MolNFT v1 · #64646 · protein + DNA

Gr DNA-binding DOMAIN:SGK 16BP complex-44

3G9M · Glucocorticoid receptor: “Gr DNA-binding DOMAIN:SGK 16BP complex-44”. X-ray diffraction, 1 ligand (ZN), 4 pockets (best druggability 0.65). MolNFT v1 #64646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 3G9M
Type: protein + DNA
Length: 188 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 0.65

Structure

x-ray diffraction · 4 distinct chains · 40% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	78	40% helix, 10% strand	P06536
B	Glucocorticoid receptor	protein	78	41% helix, 10% strand	P06536
D	DNA (5'- D(TPCPGPGPAPCPAPAPAPAPTPGPTPTPCPT)-3')	dna	16	—	—
C	DNA (5'- D(APAPGPAPAPCPAPTPTPTPTPGPTPCPCPG)-3')	dna	16	—	—

Ligands and binding sites

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

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	368	0.65	0.80	50	EDO
2	54	0.34	0.78	10	empty
3	62	0.30	0.75	15	empty
4	51	0.26	0.74	16	empty

Interfaces

6 interfaces between chains.

D–C · 645 Å² buried · 62 hydrogen bonds · nucleic-nucleic
A–B · 570 Å² buried · 11 hydrogen bonds · protein-protein
B–D · 417 Å² buried · 5 hydrogen bonds · protein-nucleic
A–C · 362 Å² buried · 6 hydrogen bonds · protein-nucleic
B–C · 358 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3G9M · GR DNA-binding domain:Sgk 16bp complex-44 · 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 0.94

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 3G9M · PDBe 3G9M · UniProt P06536

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