MolNFT v1 · #144350 · protein + DNA

Human gr (418-507) in complex with monomeric DNA binding site

6BQU · Glucocorticoid receptor: “Human gr (418-507) in complex with monomeric DNA binding site”. X-ray diffraction, 1 ligand (ZN), 2 pockets (best druggability 0.69). MolNFT v1 #144350 on GenesisL1: 3D structure, binding sites and pockets…

PDB: 6BQU
Type: protein + DNA
Length: 175 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; DNA (5'- D(P*TP*GP*CP*AP*AP*AP*TP*GP*TP*AP*CP*TP*AP*GP*CP*T)-3')…
UniProt: P04150
Ligands: ZN
Pockets: 2 · best druggability 0.69

Structure

x-ray diffraction · 4 distinct chains · 34% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
B	Glucocorticoid receptor	protein	72	32% helix, 11% strand	P04150
C	DNA (5'- D(PTPGPCPAPAPAPTPGPTPAPCPTPAPGPCPT)-3')	dna	16	—	—
D	DNA (5'- D(PAPAPGPCPTPAPGPTPAPCPAPTPTPTPGPC)-3')	dna	16	—	—
A	Glucocorticoid receptor	protein	71	37% helix, 8% strand	P04150

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

2 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	517	0.69	0.79	38	empty
2	70	0.36	0.78	18	empty

Interfaces

5 interfaces between chains.

C–D · 682 Å² buried · 69 hydrogen bonds · nucleic-nucleic
B–A · 612 Å² buried · 9 hydrogen bonds · protein-protein
B–C · 405 Å² buried · 7 hydrogen bonds · protein-nucleic
B–D · 362 Å² buried · 11 hydrogen bonds · protein-nucleic
D–A · 167 Å² buried · 5 hydrogen bonds · protein-nucleic

Compared structures

6BQU · Human GR (418-507) in complex with monomeric DNA binding site · the same entry in another collection · chain B against B, TM-score 1.00
P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain A 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 P04150
Elsewhere: RCSB PDB 6BQU · PDBe 6BQU · UniProt P04150

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