Research workbench

Gr DNA binding domain - tslp ngre complex

Analyse Gr DNA binding domain - tslp ngre complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4HN5
Type: protein + DNA
Length: 177 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: 4 · best druggability 0.54

Structure

x-ray diffraction · 4 distinct chains · 32% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	72	31% helix, 11% strand	P04150
C	DNA (5'-D(CPGPCPCPTPCPCPGPGPGPAPGPAPGPCPT)- 3')	dna	16	—	—
D	DNA (5'-D(APGPCPTPCPTPCPCPCPGPGPAPGPGPCPG)- 3')	dna	16	—	—
B	Glucocorticoid receptor	protein	73	34% helix, 11% strand	P04150

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

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	255	0.54	0.77	24	empty
2	131	0.48	0.79	16	empty
3	107	0.36	0.74	20	empty
4	52	0.23	0.72	10	empty

Interfaces

5 interfaces between chains.

C–D · 738 Å² buried · 83 hydrogen bonds · nucleic-nucleic
A–D · 383 Å² buried · 11 hydrogen bonds · protein-nucleic
D–B · 276 Å² buried · 5 hydrogen bonds · protein-nucleic
A–C · 271 Å² buried · 6 hydrogen bonds · protein-nucleic
C–B · 271 Å² buried · 7 hydrogen bonds · protein-nucleic

Compared structures

4HN5 · GR DNA Binding Domain - 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 0.97

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 4HN5 · PDBe 4HN5 · UniProt P04150

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