5CBY: AncGR2 DNA Binding Domain - (+)GRE Complex

AncGR2 DNA Binding Domain - (+)GRE Complex. Determined by X-ray diffraction at 2.0 Å resolution. Released 23 Dec 2015.

Method: X-ray diffraction
Resolution: 2.0 Å
Organisms: UNCLASSIFIED, synthetic construct
Chains: 4
Atoms: 2,020
Mol. weight: 34.81 kDa
Ligands: ZN
Released: 23 Dec 2015

Explore 5CBY in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5CBY contains 7 α-helices and 8 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 3 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	420	1	1
β-strand	427	1	1
α-helix	428	1
β-strand	430-432	3	2
β-strand	435-437	3	2
α-helix	439-450	12
α-helix	474-484	11

Chain B: 4 helices, 4 β-strands

Element	Residues	Length	Sheet
β-strand	420	1	3
β-strand	427	1	3
α-helix	428	1
β-strand	430-432	3	4
β-strand	435-437	3	4
α-helix	439-450	12
α-helix	469-471	3
α-helix	474-483	10

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
AncGR2 DNA Binding Domain	A, B	protein	105	UNCLASSIFIED	P04150 (AlphaFold model)
DNA (5'-d(cpcpapgpapapcpapgpapgptpgptptpcptpg)-3')	C	DNA	18	synthetic construct
DNA (5'-d(tpcpapgpapapcpapcptpcptpgptptpcptpg)-3')	D	DNA	18	synthetic construct

Sequence of entity 1 (A, B), FASTA

>5CBY_1 AncGR2 DNA Binding Domain (chains A, B)
MHHHHHHSSGVDLGTENLYFQSNAGPPPKICLVCSDEASGCHYGVLTCGSCKVFFKRAVE
GQHNYLCAGRNDCIIDKIRRKNCPACRFRKCLQAGMNLEARKTKK

Sequence of entity 2 (C), FASTA

>5CBY_2 DNA (5'-D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3') (chains C)
CCAGAACAGAGTGTTCTG

Sequence of entity 3 (D), FASTA

>5CBY_3 DNA (5'-D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3') (chains D)
TCAGAACACTCTGTTCTG

Ligands and cofactors

ID	Name	Formula	Copies
ZN	Zinc ion	Zn	4

Primary citation

Distal substitutions drive divergent DNA specificity among paralogous transcription factors through subdivision of conformational space. Hudson, W.H., Kossmann, B.R., de Vera, I.M. et al. Proc Natl Acad Sci U S A (2016) 113:326-331. DOI 10.1073/pnas.1518960113 · PubMed

Other PDB entries of the same protein (UniProt P04150 (AlphaFold model), which also has an AlphaFold model), best resolution first:

4UDD 1.8 Å, GR in complex with desisobutyrylciclesonide
5E69 1.85 Å, Glucocorticoid receptor DNA binding domain - IL8 NF-kB response element complex
4HN5 1.9 Å, GR DNA Binding Domain - TSLP nGRE Complex
4P6W 1.95 Å, Crystal Structure of mometasone furoate-bound glucocorticoid receptor ligand binding…
8A9G 1.96 Å, Binary complex of 14-3-3 zeta Glucocorticoid Receptor (GR) pT524 peptide stabilised by…
5CBX 2.0 Å, AncGR DNA Binding Domain - (+)GRE Complex
6X6E 2.0 Å, Glucocorticoid Receptor DNA binding domain in complex with methylated precursor for a…
5UC3 2.01 Å, Structure of the dominant negative mutant Glucocorticoid Receptor alpha (L733K/N734P)…
6YMO 2.02 Å, Binary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pS617 peptide
6YO8 2.09 Å, Binary complex of 14-3-3 zeta with Glucocorticoid Receptor (GR) pT524 peptide
3K22 2.1 Å, Glucocorticoid Receptor with Bound alaninamide 10 with TIF2 peptide
5NFP 2.1 Å, Glucocorticoid Receptor in complex with budesonide

Browse structure collections

About this viewer

MolViewer shows 5CBY directly in your browser with nothing to install. Switch between cartoon, ball-and-stick, spacefill and surface views, color by chain, secondary structure or B-factor, measure distances, angles and dihedrals, and share or embed the view.