3P5B: Proprotein convertase subtilisin/kexin type 9

The structure of the LDLR/PCSK9 complex reveals the receptor in an extended conformation. Determined by X-ray diffraction at 3.3 Å resolution. Released 26 Oct 2011.

Method: X-ray diffraction
Resolution: 3.3 Å
Organism: Homo sapiens
Chains: 3
Atoms: 7,464
Mol. weight: 112.74 kDa
Ligands: CA
Released: 26 Oct 2011

Explore 3P5B in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

3P5B contains 22 α-helices and 82 β-strands across 3 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: 14 helices, 39 β-strands

Element	Residues	Length	Sheet
α-helix	156-160	5
α-helix	168-170	3
β-strand	181-186	6	4
β-strand	201-206	6	4
α-helix	209-211	3
α-helix	225-234	10
β-strand	246-251	6	4
β-strand	258-260	3	2
α-helix	261-277	17
β-strand	283-287	5	4
β-strand	289	1	3
β-strand	291	1	5
α-helix	295-305	11
β-strand	309-314	6	4
β-strand	321	1	6
α-helix	322-324	3
β-strand	326	1	5
β-strand	334-339	6	4
β-strand	345	1	4
β-strand	347-348	2	7
β-strand	351-352	2	7
β-strand	355	1	6
β-strand	361-364	4	4
β-strand	368-371	4	8
β-strand	378-382	5	8
α-helix	385-402	18
α-helix	408-417	10
β-strand	419-421	3	4
α-helix	433-436	4
β-strand	440-442	3	4
α-helix	444-446	3
β-strand	456-461	6	9
α-helix	462-464	3
β-strand	472-475	4	10
β-strand	482-489	8	9
β-strand	495-496	2	10
β-strand	497	1	11
β-strand	498-502	5	10
β-strand	507-513	7	10
α-helix	514	1
β-strand	521-528	8	9
β-strand	533-539	7	11
β-strand	548-551	4	12
β-strand	558-565	8	11
β-strand	587-590	4	12
β-strand	595-602	8	11
β-strand	606-615	10	13
β-strand	621-625	5	9
α-helix	626-627	2
β-strand	631-638	8	13
β-strand	644-650	7	9
β-strand	653-658	6	9
β-strand	672-681	10	13

Chain L: 5 helices, 36 β-strands

Element	Residues	Length	Sheet
α-helix	301-303	3
β-strand	307-310	4	8
β-strand	315-318	4	8
β-strand	323-325	3	14
β-strand	331-333	3	14
β-strand	348	1	15
β-strand	355	1	15
α-helix	357-359	3
β-strand	360	1	16
β-strand	362	1	16
β-strand	379-384	6	17
β-strand	387-391	5	17
β-strand	399-402	4	17
β-strand	408-414	7	18
β-strand	419-424	6	18
β-strand	429-434	6	18
β-strand	445-448	4	18
β-strand	455-461	7	19
β-strand	466-471	6	19
β-strand	476-480	5	19
β-strand	487-492	6	19
β-strand	498-504	7	20
β-strand	509-514	6	20
β-strand	521-525	5	20
β-strand	532-535	4	20
β-strand	542-548	7	21
β-strand	553-558	6	21
β-strand	563-568	6	21
β-strand	575-579	5	21
β-strand	587-593	7	22
β-strand	596-601	6	22
β-strand	607-611	5	22
β-strand	619-622	4	22
β-strand	628-634	7	17
α-helix	636-638	3
α-helix	652-655	4
β-strand	659-662	4	23
α-helix	663-664	2
β-strand	673-676	4	23
β-strand	682-683	2	24
β-strand	690-691	2	24

Chain P: 3 helices, 7 β-strands

Element	Residues	Length	Sheet
β-strand	63-65	3	1
β-strand	73-82	10	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	148-150	3	2
β-strand	151	1	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proprotein convertase subtilisin/kexin type 9	P	protein	92	Homo sapiens	Q8NBP7 (AlphaFold model)
Proprotein convertase subtilisin/kexin type 9	A	protein	540	Homo sapiens	Q8NBP7 (AlphaFold model)
Low density lipoprotein receptor variant	L	protein	400	Homo sapiens	P01130 (AlphaFold model)

Sequence of entity 1 (P), FASTA

>3P5B_1 Proprotein convertase subtilisin/kexin type 9 (chains P)
TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLP
GFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ

Sequence of entity 2 (A), FASTA

>3P5B_2 Proprotein convertase subtilisin/kexin type 9 (chains A)
SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEED
GTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIR
KSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPE
VITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHV
AGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAG
WQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAH
NAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLG
THKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTL
TGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEGAVTAVAICCRSRHLAQASQELQ

Sequence of entity 3 (L), FASTA

>3P5B_3 Low density lipoprotein receptor variant (chains L)
NECLDNNGGCSHVCNDLKIGYECLCPDGFQLVAQRRCEDIDECQDPDTCSQLCVNLEGGY
KCQCEEGFQLDPHTKACKAVGSIAYLFFTNRHEVRKMTLDRSEYTSLIPNLRNVVALDTE
VASNRIYWSDLSQRMICSTQLDRAHGVSSYDTVISRDIQAPDGLAVDWIHSNIYWTDSVL
GTVSVADTKGVKRKTLFRENGSKPRAIVVDPVHGFMYWTDWGTPAKIKKGGLNGVDIYSL
VTENIQWPNGITLDLLSGRLYWVDSKLHSISSIDVNGGNRKTILEDEKRLAHPFSLAVFE
DKVFWTDIINEAIFSANRLTGSDVNLLAENLLSPEDMVLFHNLTQPRGVNWCERTTLSNG
GCQYLCLPAPQINPHSPKFTCACPDGMLLARDMRSCLTEA

Ligands and cofactors

ID	Name	Formula	Copies
CA	Calcium ion	Ca	3

Primary citation

Mechanistic implications for LDL receptor degradation from the PCSK9/LDLR structure at neutral pH. Lo Surdo, P., Bottomley, M.J., Calzetta, A. et al. EMBO Rep (2011) 12:1300-1305. DOI 10.1038/embor.2011.205 · 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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