Research workbench
Estrogen related receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen and a smrt peptide
Analyse Estrogen related receptor-gamma ligand binding domain complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GPV
- Type
- protein
- Length
- 1,331 residues
- Chains
- 9
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Estrogen-related receptor gamma; Nuclear receptor corepressor 2
- UniProt
- P62508, Q9Y618
- Ligands
- OHT
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 6 distinct chains · 68% helix, 4% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Estrogen-related receptor gamma | protein | 224 | 68% helix, 3% strand | P62508 |
| B, C | Estrogen-related receptor gamma | protein | 223 | 70% helix, 3% strand | P62508 |
| D | Estrogen-related receptor gamma | protein | 209 | 67% helix, 4% strand | P62508 |
| E | Estrogen-related receptor gamma | protein | 208 | 69% helix, 4% strand | P62508 |
| F | Estrogen-related receptor gamma | protein | 208 | 67% helix, 4% strand | P62508 |
| G, H, I | Nuclear receptor corepressor 2 | protein | 12 | 75% helix, 0% strand | Q9Y618 |
Ligands and binding sites
- OHT · 4-hydroxytamoxifen · ligand · 6 copies · chains A, G, B, H, C, I, D, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1014 | 0.80 | 0.81 | 77 | empty |
| 2 | 302 | 0.78 | 0.89 | 32 | OHT |
| 3 | 283 | 0.77 | 0.89 | 31 | OHT |
| 4 | 311 | 0.77 | 0.88 | 34 | OHT |
| 5 | 292 | 0.77 | 0.88 | 32 | OHT |
Interfaces
9 interfaces between chains.
- B–E · 1336 Ų buried · 14 hydrogen bonds · protein-protein
- C–F · 1329 Ų buried · 17 hydrogen bonds · protein-protein
- A–D · 1309 Ų buried · 13 hydrogen bonds · protein-protein
- B–D · 866 Ų buried · 3 hydrogen bonds · protein-protein
- A–E · 817 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 2GPV · Estrogen Related Receptor-gamma ligand binding domain complexed with 4-hydroxy-tamoxifen… · the same entry in another collection · chain I against I, TM-score 1.00
- P62508 · AlphaFold monomer V2.0 prediction for estrogen-related receptor gamma (P62508) · a predicted model of the same protein · chain E against A, TM-score 0.99
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 Q9Y618
- Elsewhere: RCSB PDB 2GPV · PDBe 2GPV · UniProt P62508 · UniProt Q9Y618
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.