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(-) Description

Title :  PCSK9(DELTACRD) IN COMPLEX WITH PHAGE-DERIVED INHIBITORY PEPTIDE 2-8
 
Authors :  C. Eigenbrot, S. Shia
Date :  15 Nov 13  (Deposition) - 04 Dec 13  (Release) - 29 Jan 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym./Biol. Unit :  A,B,Z
Keywords :  Subtlisin, Receptor Degradation, Ldl Receptor, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Zhang, C. Eigenbrot, L. Zhou, S. Shia, W. Li, C. Quan, J. Tom, P. Moran P. Di Lello, N. J. Skelton, M. Kong-Beltran, A. Peterson, D. Kirchhofer
Identification Of A Small Peptide That Inhibits Pcsk9 Protein Binding To The Low Density Lipoprotein Receptor.
J. Biol. Chem. V. 289 942 2014
PubMed-ID: 24225950  |  Reference-DOI: 10.1074/JBC.M113.514067

(-) Compounds

Molecule 1 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
    Chains: A
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: PROPEPTIDE (UNP RESIDUES 31-152)
    Gene: NARC1, PCSK9, PSEC0052
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9
 
Molecule 2 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
    Chains: B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Common: FALL ARMYWORM
    Expression System Taxid: 7108
    Expression System Vector Type: BACULOVIRUS
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 153-452)
    Gene: NARC1, PCSK9, PSEC0052
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9
 
Molecule 3 - PEPTIDE 2-8
    Chains: Z
    Engineered: YES
    Other Details: SYNTHETIC PEPTIDE LIBRARY DISPLAYED ON M13 PHAGE
    Synthetic: YES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 2)

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2NH21Mod. Amino AcidAMINO GROUP

(-) Sites  (0, 0)

(no "Site" information available for 4NMX)

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1B:223 -B:255
2B:323 -B:358
3B:375 -B:378

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ser B:326 -Pro B:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NMX)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NMX)

(-) Exons   (0, 0)

(no "Exon" information available for 4NMX)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhhh....eeeeee.....eeeee.hhhhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4nmx A  61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    70        80        90       100       110       120       130       140       150  


Chain B from PDB  Type:PROTEIN  Length:278
                                                                                                                                                                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh.......eeeeee.............eeeeeee.............hhhhhhhhhhhhh.........eeeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.......ee..ee........eeee...eeeee.....eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee...hhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nmx B 153 SIPWNLERITPGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFSKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPP 446
                                   162||     184       194       204       214 ||    228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438        
                                    163|                                     216|                                                                                                                                                                                                                                 
                                     176                                      221                                                                                                                                                                                                                                 


Chain Z from PDB  Type:PROTEIN  Length:15
                                               
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                 4nmx Z   0 xTVFTSWEEYLDWVx  14
                            |        9    |
                            0-ACE        14-NH2
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NMX)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NMX)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NMX)

(-) Gene Ontology  (61, 61)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ser B:326 - Pro B:327   [ RasMol ]  
 

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  4nmx
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  PCSK9_HUMAN | Q8NBP7
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PCSK9_HUMAN | Q8NBP7: 2p4e 2pmw 2qtw 2w2m 2w2n 2w2o 2w2p 2w2q 2xtj 3bps 3gcw 3gcx 3h42 3m0c 3p5b 3p5c 3sqo 4k8r 4ne9 4ov6

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4NMX)