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

(-) Description

Title :  CRYSTAL STRUCTURE OF MHV NS2 PDE DOMAIN
 
Authors :  B. K. Sui, J. H. Huang, G. Q. Peng, L. Zhao
Date :  03 Apr 15  (Deposition) - 10 Feb 16  (Release) - 04 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.05
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Murine Hepatitis Virus, Ns2 Protein, Phosphodiesterase, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  B. K. Sui, J. H. Huang, B. K. Jha, P. Yin, M. Zhou, Z. F. Fu, R. H. Silverman S. R. Weiss, G. Q. Peng, L. Zhao
Crystal Structure Of The Mouse Hepatitis Virus Ns2 Phosphodiesterase Domain That Antagonizes Rnase L Activatio
J. Gen. Virol. V. 97 880 2016
PubMed-ID: 26757803  |  Reference-DOI: 10.1099/JGV.0.000395

(-) Compounds

Molecule 1 - NON-STRUCTURAL PROTEIN 2A
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 2-199
    Gene: 2A
    Organism Common: MHV-A59
    Organism Scientific: MURINE CORONAVIRUS (STRAIN A59)
    Organism Taxid: 11142
    Other Details: PHOSPHODIESTERASE
    Strain: A59
    Synonym: NS2A,30 KDA ACCESSORY PROTEIN,30 KDA NON-STRUCTURAL PROTEIN, NS2,P30

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric/Biological Unit (1, 8)
No.NameCountTypeFull Name
1MSE8Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (0, 0)

(no "Site" information available for 4Z5V)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4Z5V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Lys B:6 -Pro B:7
2Ile B:167 -Gly B:168

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Z5V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Z5V)

(-) Exons   (0, 0)

(no "Exon" information available for 4Z5V)

(-) 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:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...hhhhhhhhhhhhhhhhhh...eee....eeeeeeee....hhhhhhhhhhhhhhhhhhhheeeeeeeeeee..eeeeeee.hhhhhhhhhhhhhhh..ee........eeeeeee...........eeeeee.............eeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z5v A   7 PNHFINFPLAQFSGFmGKYLKLQSQLVEmGLDCKLQKAPHVSITLLDIKADQYKQVEFAIQEIIDDLAAYEGDIVFDNPHmLGRCLVLDVRGFEELHEDIVEILRRRGCTADQSRHWIPHCTVAQFDEERETKGmQFYHKEPFYLKHNNLLTDAGLELVKI 167
                                    16     |  26        36        46        56        66        76        86|       96       106       116       126       136    |  146       156       166 
                                          22-MSE       35-MSE                                              87-MSE                                               141-MSE                      


Chain B from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee...hhhhhhhhhhhhhhhhhhh..eee....eeeeeee..hhhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeee..eeeeeee.hhhhhhhhhhhhhhh..........eeeeeee......eeeee......eeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4z5v B   6 KPNHFINFPLAQFSGFmGKYLKLQSQLVEmGLDCKLQKAPHVSITLLDIKADQYKQVEFAIQEIIDDLAAYEGDIVFDNPHmLGRCLVLDVRGFEELHEDIVEILRRRGCTADQSWIPHCTVAQFDEGmQFYHKEPFYLAGLELVKIG 168
                                    15      | 25        35        45        55        65        75        85 |      95       105       115    || 127      |142       160        
                                           22-MSE       35-MSE                                              87-MSE                          120|        134||       151|        
                                                                                                                                             123         140|        160        
                                                                                                                                                          141-MSE
   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 4Z5V)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Z5V)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Z5V)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
(no "Sites" information available for 4z5v)
 
  Cis Peptide Bonds
    Ile B:167 - Gly B:168   [ RasMol ]  
    Lys B:6 - Pro B:7   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit 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
  4z5v
    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
  NS2A_CVMA5 | P19738
    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
  NS2A_CVMA5 | P19738
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4Z5V)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4Z5V)