Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PCSK9 IN COMPLEX WITH LDLR PEPTIDE
 
Authors :  S. Liu
Date :  28 Oct 13  (Deposition) - 10 Sep 14  (Release) - 10 Sep 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,P
Biol. Unit 1:  A,P  (1x)
Biol. Unit 2:  B,C,D  (1x)
Keywords :  Pcsk9, Ldl Receptor, Autocatalytic Cleavage, Cholesterol Metabolism, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. I. Schroeder, J. E. Swedberg, J. M. Withka, K. J. Rosengren, M. Akcan D. J. Clayton, N. L. Daly, O. Cheneval, K. A. Borzilleri, M. Griffor, I. Stock, B. Colless, P. Walsh, P. Sunderland, A. Reyes, R. Dullea, M. Ammirati, S. Liu, K. F. Mcclure, M. Tu, S. K. Bhattacharya, S. Liras, D. A. Price, D. J. Craik
Design And Synthesis Of Truncated Egf-A Peptides That Restore Ldl-R Recycling In The Presence Of Pcsk9 In Vitro.
Chem. Biol. V. 21 284 2014
PubMed-ID: 24440079  |  Reference-DOI: 10.1016/J.CHEMBIOL.2013.11.014

(-) Compounds

Molecule 1 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
    Chains: A, B
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 153-692
    Gene: PCSK9, NARC1, 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: C, P
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 1-152
    Gene: PCSK9, NARC1, 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 - LOW-DENSITY LIPOPROTEIN RECEPTOR
    Chains: D
    Engineered: YES
    Expression System: SPODOPTERA FRUGIPERDA
    Expression System Taxid: 7108
    Fragment: UNP RESIDUES 314-339
    Gene: LDLR
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: LDL RECEPTOR

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit : ABCDP
Biological Unit 1 (1x): A   P
Biological Unit 2 (1x):  BCD 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 4)

Asymmetric Unit (3, 4)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC1Ligand/IonALPHA-L-FUCOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2FUC-1Ligand/IonALPHA-L-FUCOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:533 , FUC A:902BINDING SITE FOR RESIDUE NAG A 901
2AC2SOFTWARENAG A:901BINDING SITE FOR RESIDUE FUC A 902
3AC3SOFTWAREASN B:533BINDING SITE FOR RESIDUE NAG B 901
4AC4SOFTWARETHR D:2 , GLU D:4 , ASP D:18 , LEU D:19 , GLY D:22BINDING SITE FOR RESIDUE CA D 101

(-) SS Bonds  (26, 26)

Asymmetric Unit
No.Residues
1A:223 -A:255
2A:323 -A:358
3A:375 -A:378
4A:457 -A:527
5A:477 -A:526
6A:486 -A:509
7A:534 -A:601
8A:552 -A:600
9A:562 -A:588
10A:608 -A:679
11A:626 -A:678
12A:635 -A:654
13B:223 -B:255
14B:323 -B:358
15B:375 -B:378
16B:457 -B:527
17B:477 -B:526
18B:486 -B:509
19B:534 -B:601
20B:552 -B:600
21B:562 -B:588
22B:608 -B:679
23B:626 -B:678
24B:635 -B:654
25D:5 -D:16
26D:12 -D:25

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ser A:326 -Pro A:327
2Ser B:326 -Pro B:327

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NE9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NE9)

(-) Exons   (0, 0)

(no "Exon" information available for 4NE9)

(-) Sequences/Alignments

Asymmetric 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:491
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh.........eeeeee.............eeeeeee.......hhhhhhhh..hhhhhhhhhhhhh.........eeeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.......ee..ee........eeee...eeee.......eeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee...hhhhhhhhhh.....ee.......eeeeee..........eeee......eeeeeeee.....eeeeeeee....eeeeeee.......eeeeeeee....eeeeeee........eeee.....eeeeeeeee.........eeee....eeeeeeee...eeeeeeeeee.....eeeee.....eeeeeee......eeeeeee..eeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne9 A 153 SIPWNLERITPPRYRASLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRAVTAVAICCRSR 682
                                   162     ||181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441    || 458       468       478       488       498       508       518       528       538       548       558       568   ||  590       600       610       620       630       640       650       671       681 
                                         168|                                                                                                                                                                                                                                                                         446|                                                                                                                   572|                                                                       659|           
                                          178                                                                                                                                                                                                                                                                          454                                                                                                                    585                                                                        671           


Chain B from PDB  Type:PROTEIN  Length:490
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhh...........eeeeee.............eeeeeee.......hhhhhhhhhhhhhhhhh..........eeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.......ee..ee........eeee...eeee......eeeee.hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhh.ee...hhhhhhhhhh.....ee..........eeeeee..........eeee......eeeeeeee.....eeeeeeeee..eeeeeeee.......eeeeeeee....eeeeeee........eeee.....eeeeeeeee.........eeee....eeeeeeee...eeeeeeeeee.....eeeee.....eeeeeee......eeeeeee..eeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ne9 B 153 SIPWNLERITPPRYRAGGSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPPSTHQLFCRTVWSAHSGPTRMATAIARCAPDEELLSCSSFSRSGKRRGERMEAQGGKLVCRAHNAFGGEGVYAIARCCLLPQANCSVHTAPPAEASMGTRVHCHQQGHVLTGCSSHWEVEDLGPNQCVGHREASIHASCCHAPGLECKVKEHGIPAPQEQVTVACEEGWTLTGCSALPGTSHVLGAYAVDNTCVVRSRAVTAVAICCRSR 682
                                   162     ||179       189       199       209  ||   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445   ||  459       469       479       489       499       509       519       529       539       549       559       569  ||   591       601       611       621       631       641       651       672       682
                                         168|                                 212|                                                                                                                                                                                                                                   449|                                                                                                                   572|                                                                       659|           
                                          176                                  219                                                                                                                                                                                                                                    454                                                                                                                    585                                                                        671           


Chain C from PDB  Type:PROTEIN  Length:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhh.eeeeeeeeee....hhhhhhhhhhhhhhhhhh.....eeeeee.....eeeee.hhhhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4ne9 C  61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    70        80        90       100       110       120       130       140       150  


Chain D from PDB  Type:PROTEIN  Length:26
                                                          
               SCOP domains -------------------------- SCOP domains
               CATH domains -------------------------- CATH domains
               Pfam domains -------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh..eeee....eeee Sec.struct. author
                 SAPs(SNPs) -------------------------- SAPs(SNPs)
                    PROSITE -------------------------- PROSITE
                 Transcript -------------------------- Transcript
                 4ne9 D   1 GTNECLDNNGGCSHVCNDLKIGYECL  26
                                    10        20      


Chain P 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
                 4ne9 P  61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    70        80        90       100       110       120       130       140       150
   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 4NE9)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NE9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NE9)

(-) Gene Ontology  (96, 111)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FUC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser A:326 - Pro A:327   [ RasMol ]  
    Ser B:326 - Pro B:327   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ne9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  LDLR_HUMAN | P01130
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  PCSK9_HUMAN | Q8NBP7
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  LDLR_HUMAN | P01130
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  PCSK9_HUMAN | Q8NBP7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        LDLR_HUMAN | P01130: 1ajj 1d2j 1f5y 1f8z 1hj7 1hz8 1i0u 1ijq 1ldl 1ldr 1lrx 1n7d 1xfe 2fcw 2kri 2lgp 2m7p 2mg9 2w2m 2w2n 2w2o 2w2p 2w2q 3bps 3gcw 3gcx 3m0c 3p5b 3p5c 3so6
        PCSK9_HUMAN | Q8NBP7: 2p4e 2pmw 2qtw 2w2m 2w2n 2w2o 2w2p 2w2q 2xtj 3bps 3gcw 3gcx 3h42 3m0c 3p5b 3p5c 3sqo 4k8r 4nmx 4ov6

(-) Related Entries Specified in the PDB File

2p4e APO PCSK9