4NMX: PCSK9(deltaCRD)

PCSK9(deltaCRD) in complex with phage-derived inhibitory peptide 2-8. Determined by X-ray diffraction at 1.85 Å resolution. Released 4 Dec 2013.

Method: X-ray diffraction
Resolution: 1.85 Å
Organism: Homo sapiens
Chains: 3
Atoms: 3,348
Mol. weight: 48.54 kDa
Released: 4 Dec 2013

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

Secondary structure: helices and β-sheets

4NMX contains 16 α-helices and 28 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: 4 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	88-104	17
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: 11 helices, 21 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
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	368-372	5	7
β-strand	378-382	5	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

Chain Z: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	3	1	7
α-helix	6-12	7

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
Proprotein convertase subtilisin/kexin type 9	A	protein	125	Homo sapiens	Q8NBP7 (AlphaFold model)
Proprotein convertase subtilisin/kexin type 9	B	protein	308	Homo sapiens	Q8NBP7 (AlphaFold model)
peptide 2-8	Z	protein	15

Sequence of entity 1 (A), FASTA

>4NMX_1 Proprotein convertase subtilisin/kexin type 9 (chains A)
AGSQEDEDGDYEELVLALRSEEDGLAEAPEHGTTATFHRCAKDPWRLPGTYVVVLKEETH
LSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDS
SVFAQ

Sequence of entity 2 (B), FASTA

>4NMX_2 Proprotein convertase subtilisin/kexin type 9 (chains B)
SIPWNLERITPPRYRADEYQPPDGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEED
GTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIR
KSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPE
VITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHV
AGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHGAG
NSHHHHHH

Sequence of entity 3 (Z), FASTA

>4NMX_3 peptide 2-8 (chains Z)
XTVFTSWEEYLDWVX

Primary citation

Identification of a Small Peptide That Inhibits PCSK9 Protein Binding to the Low Density Lipoprotein Receptor. Zhang, Y., Eigenbrot, C., Zhou, L. et al. J Biol Chem (2014) 289:942-955. DOI 10.1074/jbc.M113.514067 · 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
2QTW 1.9 Å, The Crystal Structure of PCSK9 at 1.9 Angstroms Resolution Reveals structural homology…
8WFR 1.95 Å, The Crystal Structure of PCSK9 from Biortus.

Browse structure collections

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