6U2P: PCSK9

PCSK9 in complex with compound 5. Determined by X-ray diffraction at 2.04 Å resolution. Released 6 Nov 2019.

Method: X-ray diffraction
Resolution: 2.04 Å
Organism: Homo sapiens
Chains: 2
Atoms: 4,547
Mol. weight: 152.95 kDa
Ligands: PUV
Released: 6 Nov 2019

Explore 6U2P in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

6U2P contains 19 α-helices and 46 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: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	1
α-helix	70-72	3
β-strand	73-82	10	1
α-helix	83	1
α-helix	88-103	16
β-strand	110-115	6	1
β-strand	121-125	5	1
α-helix	128-130	3
α-helix	131-134	4
β-strand	140-147	8	1
β-strand	148-151	4	2

Chain B: 14 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	156-160	5
β-strand	181-186	6	3
β-strand	200-206	7	3
α-helix	209-211	3
α-helix	225-235	11
β-strand	246-251	6	3
β-strand	258-260	3	2
α-helix	261-277	17
β-strand	283-287	5	3
β-strand	289-290	2	2
β-strand	291-292	2	4
α-helix	295-306	12
β-strand	310-314	5	3
β-strand	318	1	5
β-strand	321	1	6
α-helix	322-324	3
β-strand	325-326	2	4
β-strand	334-339	6	3
α-helix	344	1
β-strand	345	1	3
α-helix	346	1
β-strand	347-348	2	5
β-strand	351-352	2	5
β-strand	355	1	6
β-strand	361-364	4	3
β-strand	368-371	4	7
β-strand	379-382	4	7
α-helix	385-402	18
α-helix	408-417	10
β-strand	420-421	2	3
α-helix	426-428	3
α-helix	433-436	4
β-strand	440-441	2	3
β-strand	456-461	6	8
β-strand	472-475	4	9
α-helix	477-478	2
β-strand	482-489	8	8
β-strand	495-496	2	9
β-strand	497	1	10
β-strand	498-503	6	9
β-strand	506-513	8	9
β-strand	521-528	8	8
β-strand	533-539	7	10
β-strand	548-551	4	11
β-strand	557-566	10	10
β-strand	587-590	4	11
β-strand	594-602	9	10
β-strand	606-615	10	12
β-strand	621-625	5	8
α-helix	626-627	2
β-strand	631-637	7	12
β-strand	644-650	7	8
β-strand	653-658	6	8
β-strand	672-681	10	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proprotein convertase subtilisin/kexin type 9	A, B	protein	707	Homo sapiens	Q8NBP7 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>6U2P_1 Proprotein convertase subtilisin/kexin type 9 (chains A, B)
QEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETHLSQ
SERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVF
AQSIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPE
EDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEF
IRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASA
PEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAA
HVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHG
AGWQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCR
AHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVED
LGTHKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGW
TLTGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQE
LQKGNSADIQHSGGRSSLEGPRFEGKPIPNPLLGLDSTRTGHHHHHH

Ligands and cofactors

ID	Name	Formula	Copies
PUV	2-fluoro-4-{[(1R)-6-methoxy-1-methyl-1-{2-oxo-2-[(1,3-thiazol-2-yl)amino]ethyl}…	C23 H22 F N3 O5 S	1

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

Primary citation

From Screening to Targeted Degradation: Strategies for the Discovery and Optimization of Small Molecule Ligands for PCSK9. Petrilli, W.L., Adam, G.C., Erdmann, R.S. et al. Cell Chem Biol (2020) 27:32-40.e3. DOI 10.1016/j.chembiol.2019.10.002 · PubMed

Other PDB entries of the same protein (UniProt Q8NBP7 (AlphaFold model), which also has an AlphaFold model), best resolution first:

7S5H 1.27 Å, PCSK9(deltaCRD) in complex with cyclic peptide 35
6XIC 1.38 Å, PCSK9(deltaCRD) in complex with cyclic peptide 40
6XIE 1.43 Å, PCSK9(deltaCRD) in complex with cyclic peptide 77
9HZ3 1.43 Å, PCSK9 AZD0780 complex
6XID 1.48 Å, PCSK9(deltaCRD) in complex with cyclic peptide 51
6U26 1.53 Å, PCSK9 in complex with compound 16
6XIB 1.55 Å, PCSK9(deltaCRD) in complex with cyclic peptide 30
9SZY 1.76 Å, PCSK9 CTD fragment structure
6XIF 1.77 Å, PCSK9(deltaCRD) in complex with cyclic peptide 83
10SB 1.83 Å, PCSK9 in complex with cyclic peptide 21
4NMX 1.85 Å, PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8
2QTW 1.9 Å, The Crystal Structure of PCSK9 at 1.9 Angstroms Resolution Reveals structural homology…

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