Research workbench
Estrogen related receptor-gamma ligand binding domain complexed with a RIP140 peptide and synthetic ligand GSK4716
Analyse Estrogen related receptor-gamma ligand binding domain complexed with a RIP140… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GPP
- Type
- protein
- Length
- 473 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen-related receptor gamma; Nuclear receptor-interacting protein 1
- UniProt
- P62508, P48552
- Ligands
- 1BA
- Pockets
- 9 · best druggability 0.79
Structure
x-ray diffraction · 4 distinct chains · 66% helix, 3% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen-related receptor gamma | protein | 225 | 64% helix, 3% strand | P62508 |
| B | Estrogen-related receptor gamma | protein | 224 | 68% helix, 4% strand | P62508 |
| C | Nuclear receptor-interacting protein 1 | protein | 11 | 64% helix, 0% strand | P48552 |
| D | Nuclear receptor-interacting protein 1 | protein | 13 | 54% helix, 0% strand | P48552 |
Ligands and binding sites
- 1BA · 4-hydroxy-N'-(4-isopropylbenzyl)benzohydrazide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 144 | 0.79 | 0.96 | 28 | 1BA |
| 2 | 85 | 0.77 | 0.98 | 18 | empty |
| 3 | 374 | 0.64 | 0.79 | 30 | empty |
| 4 | 218 | 0.62 | 0.82 | 28 | empty |
| 5 | 324 | 0.60 | 0.78 | 29 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1382 Ų buried · 17 hydrogen bonds · protein-protein
- B–D · 580 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 495 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 2GPP · Estrogen Related Receptor-gamma ligand binding domain complexed with a RIP140 peptide and… · the same entry in another collection · chain D against D, TM-score 1.00
- P62508 · AlphaFold monomer V2.0 prediction for estrogen-related receptor gamma (P62508) · a predicted model of the same protein · chain B against A, TM-score 0.99
- P48552 · AlphaFold monomer V2.0 prediction for nuclear receptor-interacting protein 1 (P48552) · a predicted model of the same protein · chain C against A, TM-score 0.62
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 P62508
- Every structure of UniProt P48552
- Elsewhere: RCSB PDB 2GPP · PDBe 2GPP · UniProt P62508 · UniProt P48552
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