MolNFT v1 · #117923 · protein + DNA

Transcription factor grdbd and mmgre complex

5EMP · Glucocorticoid receptor: “Transcription factor grdbd and mmgre complex”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.68). MolNFT v1 #117923 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5EMP
Type: protein + DNA
Length: 178 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor; DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*TP*GP*AP*TP*GP*TP*TP*CP*TP*G)…
UniProt: P04150
Ligands: ZN
Pockets: 3 · best druggability 0.68

Structure

x-ray diffraction · 3 distinct chains · 35% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Glucocorticoid receptor	protein	71	35% helix, 11% strand	P04150
C	DNA (5'- D(CPCPAPGPAPAPCPAPTPGPAPTPGPTPTPCPTPG)-3')	dna	18	—	—
D	DNA (5'-D(PCPCPAPGPAPAPCPAPTP(5CM) PAPTPGPTPTPCPTPG)-3')	dna	18	—	—

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	478	0.68	0.79	42	empty
2	95	0.38	0.76	18	empty
3	59	0.28	0.75	15	empty

Interfaces

6 interfaces between chains.

C–D · 791 Å² buried · 72 hydrogen bonds · nucleic-nucleic
A–B · 601 Å² buried · 10 hydrogen bonds · protein-protein
A–D · 377 Å² buried · 5 hydrogen bonds · protein-nucleic
B–C · 338 Å² buried · 8 hydrogen bonds · protein-nucleic
A–C · 331 Å² buried · 6 hydrogen bonds · protein-nucleic

Modifications

Observed in the structure: 1 modified (nucleotide modification).

Compared structures

5EMP · Transcription factor GRDBD and mmGRE 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 0.96

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 P04150
Elsewhere: RCSB PDB 5EMP · PDBe 5EMP · UniProt P04150

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