MolNFT v1 · #64550 · protein + DNA

Gr DNA binding DOMAIN:FKBP5 complex, 18BP

3G6P · DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*…: “Gr DNA binding DOMAIN:FKBP5 complex, 18BP”. X-ray diffraction, 1 ligand (ZN), 3 pockets (best druggability 0.66). MolNFT v1 #64550 on GenesisL1: 3D structure, binding…

PDB: 3G6P
Type: protein + DNA
Length: 191 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*CP*CP*CP*TP*GP*TP*TP*CP*TP*G)-3'); DNA (5'…
UniProt: P06536
Ligands: ZN
Pockets: 3 · best druggability 0.66

Structure

x-ray diffraction · 4 distinct chains · 33% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
C	DNA (5'- D(CPCPAPGPAPAPCPAPCPCPCPTPGPTPTPCPTPG)-3')	dna	18	—	—
D	DNA (5'- D(CPCPAPGPAPAPCPAPGPGPGPTPGPTPTPCPTPG)-3')	dna	18	—	—
A	Glucocorticoid receptor	protein	74	32% helix, 11% strand	P06536
B	Glucocorticoid receptor	protein	81	33% helix, 10% strand	P06536

Ligands and binding sites

ZN · Zinc ion · metal · 4 copies · chains A, B
ACT · Acetate ion · additive · 3 copies · chains C, D, 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	495	0.66	0.78	44	ACT
2	66	0.33	0.76	17	empty
3	75	0.32	0.75	17	empty

Interfaces

6 interfaces between chains.

C–D · 805 Å² buried · 82 hydrogen bonds · nucleic-nucleic
A–B · 583 Å² buried · 10 hydrogen bonds · protein-protein
C–A · 410 Å² buried · 7 hydrogen bonds · protein-nucleic
D–B · 408 Å² buried · 13 hydrogen bonds · protein-nucleic
D–A · 394 Å² buried · 6 hydrogen bonds · protein-nucleic

Compared structures

3G6P · GR DNA binding domain:FKBP5 complex, 18bp · the same entry in another collection · chain C against C, TM-score 1.00
P06536 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P06536) · 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 P06536
Elsewhere: RCSB PDB 3G6P · PDBe 3G6P · UniProt P06536

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