8PKN: 3-hydroxy-3-methylglutaryl-coenzyme A reductase

CryoEM structure of catalytic domain of human HMG-CoA reductase with its inhibitor atorvastatin. Determined by electron microscopy at 2.26 Å resolution. Released 15 Jan 2025.

Method: Electron microscopy
Resolution: 2.26 Å
Organism: Homo sapiens
Chains: 1
Atoms: 3,192
Mol. weight: 45.82 kDa
Ligands: 117
Released: 15 Jan 2025

Explore 8PKN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

8PKN contains 21 α-helices and 17 β-strands across 1 chain. 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: 21 helices, 17 β-strands

Element	Residues	Length	Sheet
α-helix	442-444	3
α-helix	449-453	5
α-helix	464-472	9
α-helix	478-480	3
α-helix	488-501	14
α-helix	508-511	4
β-strand	538-546	9	1
β-strand	549-556	8	1
α-helix	562-575	14
β-strand	579	1	1
β-strand	580-587	8	2
β-strand	588-590	3	3
β-strand	593-595	3	4
α-helix	599-610	12
α-helix	612-623	12
β-strand	630-631	2	3
β-strand	635-639	5	4
β-strand	642-646	5	4
β-strand	647-650	4	3
β-strand	654	1	5
α-helix	657-674	18
β-strand	679-682	4	4
α-helix	695-700	6
β-strand	703-712	10	2
α-helix	714-719	6
α-helix	725-731	7
α-helix	732-737	6
α-helix	738-742	5
β-strand	748-749	2	2
α-helix	753-763	11
α-helix	768-770	3
α-helix	771-774	4
β-strand	777-784	8	2
β-strand	790-800	11	2
β-strand	805	1	5
α-helix	807-810	4
α-helix	812-821	10
α-helix	833-859	27

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
3-hydroxy-3-methylglutaryl-coenzyme A reductase	A	protein	423	Homo sapiens	P04035 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>8PKN_1 3-hydroxy-3-methylglutaryl-coenzyme A reductase (chains A)
PREPRPNEECLQILGNAEKGAKFLSDAEIIQLVNAKHIPAYKLETLMETHERGVSIRRQL
LSKKLSEPSSLQYLPYRDYNYSLVMGACCENVIGYMPIPVGVAGPLCLDEKEFQVPMATT
EGCLVASTNRGCRAIGLGGGASSRVLADGMTRGPVVRLPRACDSAEVKAWLETSEGFAVI
KEAFDSTSRFARLQKLHTSIAGRNLYIRFQSRSGDAMGMNMISKGTEKALSKLHEYFPEM
QILAVSGNYCTDKKPAAINWIEGRGKSVVCEAVIPAKVVREVLKTTTEAMIEVNINKNLV
GSAMAGSIGGYNAHAANIVTAIYIACGQDAAQNVGSSNCITLMEASGPTNEDLYISCTMP
SIEIGTVGGGTNLLPQQACLQMLGVQGACKDNPGENARQLARIVCGTVMAGELSLMAALA
AGH

Ligands and cofactors

ID	Name	Formula	Copies
117	7-[2-(4-fluoro-phenyl)-5-isopropyl-3-phenyl-4-phenylcarbamoyl-pyrrol-1-yl]-…	C33 H35 F N2 O5	1

Primary citation

Cryo-EM structures of apo and atorvastatin-bound human 3-hydroxy-3-methylglutaryl-coenzyme A reductase. Karuppasamy, M., van Rooyen, J. Acta Crystallogr F Struct Biol Commun (2025) 81:118-122. DOI 10.1107/S2053230X25001098 · PubMed

Other PDB entries of the same protein (UniProt P04035 (AlphaFold model), which also has an AlphaFold model), best resolution first:

2R4F 1.7 Å, Substituted Pyrazoles as Hepatselective HMG-COA reductase inhibitors
3CCZ 1.7 Å, Thermodynamic and structure guided design of statin hmg-coa reductase inhibitors
1DQA 2.0 Å, Complex of the catalytic portion of human hmg-CoA reductase with hmg, CoA, and NADP+
2Q6B 2.0 Å, Design and synthesis of novel, conformationally restricted HMG-COA reductase inhibitors
2Q6C 2.0 Å, Design and synthesis of novel, conformationally restricted HMG-COA reductase inhibitors
2Q1L 2.05 Å, Design and Synthesis of Pyrrole-based, Hepatoselective HMG-CoA Reductase Inhibitors
3CD7 2.05 Å, Thermodynamic and structure guided design of statin hmg-coa reductase inhibitors
8S6B 2.06 Å, CryoEM structure of Apo form of catalytic domain of human HMG-CoA reductase
3CDA 2.07 Å, Thermodynamic and structure guided design of statin hmg-coa reductase inhibitors
1DQ8 2.1 Å, Complex of the catalytic portion of human hmg-CoA reductase with hmg and CoA
1HW8 2.1 Å, Complex of the catalytic portion of human hmg-CoA reductase with compactin (also known…
1HWL 2.1 Å, Complex of the catalytic portion of human hmg-CoA reductase with rosuvastatin (formally…

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