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 :  CRYSTAL STRUCTURE OF PCSK9(53-451) WITH ADNECTIN
 
Authors :  J. A. Khan
Date :  20 Feb 14  (Deposition) - 02 Jul 14  (Release) - 16 Jul 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.69
Chains :  Asym. Unit :  A,B,D,E,F,G
Biol. Unit 1:  A,B,F  (1x)
Biol. Unit 2:  D,E,G  (1x)
Keywords :  Pcsk9, Adnectin, Ldl-Cholesterol, Hydrolase-Protein Binding Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Mitchell, G. Chao, D. Sitkoff, F. Lo, H. Monshizadegan, D. Meyers, S. Low, K. Russo, R. Dibella, F. Denhez, M. Gao, J. Myers, G. Duke, M. Witmer, B. Miao, S. P. Ho, J. Khan, R. A. Parker
Pharmacologic Profile Of The Adnectin Bms-962476, A Small Protein Biologic Alternative To Pcsk9 Antibodies For Low-Density Lipoprotein Lowering.
J. Pharmacol. Exp. Ther. V. 350 412 2014
PubMed-ID: 24917546  |  Reference-DOI: 10.1124/JPET.114.214221

(-) Compounds

Molecule 1 - PROPROTEIN CONVERTASE SUBTILISIN/KEXIN TYPE 9
    Chains: A, D
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PACHLT
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: PRODOMAIN (UNP RESIDUES 60-152)
    Gene: PCSK9, NARC1, PSEC0052
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PCSK9, 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, E
    EC Number: 3.4.21.-
    Engineered: YES
    Expression System: TRICHOPLUSIA NI
    Expression System Cell Line: HIGH FIVE CELLS
    Expression System Common: CABBAGE LOOPER
    Expression System Plasmid: PACHLT
    Expression System Taxid: 7111
    Expression System Vector Type: BACULOVIRUS
    Fragment: CATALYTIC DOMAIN (UNP RESIDUES 153-446)
    Gene: PCSK9, NARC1, PSEC0052
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PCSK9, NEURAL APOPTOSIS-REGULATED CONVERTASE 1, NARC-1, PROPROTEIN CONVERTASE 9, PC9, SUBTILISIN/KEXIN-LIKE PROTEASE PC9
 
Molecule 3 - ADNECTIN
    Chains: F, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-9D
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit : ABDEFG
Biological Unit 1 (1x): AB  F 
Biological Unit 2 (1x):   DE G

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:72 , PHE A:150 , LYS B:258 , HIS F:80BINDING SITE FOR RESIDUE EDO A 201
2AC2SOFTWAREPHE B:318 , ARG B:319BINDING SITE FOR RESIDUE EDO B 501
3AC3SOFTWAREPHE B:379BINDING SITE FOR RESIDUE EDO B 502
4AC4SOFTWAREGLN B:413 , ILE B:416 , GLN E:413BINDING SITE FOR RESIDUE PG4 B 503
5AC5SOFTWARELEU D:108 , LYS D:125 , MET D:126 , HOH D:308BINDING SITE FOR RESIDUE PG4 D 201

(-) SS Bonds  (6, 6)

Asymmetric Unit
No.Residues
1B:223 -B:255
2B:323 -B:358
3B:375 -B:378
4E:223 -E:255
5E:323 -E:358
6E:375 -E:378

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Ser B:326 -Pro B:327
2Ser E:326 -Pro E:327
3Tyr F:29 -Gly F:30

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OV6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OV6)

(-) Exons   (0, 0)

(no "Exon" information available for 4OV6)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee...hhh.eeeeeeeeee......hhhhhhhhhhhhhhhhh....eeeeee.....eeeee.hhhhhhhhhh...eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4ov6 A  61 TATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    70        80        90       100       110       120       130       140       150  


Chain B from PDB  Type:PROTEIN  Length:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhh......eeeeee.............eeeeeee......hhhhh......hhhhhhhhhhhhh.........eeeeee......eeehhhhhhhhhhhhhhhhhh....eeeee.eeee.hhhhhhhhhhhhhh..eeeee......hhh.ee.......eeeeee.....................eeee...eeee.......eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhee...hhhhhhhhhh.....ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ov6 B 153 SIPWNLERITPPSLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDGTRFHRQASKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALPP 446
                                   162 ||    185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445 
                                     164|                                                                                                                                                                                                                                                                            
                                      178                                                                                                                                                                                                                                                                            


Chain D from PDB  Type:PROTEIN  Length:93
                                                                                                                             
               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
                 4ov6 D  60 TTATFHRCAKDPWRLPGTYVVVLKEETHLSQSERTARRLQAQAARRGYLTKILHVFHGLLPGFLVKMSGDLLELALKLPHVDYIEEDSSVFAQ 152
                                    69        79        89        99       109       119       129       139       149   


Chain E from PDB  Type:PROTEIN  Length:270
                                                                                                                                                                                                                                                                                                              
               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.....................eeee...eeee.......eeeeehhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhee...hhhhhhhhhh.....ee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ov6 E 153 SIPWNLERITPLVEVYLLDTSIQSDHREIEGRVMVTDFENVPEEDSKCDSHGTHLAGVVSGRDAGVAKGASMRSLRVLNCQGKGTVSGTLIGLEFIRKSQLVQPVGPLVVLLPLAGGYSRVLNAACQRLARAGVVLVTAAGNFRDDACLYSPASAPEVITVGATNAQDQPVTLGTLGTNFGRCVDLFAPGEDIIGASSDCSTCFVSQSGTSQAAAHVAGIAAMMLSAEPELTLAELRQRLIHFSAKDVINEAWFPEDQRVLTPNLVAALP 445
                                   162||     187       197       207    || 225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445
                                    163|                              212|                                                                                                                                                                                                                                
                                     179                               221                                                                                                                                                                                                                                


Chain F from PDB  Type:PROTEIN  Length:99
                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeee....eeee.........eeeeeeee.......eeeeehhhh.eeee.......eeeeeeeee........eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------- Transcript
                 4ov6 F  -1 GVSDVPRDLEVVAATPTSLLISWPPPSHGYGYYRITYGETGGNSPVQEFTVPPGKGTATISGLKPGVDYTITVYAVEYPYKHSGYYHRPISINYRTEID  97
                            ||       9        19        29        39        49        59        69        79|       88         
                           -1|                                                                            79A                  
                             1                                                                                                 


Chain G from PDB  Type:PROTEIN  Length:96
                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........eeeee....eeee.........eeeeeeee.......eeeeehhhh.eeee.......eeeeeeeee........eeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------ Transcript
                 4ov6 G  -1 GVSDVPRDLEVVAATPTSLLISWPPPSHGYGYYRITYGETGGNSPVQEFTVPPGKGTATISGLKPGVDYTITVYAVEYPYKHSGYYHRPISINYRT  94
                            ||       9        19        29        39        49        59        69        79|       88      
                           -1|                                                                            79A               
                             1
   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 4OV6)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OV6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OV6)

(-) Gene Ontology  (61, 61)

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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ser B:326 - Pro B:327   [ RasMol ]  
    Ser E:326 - Pro E:327   [ RasMol ]  
    Tyr F:29 - Gly F:30   [ 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
  4ov6
    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
  A0A075B5G3_H | A0A075B5G3
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
  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
  A0A075B5G3_H | A0A075B5G3
    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
        PCSK9_HUMAN | Q8NBP7: 2p4e 2pmw 2qtw 2w2m 2w2n 2w2o 2w2p 2w2q 2xtj 3bps 3gcw 3gcx 3h42 3m0c 3p5b 3p5c 3sqo 4k8r 4ne9 4nmx

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4OV6)