Research workbench

DNA binding DOMAIN:GILZ 16BP complex-5

Analyse DNA binding DOMAIN:GILZ 16BP complex-5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3G8U
Type: protein + DNA
Length: 183 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; DNA (5'-D(*TP*GP*GP*AP*AP*CP*CP*CP*AP*AP*TP*GP*TP*TP*CP*T)- 3')…
UniProt: P06536
Ligands: ZN
Pockets: 4 · best druggability 0.68

Structure

x-ray diffraction · 4 distinct chains · 38% helix, 8% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	79	39% helix, 8% strand	P06536
B	Glucocorticoid receptor	protein	72	38% helix, 8% strand	P06536
D	DNA (5'-D(TPGPGPAPAPCPCPCPAPAPTPGPTPTPCPT)- 3')	dna	16	—	—
C	DNA (5'-D(APAPGPAPAPCPAPTPTPGPGPGPTPTPCPC)- 3')	dna	16	—	—

Ligands and binding sites

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

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

Pockets

4 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	489	0.68	0.79	41	empty
2	59	0.39	0.80	11	empty
3	68	0.32	0.76	17	empty
4	59	0.28	0.75	14	empty

Interfaces

6 interfaces between chains.

D–C · 616 Å² buried · 64 hydrogen bonds · nucleic-nucleic
A–B · 585 Å² buried · 9 hydrogen bonds · protein-protein
A–C · 396 Å² buried · 4 hydrogen bonds · protein-nucleic
B–C · 367 Å² buried · 7 hydrogen bonds · protein-nucleic
A–D · 362 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3G8U · DNA binding domain:GilZ 16bp complex-5 · 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 B against A, TM-score 0.97

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 3G8U · PDBe 3G8U · UniProt P06536

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