Research workbench
X-ray co-structure of nuclear receptor ror-gammat ligand binding domain with an inverse agonist and SRC2 peptide
Analyse X-ray co-structure of nuclear receptor ror-gammat ligand binding domain with an… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VB5
- Type
- protein
- Length
- 259 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Nuclear receptor ror-gamma, SRC2 chimera
- UniProt
- P51449
- Ligands
- 92A, NA
- Pockets
- 4 · best druggability 0.83
Structure
x-ray diffraction · 1 distinct chain · 71% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Nuclear receptor ror-gamma, SRC2 chimera | protein | 259 | 71% helix, 4% strand | P51449 |
Ligands and binding sites
- 92A · N-[(2R)-3-(4-{[3-(4-chlorophenyl) propanoyl]amino}phenyl)-1-(4-methylpiperidin-1-yl)-1-oxopropan-2-yl]-4-methylpentanamide · ligand · chains A
- NA · Sodium ion · metal · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 397 | 0.83 | 0.91 | 36 | 92A |
| 2 | 148 | 0.52 | 0.79 | 19 | empty |
| 3 | 65 | 0.38 | 0.79 | 13 | NA |
| 4 | 98 | 0.35 | 0.74 | 18 | empty |
Compared structures
- 5VB5 · X-ray co-structure of nuclear receptor ROR-gammat Ligand Binding Domain with an inverse… · 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 5VB5 · PDBe 5VB5 · UniProt P51449
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