8VDV: Pcsk9

pcsk9 in complex with inhibitor. Determined by X-ray diffraction at 1.97 Å resolution. Released 26 Mar 2025.

Method: X-ray diffraction
Resolution: 1.97 Å
Organisms: Homo sapiens, synthetic construct
Chains: 3
Atoms: 4,633
Mol. weight: 67.83 kDa
Released: 26 Mar 2025

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

Secondary structure: helices and β-sheets

8VDV contains 21 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	131-135	5
β-strand	140-147	8	1
β-strand	148-151	4	2

Chain B: 16 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	431-433	3
β-strand	440-441	2	3
α-helix	444-446	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	495-496	2	9
β-strand	497	1	10
β-strand	498-503	6	9
β-strand	506-513	8	9
α-helix	514	1
β-strand	521-528	8	8
β-strand	533-539	7	10
β-strand	548-551	4	11
β-strand	558-566	9	10
β-strand	587-590	4	11
β-strand	594-602	9	10
β-strand	607-615	9	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	672-680	9	12

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proprotein convertase subtilisin/kexin type 9	A	protein	92	Homo sapiens	Q8NBP7 (AlphaFold model)
Proprotein convertase subtilisin/kexin type 9	B	protein	529	Homo sapiens	Q8NBP7 (AlphaFold model)
Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH	L	protein	11	synthetic construct

Sequence of entity 1 (A), FASTA

>8VDV_1 Proprotein convertase subtilisin/kexin type 9 (chains A)
TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLP
GFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ

Sequence of entity 2 (B), FASTA

>8VDV_2 Proprotein convertase subtilisin/kexin type 9 (chains B)
SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEED
GTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIR
KSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPE
VITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHV
AGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAG
WQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAH
NAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLG
THKPPVLRPRGQPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTL
TGCSALPGTSHVLGAYAVDNTCVVRSRDVSTTGSTSEGAVTAVAICCRS

Sequence of entity 3 (L), FASTA

>8VDV_3 Inhibitor YBX-PHE-VAL-GLY-THR-THR-PHA-MAA-BIF-EME-NEH (chains L)
XFVGTTFAFXX

Primary citation

PCSK9 in complex with inhibitor. Xu, M., Xu, M. To be published.

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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