Research workbench

Gr DNA binding DOMAIN:CGT complex

Analyse Gr DNA binding DOMAIN:CGT complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FYL
Type: protein + DNA
Length: 182 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; DNA (5'-D(*AP*AP*GP*AP*AP*CP*AP*TP*TP*TP*TP*GP*TP*CP*CP*G)- 3')…
UniProt: P06536
Ligands: ZN
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	74	35% helix, 11% strand	P06536
B	Glucocorticoid receptor	protein	76	36% helix, 11% strand	P06536
C	DNA (5'-D(APAPGPAPAPCPAPTPTPTPTPGPTPCPCPG)- 3')	dna	16	—	—
D	DNA (5'-D(TPCPGPGPAPCPAPAPAPAPTPGPTPTPCPT)- 3')	dna	16	—	—

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · chains A, B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	359	0.66	0.81	48	empty
2	75	0.33	0.75	15	empty
3	50	0.26	0.74	18	empty

Interfaces

6 interfaces between chains.

C–D · 654 Å² buried · 67 hydrogen bonds · nucleic-nucleic
A–B · 592 Å² buried · 12 hydrogen bonds · protein-protein
A–C · 428 Å² buried · 8 hydrogen bonds · protein-nucleic
B–D · 424 Å² buried · 7 hydrogen bonds · protein-nucleic
B–C · 350 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3FYL · GR DNA binding domain:CGT complex · the same entry in another collection · chain A against A, TM-score 1.00
P06536 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P06536) · a predicted model of the same protein · chain A against A, TM-score 0.96

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 P06536
Elsewhere: RCSB PDB 3FYL · PDBe 3FYL · UniProt P06536

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