 0.86 | 38 | 4P3 |
| 4 | 692 | 0.78 | 0.82 | 58 | 4P3 |
| 5 | 179 | 0.53 | 0.79 | 18 | empty |
Interfaces
4 interfaces between chains.
- A–B · 861 Ų buried · 8 hydrogen bonds · protein-protein
- C–D · 802 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 56 Ų buried · 0 hydrogen bonds · protein-protein
- B–D · 48 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4ZJR · RORgamma in complex with inverse agonist 48 · 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 4ZJR · PDBe 4ZJR · UniProt P51449
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