MolNFT v1 · #145150 · protein

Crystal structure of the DNA-free glucocorticoid receptor DNA binding domain

6CFN: “Crystal structure of the DNA-free glucocorticoid receptor DNA binding domain”. X-ray diffraction, 1 ligand (ZN), 5 pockets (best druggability 0.64). MolNFT v1 #145150 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6CFN
Type: protein
Length: 595 residues
Chains: 8
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Glucocorticoid receptor
UniProt: P04150
Ligands: ZN
Pockets: 5 · best druggability 0.64

Structure

x-ray diffraction · 8 distinct chains · 39% helix, 10% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Glucocorticoid receptor	protein	80	46% helix, 10% strand	P04150
B	Glucocorticoid receptor	protein	70	30% helix, 11% strand	P04150
C	Glucocorticoid receptor	protein	81	42% helix, 7% strand	P04150
D	Glucocorticoid receptor	protein	68	37% helix, 9% strand	P04150
E	Glucocorticoid receptor	protein	79	42% helix, 10% strand	P04150
F	Glucocorticoid receptor	protein	78	36% helix, 10% strand	P04150
G	Glucocorticoid receptor	protein	70	36% helix, 11% strand	P04150
H	Glucocorticoid receptor	protein	69	39% helix, 12% strand	P04150

Ligands and binding sites

ZN · Zinc ion · metal · 16 copies · chains A, B, C, D, E, F, G, H

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	325	0.64	0.80	23	empty
2	174	0.52	0.78	25	empty
3	146	0.42	0.74	22	empty
4	54	0.31	0.77	17	empty
5	51	0.28	0.75	17	empty

Interfaces

8 interfaces between chains.

D–E · 522 Å² buried · 3 hydrogen bonds · protein-protein
A–D · 371 Å² buried · 0 hydrogen bonds · protein-protein
B–C · 370 Å² buried · 1 hydrogen bond · protein-protein
E–G · 370 Å² buried · 1 hydrogen bond · protein-protein
F–H · 367 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

6CFN · Crystal Structure of the DNA-free Glucocorticoid Receptor DNA Binding Domain · the same entry in another collection · chain H against H, TM-score 1.00
P04150 · AlphaFold monomer V2.0 prediction for glucocorticoid receptor (P04150) · a predicted model of the same protein · chain D 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 6CFN · PDBe 6CFN · UniProt P04150

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