5VLP: Proprotein convertase subtilisin/kexin type 9

PCSK9 complex with LDLR antagonist peptide and Fab7G7. Determined by X-ray diffraction at 2.9 Å resolution. Released 16 Aug 2017.

Method: X-ray diffraction
Resolution: 2.9 Å
Organisms: Homo sapiens, Mus musculus, synthetic construct
Chains: 4
Atoms: 7,814
Mol. weight: 125.32 kDa
Released: 16 Aug 2017

Explore 5VLP in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5VLP contains 39 α-helices and 87 β-strands across 4 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: 20 helices, 44 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	88-104	17
β-strand	110-115	6	1
β-strand	121-125	5	1
α-helix	128-130	3
α-helix	131-136	6
β-strand	140-147	8	1
β-strand	148-151	4	2
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	261-276	16
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	321	1	5
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	6
β-strand	351-352	2	6
β-strand	355	1	5
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	408-418	11
β-strand	420-421	2	3
α-helix	426-428	3
α-helix	431-434	4
β-strand	440-441	2	3
β-strand	456-461	6	8
α-helix	462-464	3
β-strand	472-475	4	9
β-strand	482-489	8	8
β-strand	495-503	9	9
β-strand	506-513	8	9
β-strand	521-528	8	8
β-strand	533-539	7	9
β-strand	549	1	10
β-strand	557-566	10	9
α-helix	576-578	3
β-strand	579	1	11
α-helix	580-581	2
β-strand	591	1	11
β-strand	594-602	9	9
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

Chain H: 9 helices, 22 β-strands

Element	Residues	Length	Sheet
β-strand	3-6	4	13
α-helix	7-9	3
β-strand	10-12	3	14
β-strand	18-25	8	13
α-helix	29-31	3
β-strand	34-39	6	14
β-strand	46-52	7	14
β-strand	57-60	4	14
α-helix	62-64	3
β-strand	68-73	6	13
β-strand	78-83	6	13
α-helix	88-90	3
β-strand	92-101	10	14
β-strand	105	1	10
β-strand	109-114	6	14
β-strand	118-122	5	14
α-helix	126-127	2
β-strand	128	1	15
α-helix	129-130	2
β-strand	131-135	5	16
β-strand	146-156	11	16
β-strand	157	1	15
β-strand	162-165	4	17
β-strand	173-176	4	16
α-helix	177-179	3
β-strand	180-182	3	16
β-strand	185-195	11	16
α-helix	198-201	4
β-strand	204-210	7	17
α-helix	211-213	3
β-strand	215-221	7	17

Chain L: 9 helices, 21 β-strands

Element	Residues	Length	Sheet
α-helix	2-3	2
β-strand	4-6	3	18
β-strand	11-12	2	18
β-strand	18-25	8	18
β-strand	33-38	6	14
β-strand	45-49	5	14
β-strand	53-54	2	14
α-helix	55	1
β-strand	62-67	6	18
β-strand	70-76	7	18
α-helix	80-82	3
β-strand	85-90	6	14
α-helix	96	1
β-strand	97-98	2	14
β-strand	102-103	2	14
β-strand	111	1	19
β-strand	114-118	5	20
α-helix	119-121	3
α-helix	122-126	5
β-strand	129-139	11	20
β-strand	140	1	19
β-strand	144-150	7	21
β-strand	153-155	3	21
β-strand	159-163	5	20
α-helix	164-167	4
β-strand	173-182	10	20
α-helix	183-187	5
β-strand	191-198	8	21
α-helix	204	1
β-strand	205-210	6	21

Chain Z: 1 helix, 0 β-strands

Element	Residues	Length	Sheet
α-helix	1-5	5

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proprotein convertase subtilisin/kexin type 9	A	protein	700	Homo sapiens	Q8NBP7 (AlphaFold model)
Fab7G7 heavy chain	H	protein	223	Mus musculus
Fab7G7 light chain	L	protein	214	Mus musculus	A0A0U5BC76 (AlphaFold model)
LDLR antagonist peptide	Z	protein	17	synthetic construct

Sequence of entity 1 (A), FASTA

>5VLP_1 Proprotein convertase subtilisin/kexin type 9 (chains A)
MGTVSSRRSWWPLPLLLLLLLLLGPAGARAQEDEDGDYEELVLALRSEEDGLAEAPEHGT
TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLP
GFLVKMSGDLLELALKLPHVDYIEEDSSVFAQSIPWNLERITPPRYRADEYQPPDGGSLV
EVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAG
VAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAA
CQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVD
LFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSA
KDVINEAWFPEDQRVLTPNLVAALPPSTHGAGWQLFCRTVWSAHSGPTRMATAIARCAPD
EELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAP
PAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGTHKPPVLRPRGQPNQCVGHREASIHASC
CHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRD
VSTTGSTSEEAVTAVAICCRSRHLAQASQELQHHHHHHHH

Sequence of entity 2 (H), FASTA

>5VLP_2 Fab7G7 heavy chain (chains H)
QVQLKQSGAELVRPGASVKLSCKASGYIFTDYYINWLKKRPGQGLEWIARIYPGSGHTYY
NENFKDKATLTAEKSSSNVYMQLSSLTSEDSAVYFCARENFYGSSYVDWYFDVWGTGTTV
TVSSAKTTPPSVYPLAPGCGDTTGSSVTLGCLVKGYFPESVTVTWNSGSLSSSVHTFPAL
LQSGLYTMSSSVTVPSSTWPSQTVTCSVAHPASSTTVDKKLEP

Sequence of entity 3 (L), FASTA

>5VLP_3 Fab7G7 light chain (chains L)
DIVMTQSQKFMSTSGGDRVSITCKTSQNVGTAVAWFQQKPGQSPKLLIYSASNRYTGVSD
RFTGSGSGTEFIFTISYAQSEDLADYFCHQYSSYPLTFGAGTKLELKRADAAPTVSIFPP
SSEQLTSGGASVVCFLNNFYPKDINVKWKIDGSERQNGVLNSWTDQDSKDSTYSMSSTLT
LTKDEYERHNSYTCEATHKTSTSPIVKSFNRNEC

Sequence of entity 4 (Z), FASTA

>5VLP_4 LDLR antagonist peptide (chains Z)
XMESFPGWNLVRIGLLR

Primary citation

Discovery of a cryptic peptide-binding site on PCSK9 and design of antagonists. Zhang, Y., Ultsch, M., Skelton, N.J. et al. Nat Struct Mol Biol (2017) 24:848-856. DOI 10.1038/nsmb.3453 · 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…

Browse structure collections

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