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 :  STRUCTURE OF THE NUCLEOCAPSID-BINDING DOMAIN FROM THE MUMPS VIRUS PHOSPHOPROTEIN
 
Authors :  R. L. Kingston, L. S. Gay, W. S. Baase, B. W. Matthews
Date :  11 Nov 07  (Deposition) - 27 May 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A (1x),B (1x)
Keywords :  Molten Globule, Viral Protein, Replication (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. L. Kingston, L. S. Gay, W. S. Baase, B. W. Matthews
Structure Of The Nucleocapsid-Binding Domain From The Mumps Virus Polymerase; An Example Of Protein Folding Induced By Crystallization
J. Mol. Biol. V. 379 719 2008
PubMed-ID: 18468621  |  Reference-DOI: 10.1016/J.JMB.2007.12.080
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - P PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET41A(+)
    Expression System Strain: BL21-STAR (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: NUCLEOCAPSID-BINDING DOMAIN, UNP RESIDUES 343- 391
    Mutation: YES
    Organism Scientific: MUMPS VIRUS
    Organism Taxid: 11161
    Strain: JERYL-LYNN VACCINE
    Synonym: PHOSPHOPROTEIN

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (1x): A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1BR2Ligand/IonBROMIDE ION
2FMT6Ligand/IonFORMIC ACID
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2FMT3Ligand/IonFORMIC ACID
Biological Unit 2 (1, 3)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2FMT3Ligand/IonFORMIC ACID
Biological Unit 3 (1, 3)
No.NameCountTypeFull Name
1BR-1Ligand/IonBROMIDE ION
2FMT3Ligand/IonFORMIC ACID

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREMET B:348 , ALA B:365 , HOH B:418BINDING SITE FOR RESIDUE BR B 64
2AC2SOFTWAREGLY A:344 , GLN A:345 , LYS A:346 , LYS B:346BINDING SITE FOR RESIDUE FMT A 1
3AC3SOFTWARESER A:356 , ALA A:358 , ASN A:359BINDING SITE FOR RESIDUE FMT A 4
4AC4SOFTWAREARG A:369 , ALA A:373BINDING SITE FOR RESIDUE FMT A 8
5AC5SOFTWARELYS A:346 , GLY B:344 , GLN B:345 , LYS B:346BINDING SITE FOR RESIDUE FMT B 2
6AC6SOFTWAREASP B:377 , ASN B:380BINDING SITE FOR RESIDUE FMT B 3
7AC7SOFTWAREGLN A:364 , PRO B:360 , LYS B:363 , GLN B:364BINDING SITE FOR RESIDUE FMT B 7

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3BBZ)

(-) 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:48
 aligned with Q9J4L6_MUMPJ | Q9J4L6 from UniProtKB/TrEMBL  Length:391

    Alignment length:48
                                   353       363       373       383        
         Q9J4L6_MUMPJ   344 GQKVMITKMITDCVANPQMKQAFEQRLAKASTEDALNDIKRDIIRSAI 391
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 3bbz A 344 GQKVMITKMITDSVANPQMKQAFEQRLAKASTEDALNDIKRDIIRSAI 391
                                   353       363       373       383        


Chain B from PDB  Type:PROTEIN  Length:48
 aligned with Q9J4L6_MUMPJ | Q9J4L6 from UniProtKB/TrEMBL  Length:391

    Alignment length:48
                                   353       363       373       383        
         Q9J4L6_MUMPJ   344 GQKVMITKMITDCVANPQMKQAFEQRLAKASTEDALNDIKRDIIRSAI 391
               SCOP domains ------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhh.hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------ Transcript
                 3bbz B 344 GQKVMITKMITDSVANPQMKQAFEQRLAKASTEDALNDIKRDIIRSAI 391
                                   353       363       373       383
   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 3BBZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3BBZ)

 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
    BR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ 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 3bbz)
 
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
  3bbz
    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
  Q9J4L6_MUMPJ | Q9J4L6
    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)
  (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
  Q9J4L6_MUMPJ | Q9J4L6
    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 3BBZ)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3BBZ)