3D90: Progesterone receptor

Crystal structure of the human progesterone receptor ligand-binding domain bound to levonorgestrel. Determined by X-ray diffraction at 2.26 Å resolution. Released 26 May 2009.

Method: X-ray diffraction
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,365
Mol. weight: 60.1 kDa
Ligands: NOG
Released: 26 May 2009

Explore 3D90 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3D90 contains 24 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	695-700	6
α-helix	711-733	23
α-helix	739-741	3
α-helix	744-770	27
β-strand	776-779	4	1
β-strand	782-784	3	1
α-helix	786-788	3
α-helix	792-801	10
α-helix	803-811	9
α-helix	815-826	12
β-strand	829-830	2	2
α-helix	838-856	19
α-helix	864-896	33
α-helix	907-921	15
β-strand	926-927	2	2

Chain B: 12 helices, 4 β-strands

Element	Residues	Length	Sheet
α-helix	686-693	8
α-helix	697-699	3
α-helix	711-735	25
α-helix	739-741	3
α-helix	744-769	26
β-strand	776-779	4	3
β-strand	782-784	3	3
α-helix	786-790	5
α-helix	795-811	17
α-helix	815-826	12
β-strand	829-830	2	4
α-helix	838-857	20
α-helix	865-896	32
α-helix	898-901	4
α-helix	907-922	16
β-strand	926-927	2	4

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Progesterone receptor	A, B	protein	258	Homo sapiens	P06401 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>3D90_1 Progesterone receptor (chains A, B)
SPGQDIQLIPPLINLLMSIEPDVIYAGHDNTKPDTSSSLLTSLNQLGERQLLSVVKWSKS
LPGFRNLHIDDQITLIQYSWMSLMVFGLGWRSYKHVSGQMLYFAPDLILNEQRMKESSFY
SLCLTMWQIPQEFVKLQVSQEEFLCMKVLLLLNTIPLEGLRSQTQFEEMRSSYIRELIKA
IGLRQKGVVSSSQRFYQLTKLLDNLHDLVKQLHLYCLNTFIQSRALSVEFPEMMSEVIAA
QLPKILAGMVKPLLFHKK

Ligands and cofactors

ID	Name	Formula	Copies
NOG	13-beta-ethyl-17-alpha-ethynyl-17-beta-hydroxygon-4-en-3-one	C21 H28 O2	2

Primary citation

Met909 plays a key role in the activation of the progesterone receptor and also in the high potency of 13-ethyl progestins. Petit-Topin, I., Turque, N., Fagart, J. et al. Mol Pharmacol (2009) 75:1317-1324. DOI 10.1124/mol.108.054312 · 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
2W8Y 1.8 Å, RU486 bound to the progesterone receptor in a destabilized agonistic conformation
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

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