Research workbench

Gr DNA binding DOMAIN:FKBP5 complex-52, 18BP

Analyse Gr DNA binding DOMAIN:FKBP5 complex-52, 18BP in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G6R
Type: protein + DNA
Length: 189 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*GP*GP*TP*GP*TP*TP*CP*TP*G)-3'); DNA (5'…
UniProt: P06536
Ligands: ZN
Pockets: 3 · best druggability 0.65

Structure

x-ray diffraction · 4 distinct chains · 35% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'- D(CPCPAPGPAPAPCPAPGPGPGPTPGPTPTPCPTPG)-3')	dna	18	—	—
D	DNA (5'- D(CPCPAPGPAPAPCPAPCPCPCPTPGPTPTPCPTPG)-3')	dna	18	—	—
B	Glucocorticoid receptor	protein	74	31% helix, 11% strand	P06536
A	Glucocorticoid receptor	protein	79	39% helix, 10% strand	P06536

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains B, A

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	378	0.65	0.79	53	empty
2	87	0.38	0.77	17	empty
3	62	0.30	0.75	16	empty

Interfaces

6 interfaces between chains.

C–D · 838 Å² buried · 80 hydrogen bonds · nucleic-nucleic
B–A · 567 Å² buried · 11 hydrogen bonds · protein-protein
D–A · 468 Å² buried · 12 hydrogen bonds · protein-nucleic
C–A · 361 Å² buried · 6 hydrogen bonds · protein-nucleic
C–B · 343 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3G6R · GR DNA binding domain:FKBP5 complex-52, 18bp · the same entry in another collection · chain D against D, TM-score 1.00
P06536 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P06536) · a predicted model of the same protein · chain B 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 3G6R · PDBe 3G6R · UniProt P06536

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