MolNFT v1 · #17949 · protein

Crystal structure of the agonist form of glucocorticoid receptor

1P93: “Crystal structure of the agonist form of glucocorticoid receptor”. X-ray diffraction, 1 ligand (DEX), 19 pockets (best druggability 0.84). MolNFT v1 #17949 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 1P93
Type: protein
Length: 1,022 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; Nuclear receptor coactivator 2
UniProt: P04150, Q15596
Ligands: DEX
Pockets: 19 · best druggability 0.84

Structure

x-ray diffraction · 3 distinct chains · 62% helix, 3% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C, D	Glucocorticoid receptor	protein	247	61% helix, 3% strand	P04150
E, F, G, H	Nuclear receptor coactivator 2	protein	9	67% helix, 0% strand	Q15596
B	Glucocorticoid receptor	protein	245	62% helix, 4% strand	P04150

Ligands and binding sites

DEX · Dexamethasone · ligand · 4 copies · chains A, B, C, D

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	248	0.84	0.96	30	DEX
2	248	0.84	0.95	30	DEX
3	211	0.84	0.97	30	DEX
4	223	0.83	0.96	35	DEX
5	412	0.76	0.85	50	empty

Interfaces

11 interfaces between chains.

C–D · 558 Å² buried · 0 hydrogen bonds · protein-protein
A–C · 502 Å² buried · 11 hydrogen bonds · protein-protein
A–B · 409 Å² buried · 1 hydrogen bond · protein-protein
A–E · 328 Å² buried · 2 hydrogen bonds · protein-protein
C–G · 327 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

1P93 · Crystal structure of the agonist form of glucocorticoid receptor · the same entry in another collection · chain H against H, TM-score 1.00
P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P04150
Every structure of UniProt Q15596
Elsewhere: RCSB PDB 1P93 · PDBe 1P93 · UniProt P04150 · UniProt Q15596

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