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

(-) Description

Title :  CRYSTAL STRUCTURE OF NADE FROM STREPTOCOCCUS PYOGENES
 
Authors :  W. T. Booth, M. Chruszcz
Date :  27 Jan 16  (Deposition) - 25 Jan 17  (Release) - 12 Jul 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. T. Booth, T. L. Morris, D. P. Mysona, M. J. Shah, L. K. Taylor, T. W. Karlin, K. Clary, K. A. Majorek, L. R. Offermann, M. Chruszcz
Streptococcus Pyogenes Quinolinate-Salvage Pathway - Structural And Functional Studies Of Quinolinate Phosphoribosyl Transferase And Nh3 -Dependent Nad(+) Synthetase.
Febs J. 2017
PubMed-ID: 28618168  |  Reference-DOI: 10.1111/FEBS.14136

(-) Compounds

Molecule 1 - NH(3)-DEPENDENT NAD(+) SYNTHETASE
    Chains: A, B
    EC Number: 6.3.1.5
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PJEXPRESS411
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Gene: NADE, SPY49_1281C
    Organism Scientific: STREPTOCOCCUS PYOGENES SEROTYPE M49 (STRAIN NZ131)
    Organism Taxid: 471876
    Strain: NZ131

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1CL1Ligand/IonCHLORIDE ION

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP B:279 , PHE B:280binding site for residue CL B 301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5HUJ)

(-) 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:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhh.eee....hhhhhh....................hhhhhhhhhhhh..hhhhh..hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huj A   9 MTLQEEIIRQLGVKASIDPQEEIRKTVDFLKAYLRKHSFLKTYVLGISGGQDSTLAGKLAQMAIAELREETSDQAYQFIAVRLPYGVQDEADAQKALAFIAPDQTLTINIKAAVDGQVEALQAAGVEISDFNKGNIKARQRMISQYAIAGQMAGAVIGTDHAAENITGFFTKFGDGGADILPLFRLNKRQGKALLKVLGADAALYELADEVALGVTYQDIDDYLEGKLISKVAQATIEKWWHKGQHKRHLPITIFADFWK 282
                                    18        28        38        48        58        68        78        88       |99       109       119       129       139       149       159       169       179       189       199       209     ||232       242       252       262       272       282
                                                                                                                  96|                                                                                                                  215|                                                     
                                                                                                                   98                                                                                                                   229                                                     


Chain B from PDB  Type:PROTEIN  Length:260
                                                                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh....eeeee...hhhhhhhhhhhhhhhhhhhhhhh....eeeeee.......hhhhhhhhhhhh..eeee..hhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhheee....hhhhhh....................hhhhhhhhhhhh..hhhhhh.hhhhhhh.hhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5huj B   9 MTLQEEIIRQLGVKASIDPQEEIRKTVDFLKAYLRKHSFLKTYVLGISGGQDSTLAGKLAQMAIAELREETSDQAYQFIAVRLPYGVQDEADAQKALAFIAPDQTLTINIKAAVDGQVEALQAAGVEISDFNKGNIKARQRMISQYAIAGQMAGAVIGTDHAAENITGFFTKFGDGGADILPLFRLNKRQGKALLKVLGADAALYELADEVALGVTYQDIDDYLEGKLISKVAQATIEKWWHKGQHKRHLPITIFADFWK 282
                                    18        28        38        48        58        68        78        88       |99       109       119       129       139       149       159       169       179       189       199       209     ||232       242       252       262       272       282
                                                                                                                  96|                                                                                                                  215|                                                     
                                                                                                                   98                                                                                                                   229
   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 5HUJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 5HUJ)

 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5huj)
 

(-) 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 | Asym./Biol. Unit - sites 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
  5huj
    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
  A0A0H3BZ89_S | A0A0H3BZ89
    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)
  6.3.1.5
    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
  A0A0H3BZ89_S | A0A0H3BZ89
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        A0A0H3BZ89_S | A0A0H3BZ89: 5huh

(-) Related Entries Specified in the PDB File

5huh 5HUH CONTAINS THE SAME PROTEIN.
5hul
5huo
5hup