MolNFT v1 · #64643 · protein + DNA

Gr DNA binding DOMAIN:PAL, 18BP complex-36

3G9J · DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*…: “Gr DNA binding DOMAIN:PAL, 18BP complex-36”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.64). MolNFT v1 #64643 on GenesisL1: 3D structure, binding…

PDB: 3G9J
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*AP*AP*AP*TP*GP*TP*TP*CP*TP*G)-3'); DNA (5'…
UniProt: P06536
Ligands: ZN
Pockets: 3 · best druggability 0.64

Structure

x-ray diffraction · 4 distinct chains · 37% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'- D(CPCPAPGPAPAPCPAPAPAPAPTPGPTPTPCPTPG)-3')	dna	18	—	—
D	DNA (5'- D(CPCPAPGPAPAPCPAPTPTPTPTPGPTPTPCPTPG)-3')	dna	18	—	—
A	Glucocorticoid receptor	protein	74	36% helix, 11% strand	P06536
B	Glucocorticoid receptor	protein	79	38% helix, 10% strand	P06536

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · chains C, D, 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	363	0.64	0.80	51	EDO
2	71	0.36	0.77	14	empty
3	69	0.36	0.78	18	empty

Interfaces

6 interfaces between chains.

C–D · 820 Å² buried · 69 hydrogen bonds · nucleic-nucleic
A–B · 569 Å² buried · 10 hydrogen bonds · protein-protein
D–B · 455 Å² buried · 14 hydrogen bonds · protein-nucleic
C–A · 396 Å² buried · 8 hydrogen bonds · protein-nucleic
C–B · 358 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3G9J · GR DNA binding domain:Pal, 18bp complex-36 · the same entry in another collection · chain C against C, 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 3G9J · PDBe 3G9J · UniProt P06536

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