MolNFT v1 · #64649 · protein + DNA

Gr DNA binding DOMAIN:SGK 16BP complex-7

3G9P · Glucocorticoid receptor: “Gr DNA binding DOMAIN:SGK 16BP complex-7”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.67). MolNFT v1 #64649 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3G9P
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(*TP*CP*GP*GP*AP*CP*AP*AP*AP*AP*TP*GP*TP*TP*CP*T)- 3')…
UniProt: P06536
Ligands: ZN
Pockets: 4 · best druggability 0.67

Structure

x-ray diffraction · 3 distinct chains · 33% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B, A	Glucocorticoid receptor	protein	75	33% helix, 11% strand	P06536
C	DNA (5'-D(TPCPGPGPAPCPAPAPAPAPTPGPTPTPCPT)- 3')	dna	16	—	—
D	DNA (5'-D(APAPGPAPAPCPAPTPTPTPTPGPTPCPCPG)- 3')	dna	16	—	—

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

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	377	0.67	0.81	44	empty
2	93	0.44	0.80	22	empty
3	59	0.28	0.74	17	empty
4	50	0.24	0.73	17	empty

Interfaces

6 interfaces between chains.

C–D · 629 Å² buried · 61 hydrogen bonds · nucleic-nucleic
B–A · 592 Å² buried · 10 hydrogen bonds · protein-protein
A–C · 421 Å² buried · 9 hydrogen bonds · protein-nucleic
B–D · 409 Å² buried · 7 hydrogen bonds · protein-nucleic
B–C · 385 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3G9P · GR DNA binding domain:Sgk 16bp complex-7 · the same entry in another collection · chain B against B, 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 3G9P · PDBe 3G9P · UniProt P06536

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