2W8Y: RU486

Name: PDB 2W8Y: RU486 bound to the progesterone receptor in a destabilized agonistic conformation
Published: 2009-04-28
License: https://creativecommons.org/publicdomain/zero/1.0/
Keywords: receptor

RU486 bound to the progesterone receptor in a destabilized agonistic conformation. Determined by X-ray diffraction at 1.8 Å resolution. Released 28 Apr 2009.

Method: X-ray diffraction
Resolution: 1.8 Å
Organism: HOMO SAPIENS
Chains: 2
Atoms: 4,370
Mol. weight: 60.82 kDa
Ligands: 486, NDR
Released: 28 Apr 2009

Explore 2W8Y in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

2W8Y contains 26 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: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	686-693	8
α-helix	695-698	4
α-helix	711-735	25
α-helix	739-741	3
α-helix	744-771	28
β-strand	776-779	4	1
β-strand	782-784	3	1
α-helix	786-791	6
α-helix	795-811	17
α-helix	815-826	12
β-strand	829-830	2	2
α-helix	838-857	20
α-helix	863-896	34
α-helix	898-901	4
α-helix	907-921	15
β-strand	926-927	2	2

Chain B: 14 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	686-693	8
α-helix	696-698	3
α-helix	708-709	2
α-helix	711-735	25
α-helix	739-741	3
α-helix	744-771	28
β-strand	776-779	4	3
β-strand	782-784	3	3
α-helix	786-788	3
α-helix	792-801	10
α-helix	803-811	9
α-helix	815-826	12
β-strand	829-831	3	4
α-helix	838-857	20
α-helix	863-896	34
α-helix	898-901	4
α-helix	907-921	15
β-strand	925-927	3	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Progesterone receptor	A, B	protein	260	HOMO SAPIENS	P06401 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>2W8Y_1 PROGESTERONE RECEPTOR (chains A, B)
GSHMGQDIQLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWS
KSLPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESS
FYSLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELI
KAIGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVI
AAQLPKILAGMVKPLLFHKK

Ligands and cofactors

ID	Name	Formula	Copies
486	11-(4-dimethylamino-phenyl)-17-hydroxy-13-methyl-17-prop-1-ynyl-1,2,6,7,8,11,12…	C29 H35 N O2	1
NDR	Norethindrone	C20 H26 O2	1

Water and common crystallization additives (SO4, EDO) are not listed.

Primary citation

The X-Ray Structure of Ru486 Bound to the Progesterone Receptor in a Destabilized Agonistic Conformation. Raaijmakers, H.C.A., Versteegh, J., Uitdehaag, J.C.M. J Biol Chem (2009) 284:19572. DOI 10.1074/JBC.M109.007872 · PubMed

Other PDB entries of the same protein (UniProt P06401 (AlphaFold model), which also has an AlphaFold model), best resolution first:

1SQN 1.45 Å, Progesterone Receptor Ligand Binding Domain with bound Norethindrone
1SR7 1.46 Å, Progesterone Receptor Hormone Binding Domain with Bound Mometasone Furoate
3ZR7 1.65 Å, Structural basis for agonism and antagonism for a set of chemically related progesterone…
1A28 1.8 Å, Hormone-bound human progesterone receptor ligand-binding domain
3ZRB 1.8 Å, Structural basis for agonism and antagonism for a set of chemically related progesterone…
3G8O 1.9 Å, Progesterone Receptor with bound Pyrrolidine 1
3ZRA 1.9 Å, Structural basis for agonism and antagonism for a set of chemically related progesterone…
4APU 1.9 Å, PR X-Ray structures in agonist conformations reveal two different mechanisms for partial…
1ZUC 2.0 Å, Progesterone receptor ligand binding domain in complex with the nonsteroidal agonist…
2OVH 2.0 Å, Progesterone Receptor with Bound Asoprisnil and a Peptide from the Co-Repressor SMRT
3KBA 2.0 Å, Progesterone receptor bound to sulfonamide pyrrolidine partial agonist
4A2J 2.0 Å, PR X-Ray structures in agonist conformations reveal two different mechanisms for partial…

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