Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Biological Unit 1
(-)Biological Unit 2
(-)Biological Unit 3
(-)Biological Unit 4
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURES OF UNLINKED NS2B-NS3 PROTEASE FROM ZIKA VIRUS AND ITS COMPLEX WITH A REVERSE PEPTIDE INHIBITOR
 
Authors :  W. W. Phoo, Z. Z. Zhang
Date :  02 Aug 16  (Deposition) - 14 Dec 16  (Release) - 25 Jan 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.58
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  G,H  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  A,B  (1x)
Biol. Unit 4:  E,F  (1x)
Keywords :  Zika Virus Protease, Serine Protease, Non-Structural Protein 3, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Zhang, Y. Li, Y. R. Loh, W. W. Phoo, A. W. Hung, C. Kang, D. Luo
Crystal Structure Of Unlinked Ns2B-Ns3 Protease From Zika Virus
Science V. 354 1597 2016
PubMed-ID: 27940580  |  Reference-DOI: 10.1126/SCIENCE.AAI9309

(-) Compounds

Molecule 1 - NS3 PROTEASE
    Chains: H, D, B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ZIKA VIRUS
    Organism Taxid: 64320
 
Molecule 2 - NS2B COFACTOR
    Chains: C, A, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Scientific: ZIKA VIRUS
    Organism Taxid: 64320

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x):       GH
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x): AB      
Biological Unit 4 (1x):     EF  

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 5GPI)

(-) Sites  (0, 0)

(no "Site" information available for 5GPI)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5GPI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5GPI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5GPI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5GPI)

(-) Exons   (0, 0)

(no "Exon" information available for 5GPI)

(-) 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:38
                                                                      
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........ee.....eeeeee.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 5gpi A  50 DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLV  87
                                    59        69        79        


Chain B from PDB  Type:PROTEIN  Length:154
                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeeee....eeeeeeeeee..eeeehhhhhh...eee..eee.eeeee....eeee...............eeeee.......eeeee..eeeee..eeeeee....hhhhh..eee.....eeee...eee.....eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gpi B  17 ETTDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR 170
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166    


Chain C from PDB  Type:PROTEIN  Length:37
                                                                     
               SCOP domains ------------------------------------- SCOP domains
               CATH domains ------------------------------------- CATH domains
               Pfam domains ------------------------------------- Pfam domains
         Sec.struct. author .eeeeee........ee.....eeeeee.....eee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------- PROSITE
                 Transcript ------------------------------------- Transcript
                 5gpi C  51 MYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLV  87
                                    60        70        80       


Chain D from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...eeeeeeee..eeeehhhhhh...eee..eee.eeeee....eeee...............eeeee.......eeeee..eeeee..eeeeee...........eee.....eeee...eee.....eeee...... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gpi D  18 TTDGVYRVMTSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR 170
                                    27|       42        52        62        72        82        92       102       112       122       132       142       152       162        
                                    27|                                                                                                                                         
                                     33                                                                                                                                         


Chain E from PDB  Type:PROTEIN  Length:38
                                                                      
               SCOP domains -------------------------------------- SCOP domains
               CATH domains -------------------------------------- CATH domains
               Pfam domains -------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........ee.....eeeeee.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------- PROSITE
                 Transcript -------------------------------------- Transcript
                 5gpi E  50 DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLV  87
                                    59        69        79        


Chain F from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeee......eeeeeeeee..eeeehhhhhh...ee....ee.eeeee....eeee...............eeeee.......eeeee..eeeee..eeeeee....hhhhh.eeee.....eeeee..eee.....eeee...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gpi F  19 TDGVYRVMTRRLLGSTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR 170
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168  


Chain G from PDB  Type:PROTEIN  Length:40
                                                                        
               SCOP domains ---------------------------------------- SCOP domains
               CATH domains ---------------------------------------- CATH domains
               Pfam domains ---------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee........ee.....eeeeee.....eee... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------- PROSITE
                 Transcript ---------------------------------------- Transcript
                 5gpi G  50 DMYIERAGDITWEKDAEVTGNSPRLDVALDESGDFSLVEE  89
                                    59        69        79        89


Chain H from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeeeee....eeeeee..eeeeehhhhh...eee..eee.eeeee....eeee...............eeeee.......eeeee..eeeee..eeeeee....hhhhh.eeee.....eeeee..eee.....eeee...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5gpi H  12 EVKKGETTDGVYRVMTTQVGVGVMQEGVFHTMWHVTKGAALRSGEGRLDPYWGDVKQDLVSYCGPWKLDAAWDGLSEVQLLAVPPGERAKNIQTLPGIFKTKDGDIGAVALDYPAGTSGSPILDKCGRVIGLYGNGVVIKNGSYVSAITQGKR 170
                                    21     || 37        47        57        67        77        87        97       107       117       127       137       147       157       167   
                                          27|                                                                                                                                        
                                           34
   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 5GPI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5GPI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5GPI)

(-) Gene Ontology  (58, 58)

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
(no "Ligands, Modified Residues, Ions" information available for 5gpi)
 
  Sites
(no "Sites" information available for 5gpi)
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5gpi)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ 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 | Biol. Unit 1 PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 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
  5gpi
    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
  POLG_ZIKV | Q32ZE1
    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)
  (no 'Enzyme Classificator' available)
    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
  POLG_ZIKV | Q32ZE1
    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
        POLG_ZIKV | Q32ZE1: 5gj4 5jps 5jrz 5k6k 5t1v 5tfr 5tmh 5u04 5u0b 5u0c

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5GPI)