MolNFT v1 · #94123 · protein + DNA

Gr DNA binding domain R460D/D462R - tslp ngre complex

4HN6 · Glucocorticoid receptor: “Gr DNA binding domain R460D/D462R - tslp ngre complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.56). MolNFT v1 #94123 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4HN6
Type: protein + DNA
Length: 176 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; DNA (5'-D(*CP*GP*CP*CP*TP*CP*CP*GP*GP*GP*AP*GP*AP*GP*CP*T)- 3')…
UniProt: P04150
Ligands: ZN
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 3 distinct chains · 32% helix, 8% strand (DSSP).

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

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	271	0.56	0.77	20	empty
2	106	0.48	0.80	16	empty
3	96	0.33	0.73	17	empty

Interfaces

5 interfaces between chains.

C–D · 736 Å² buried · 80 hydrogen bonds · nucleic-nucleic
A–D · 397 Å² buried · 7 hydrogen bonds · protein-nucleic
A–C · 282 Å² buried · 5 hydrogen bonds · protein-nucleic
C–B · 277 Å² buried · 6 hydrogen bonds · protein-nucleic
D–B · 263 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

4HN6 · GR DNA Binding Domain R460D/D462R - TSLP nGRE Complex · the same entry in another collection · chain A against A, TM-score 1.00
P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 4HN6 · PDBe 4HN6 · UniProt P04150

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