4NE9: PCSK9

PCSK9 in complex with LDLR peptide. Determined by X-ray diffraction at 2.6 Å resolution. Released 10 Sept 2014.

Method: X-ray diffraction
Resolution: 2.6 Å
Organism: Homo sapiens
Chains: 5
Atoms: 8,999
Mol. weight: 152.36 kDa
Ligands: CA, NAG
Released: 10 Sept 2014

Explore 4NE9 in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

4NE9 contains 44 α-helices and 93 β-strands across 5 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: 15 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	156-161	6
β-strand	181-186	6	1
β-strand	200-206	7	1
α-helix	209-211	3
α-helix	215-220	6
α-helix	225-235	11
β-strand	246-251	6	1
β-strand	258-260	3	2
α-helix	261-277	17
β-strand	283-287	5	1
β-strand	289-292	4	2
α-helix	295-306	12
β-strand	310-314	5	1
β-strand	318	1	3
β-strand	321	1	4
α-helix	322-324	3
β-strand	325-326	2	2
β-strand	334-339	6	1
α-helix	344	1
β-strand	345	1	1
α-helix	346	1
β-strand	347-348	2	3
β-strand	351-352	2	3
β-strand	355	1	4
β-strand	361-364	4	1
β-strand	368-371	4	5
β-strand	379-382	4	5
α-helix	385-402	18
α-helix	408-417	10
β-strand	420-421	2	1
α-helix	426-428	3
α-helix	431-433	3
β-strand	440-441	2	1
β-strand	456-461	6	6
α-helix	462-464	3
β-strand	472-475	4	7
β-strand	482-489	8	6
β-strand	495-496	2	7
β-strand	497	1	8
β-strand	498-502	5	7
β-strand	507-513	7	7
β-strand	521-528	8	6
β-strand	533-539	7	8
β-strand	548-551	4	9
β-strand	557-565	9	8
β-strand	587-590	4	9
β-strand	595-602	8	8
β-strand	606-615	10	10
β-strand	621-625	5	6
α-helix	626-627	2
β-strand	631-637	7	10
β-strand	644-650	7	6
β-strand	653-658	6	6
β-strand	672-681	10	10

Chain B: 17 helices, 40 β-strands

Element	Residues	Length	Sheet
α-helix	156-161	6
β-strand	181-186	6	11
β-strand	200-206	7	11
α-helix	209-211	3
α-helix	220-223	4
α-helix	225-235	11
β-strand	247-251	5	11
β-strand	258-260	3	12
α-helix	261-277	17
α-helix	279-280	2
β-strand	283-287	5	11
β-strand	289-290	2	12
β-strand	291-292	2	13
α-helix	295-306	12
β-strand	310-314	5	11
β-strand	318	1	14
β-strand	321	1	15
α-helix	322-324	3
β-strand	325-326	2	13
β-strand	334-339	6	11
α-helix	344	1
β-strand	345	1	11
α-helix	346	1
β-strand	347-348	2	14
β-strand	351-352	2	14
β-strand	355	1	15
β-strand	361-364	4	11
β-strand	368-371	4	16
β-strand	378-382	5	16
α-helix	385-402	18
α-helix	408-417	10
β-strand	420-421	2	11
α-helix	426-428	3
α-helix	431-433	3
β-strand	440-441	2	11
α-helix	444-446	3
β-strand	456-461	6	17
α-helix	462-464	3
β-strand	472-475	4	18
β-strand	482-489	8	17
β-strand	495-496	2	18
β-strand	497	1	19
β-strand	498-503	6	18
β-strand	506-513	8	18
β-strand	521-528	8	17
β-strand	533-539	7	19
β-strand	548-551	4	20
β-strand	557-565	9	19
β-strand	587-590	4	20
β-strand	595-602	8	19
β-strand	606-615	10	21
β-strand	621-625	5	17
α-helix	626-627	2
β-strand	631-637	7	21
β-strand	644-650	7	17
β-strand	653-658	6	17
β-strand	672-681	10	21

Chain C: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	22
α-helix	70-72	3
β-strand	73-82	10	22
α-helix	83	1
α-helix	88-103	16
β-strand	110-115	6	22
β-strand	121-125	5	22
α-helix	128-130	3
α-helix	131-135	5
β-strand	140-147	8	22
β-strand	148-151	4	12

Chain D: 2 helices, 2 β-strands

Element	Residues	Length	Sheet
α-helix	4-6	3
α-helix	8-11	4
β-strand	16-18	3	16
β-strand	23-25	3	16

Chain P: 5 helices, 6 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	23
α-helix	70-72	3
β-strand	73-82	10	23
α-helix	83	1
α-helix	88-104	17
β-strand	110-115	6	23
β-strand	121-125	5	23
α-helix	128-130	3
α-helix	131-135	5
β-strand	140-147	8	23
β-strand	148-151	4	2

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proprotein convertase subtilisin/kexin type 9	A, B	protein	540	Homo sapiens	Q8NBP7 (AlphaFold model)
Proprotein convertase subtilisin/kexin type 9	C, P	protein	152	Homo sapiens	Q8NBP7 (AlphaFold model)
Low-density lipoprotein receptor	D	protein	26	Homo sapiens	P01130 (AlphaFold model)

Sequence of entity 1 (A, B), FASTA

>4NE9_1 Proprotein convertase subtilisin/kexin type 9 (chains A, B)
SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEED
GTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIR
KSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPE
VITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHV
AGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAG
WQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAH
NAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLG
THKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTL
TGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEEAVTAVAICCRSRHLAQASQELQ

Sequence of entity 2 (C, P), FASTA

>4NE9_2 Proprotein convertase subtilisin/kexin type 9 (chains C, P)
MGTVSSRRSWWPLPLLLLLLLLLGPAGARAQEDEDGDYEELVLALRSEEDGLAEAPEHGT
TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLP
GFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ

Sequence of entity 3 (D), FASTA

>4NE9_3 Low-density lipoprotein receptor (chains D)
GTNECLDNNGGCSHVCNDLKIGYECL

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	1
NAG	2-acetamido-2-deoxy-beta-D-glucopyranose	C8 H15 N O6	1

Primary citation

Design and synthesis of truncated EGF-A peptides that restore LDL-R recycling in the presence of PCSK9 in vitro. Schroeder, C.I., Swedberg, J.E., Withka, J.M. et al. Chem Biol (2014) 21:284-294. DOI 10.1016/j.chembiol.2013.11.014 · 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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