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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF TELLINA VIRUS 1 VP4 PROTEASE IN THE FORM OF AN INTRA-MOLECULAR(CIS)ACYL-ENZYME COMPLEX.
 
Authors :  I. Y. W. Chung, M. Paetzel
Date :  27 Sep 10  (Deposition) - 02 Feb 11  (Release) - 20 Apr 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  A  (2x)
Biol. Unit 3:  A  (4x)
Keywords :  Cis-Cleavage, Intramolecular Acyl-Enzyme, Ester-Linkage, Alpha/Beta Protein, Protease, Polyprotein Processing, Acyl-Enzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Y. Chung, M. Paetzel
Crystal Structure Of A Viral Protease Intramolecular Acyl-Enzyme Complex: Insights Into Cis-Cleavage At The Vp4/Vp3 Junction Of Tellina Birnavirus.
J. Biol. Chem. V. 286 12475 2011
PubMed-ID: 21288899  |  Reference-DOI: 10.1074/JBC.M110.198812
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - VP4 PROTEIN
    Chains: A
    EC Number: 3.4.21.115
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B+
    Expression System Strain: TUNER (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 637-830
    Gene: VIRAL PROTEIN 4 (VP4)
    Organism Scientific: TELLINA VIRUS 1
    Organism Taxid: 321302

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (1x): A
Biological Unit 2 (2x): A
Biological Unit 3 (4x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 12)

Asymmetric Unit (6, 12)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CL1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4MSE5Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
6URE1Ligand/IonUREA
Biological Unit 1 (5, 11)
No.NameCountTypeFull Name
1BME1Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3GOL3Ligand/IonGLYCEROL
4MSE5Mod. Amino AcidSELENOMETHIONINE
5SO41Ligand/IonSULFATE ION
6URE1Ligand/IonUREA
Biological Unit 2 (5, 22)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3GOL6Ligand/IonGLYCEROL
4MSE10Mod. Amino AcidSELENOMETHIONINE
5SO42Ligand/IonSULFATE ION
6URE2Ligand/IonUREA
Biological Unit 3 (5, 44)
No.NameCountTypeFull Name
1BME4Ligand/IonBETA-MERCAPTOETHANOL
2CL-1Ligand/IonCHLORIDE ION
3GOL12Ligand/IonGLYCEROL
4MSE20Mod. Amino AcidSELENOMETHIONINE
5SO44Ligand/IonSULFATE ION
6URE4Ligand/IonUREA

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:738 , THR A:760 , GLY A:761 , ASN A:771 , LEU A:772 , LEU A:773 , ALA A:774 , LYS A:777BINDING SITE FOR RESIDUE SO4 A 100
2AC2SOFTWAREHOH A:7 , HOH A:12 , LYS A:783 , GLY A:786BINDING SITE FOR RESIDUE GOL A 101
3AC3SOFTWAREASN A:637 , HIS A:673BINDING SITE FOR RESIDUE GOL A 102
4AC4SOFTWAREGLY A:660 , GLY A:661 , LEU A:780 , VAL A:781 , ALA A:785 , THR A:820 , PHE A:821 , SER A:822BINDING SITE FOR RESIDUE GOL A 103
5AC5SOFTWAREGLY A:661 , ALA A:662 , PRO A:716 , VAL A:717 , PRO A:732 , SER A:822 , SER A:823 , GLY A:824BINDING SITE FOR RESIDUE BME A 104
6AC6SOFTWAREHOH A:15 , GLN A:753 , VAL A:809 , GLY A:810 , LYS A:812BINDING SITE FOR RESIDUE URE A 105
7AC7SOFTWARELYS A:798BINDING SITE FOR RESIDUE CL A 106

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3P06)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3P06)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3P06)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3P06)

(-) Exons   (0, 0)

(no "Exon" information available for 3P06)

(-) 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:194
 aligned with Q2PBR5_9VIRU | Q2PBR5 from UniProtKB/TrEMBL  Length:1114

    Alignment length:194
                                   646       656       666       676       686       696       706       716       726       736       746       756       766       776       786       796       806       816       826    
         Q2PBR5_9VIRU   637 NGVELSAVGVLLPVLMDSGRRISGGAFMAVKGDLSEHIKNPKNTRIAQTVAGGTIYGLSEMVNIDEAEKLPIKGAITVLPVVQATATSILVPDNQPQLAFNSWEAAACAADTLESQQTPFLMVTGAVESGNLSPNLLAVQKQLLVAKPAGIGLAANSDRALKVVTLEQLRQVVGDKPWRKPMVTFSSGKNVAQA 830
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..eeeeeeeeee..eeeeeeeeeee..hhhhh......eeee.....eeeee....hhhhhh......eeeeeee.ee...eeeee.....ee...hhhhhhhhhh.........ee...ee..ee....hhhhhhhhhhhhhh..eee.....ee..hhhhhhhhhh........ee.......ee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3p06 A 637 NGVELSAVGVLLPVLmDSGRRISGGAFmAVKGDLSEHIKNPKNTRIAQTVAGGTIYGLSEmVNIDEAEKLPIKGAITVLPVVQATATSILVPDNQPQLAFNSWEAAACAADTLESQQTPFLmVTGAVESGNLSPNLLAVQKQLLVAKPAGIGLAANSDRALKVVTLEQLRQVVGDKPWRKPmVTFSSGKNVAQA 830
                                   646     | 656       666       676       686       696|      706       716       726       736       746       756 |     766       776       786       796       806       816 |     826    
                                         652-MSE     664-MSE                          697-MSE                                                      758-MSE                                                     818-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 3P06)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3P06)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3P06)

(-) Gene Ontology  (1, 1)

Asymmetric Unit(hide GO term definitions)
Chain A   (Q2PBR5_9VIRU | Q2PBR5)
molecular function
    GO:0005198    structural molecule activity    The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.

 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
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    URE  [ 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 ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3p06)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  3p06
    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
  Q2PBR5_9VIRU | Q2PBR5
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.4.21.115
    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
  Q2PBR5_9VIRU | Q2PBR5
    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 3P06)

(-) Related Entries Specified in the PDB File

2gef BIRNAVIRUS VP4 PROTEASE
2pnl BIRNAVIRUS VP4 PROTEASE
2pnm BIRNAVIRUS VP4 PROTEASE