MolNFT v1 · #141516 · protein
Ligand complex of rorgt lbd
5ZA1 · Nuclear receptor ror-gamma: “Ligand complex of rorgt lbd”. X-ray diffraction, 1 ligand (9A0), 7 pockets (best druggability 0.83). MolNFT v1 #141516 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ZA1
- Type
- protein
- Length
- 454 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma
- UniProt
- P51449
- Ligands
- 9A0
- Pockets
- 7 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 67% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma | protein | 230 | 67% helix, 5% strand | P51449 |
| B | Nuclear receptor ror-gamma | protein | 224 | 66% helix, 5% strand | P51449 |
Ligands and binding sites
- 9A0 · 2-[4-({[4-(ethylsulfonyl)phenyl]acetyl}amino)phenyl]-2-methyl-N-phenylpropanamide · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- DMF · Dimethylformamide · additive · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 335 | 0.83 | 0.92 | 34 | 9A0, EDO |
| 2 | 895 | 0.81 | 0.83 | 78 | 9A0, EDO |
| 3 | 216 | 0.65 | 0.83 | 30 | empty |
| 4 | 219 | 0.55 | 0.78 | 22 | empty |
| 5 | 76 | 0.49 | 0.83 | 13 | EDO |
Interfaces
1 interface between chains.
- A–B · 797 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 5ZA1 · Ligand complex of RORgt LBD · 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 5ZA1 · PDBe 5ZA1 · UniProt P51449
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