Research workbench
Crystal structure of mineralocorticoid receptor ligand binding domain in complex with esaxerenone
Analyse Crystal structure of mineralocorticoid receptor ligand binding domain in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6L88
- Type
- protein
- Length
- 755 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mineralocorticoid receptor
- UniProt
- P08235
- Ligands
- E6R
- Pockets
- 6 · best druggability 0.77
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mineralocorticoid receptor | protein | 195 | 65% helix, 4% strand | P08235 |
| B | Mineralocorticoid receptor | protein | 183 | 66% helix, 3% strand | P08235 |
| C | Mineralocorticoid receptor | protein | 188 | 65% helix, 3% strand | P08235 |
| D | Mineralocorticoid receptor | protein | 189 | 67% helix, 3% strand | P08235 |
Ligands and binding sites
- E6R · 1-(2-hydroxyethyl)-4-methyl-N-(4-methylsulfonylphenyl)-5-[2-(trifluoromethyl)phenyl]pyrrole-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
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 984 | 0.77 | 0.79 | 79 | E6R |
| 2 | 681 | 0.72 | 0.78 | 61 | E6R |
| 3 | 646 | 0.71 | 0.78 | 57 | E6R |
| 4 | 555 | 0.67 | 0.77 | 63 | E6R |
| 5 | 324 | 0.56 | 0.75 | 35 | empty |
Interfaces
3 interfaces between chains.
- B–C · 2090 Ų buried · 28 hydrogen bonds · protein-protein
- A–D · 2055 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 593 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 6L88 · Crystal structure of mineralocorticoid receptor ligand binding domain in complex with… · the same entry in another collection · chain D against D, TM-score 1.00
- P08235 · AlphaFold monomer V2.0 prediction for mineralocorticoid receptor (P08235) · a predicted model of the same protein · chain A against A, TM-score 0.83
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 P08235
- Elsewhere: RCSB PDB 6L88 · PDBe 6L88 · UniProt P08235
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