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 :  STRUCTURE OF BACTERIAL DNA LIGASE WITH SMALL-MOLECULE LIGAND PYRIMIDIN-2-AMINE (AT371) IN AN ALTERNATE BINDING SITE.
 
Authors :  H. Jhoti, R. F. Ludlow, P. Pathuri, H. K. Saini, I. J. Tickle, D. Tisi, M. V P. A. Williams
Date :  02 Dec 15  (Deposition) - 16 Dec 15  (Release) - 13 Jan 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Ligase, Antibiotic Design, Protein-Ligand Complex, Fragment Screening, Alternate Binding Site, At371. (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. F. Ludlow, M. L. Verdonk, H. K. Saini, I. J. Tickle, H. Jhoti
Detection Of Secondary Binding Sites In Proteins Using Fragment Screening.
Proc. Natl. Acad. Sci. Usa V. 112 15910 2015
PubMed-ID: 26655740  |  Reference-DOI: 10.1073/PNAS.1518946112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - DNA LIGASE
    Chains: A
    EC Number: 6.5.1.2, 6.5.1.1
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET17
    Expression System Vector Type: PLASMID
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280
    Synonym: POLYDEOXYRIBONUCLEOTIDE SYNTHASE NAD(+)

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1LGA1Ligand/IonPYRIMIDIN-2-AMINE
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:182 , PHE A:190 , GLY A:199 , GLN A:203 , ARG A:212BINDING SITE FOR RESIDUE SO4 A1310
2AC2SOFTWAREGLY A:115 , LEU A:116 , ALA A:117 , ARG A:133 , ARG A:194 , HOH A:2316 , HOH A:2317 , HOH A:2333 , HOH A:2391BINDING SITE FOR RESIDUE SO4 A1311
3AC3SOFTWARETYR A:18 , TYR A:22 , PRO A:28 , VAL A:30 , PRO A:31 , ASP A:32 , TYR A:35 , GLN A:297 , HOH A:2083BINDING SITE FOR RESIDUE LGA A1312

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5FPR)

(-) 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:307
                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhh........eee.........ee.hhhhhhhhhhhhhhhhh...eeeeeee..eeeeeeee..eeeeeee.....eee.hhhhhh..............eeeeeeee.hhhhhhhhhhhhhhh......hhhhhhhhhhh..hhhhhhh...eeeeeee.........hhhhhhhhhhhh........eee.hhhhhhhhhhhhhhhhhhh...eeeeeeee.hhhhhhhhh........eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5fpr A   3 DLSSRVNELHDLLNQYSYEYYVEDNPSVPDSEYDKLLHELIKIEEEHPEYKTVDSPTVRVGGEAQASFNKVNHDTPMLSLGNAFNEDDLRKFDQRIREQIGNVEYMCELKIDGLAVSLKYVDGYFVQGLTRGDGTTGEDITENLKTIHAIPLKMKEPLNVEVRGEAYMPRRSFLRLNEEKEKNDEQLFANPRNAAAGSLRQLDSKLTAKRKLSVFIYSVNDFTDFNARSQSEALDELDKLGFTTNKNRARVNNIDGVLEYIEKWTSQRESLPYDIDGIVIKVNDLDQQDEMGFTQKSPRWAIAYKFP 309
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302
   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 5FPR)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (9, 9)

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
    LGA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5fpr)
 

(-) 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
  5fpr
    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
  DNLJ_STAAU | Q9AIU7
    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)
  6.5.1.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  6.5.1.2
    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
  DNLJ_STAAU | Q9AIU7
    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
        DNLJ_STAAU | Q9AIU7: 3jsl 3jsn 4cc5 4cc6 5fpo

(-) Related Entries Specified in the PDB File

5fp5 STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 WITH SMALL- MOLECULE LIGAND 4-FLUOROBENZOIC ACID (AT222) IN AN ALTERNATE BINDING SITE.
5fp6 STRUCTURE OF CYCLIN-DEPENDENT KINASE 2 WITH SMALL- MOLECULE LIGAND 3-(4,7-DICHLORO-1H-INDOL-3-YL)PROP -2-YN-1-OL (AT17833) IN AN ALTERNATE BINDING SITE.
5fpd STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND PYRAZINE-2-CARBOXAMIDE (AT513) IN AN ALTERNATE BINDING SITE.
5fpe STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND 1H-1,2,4-TRIAZOL-3-AMINE ( AT485) IN AN ALTERNATE BINDING SITE.
5fpm STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND 5-PHENYL-1,3,4-OXADIAZOLE-2- THIOL (AT809) IN AN ALTERNATE BINDING SITE.
5fpn STRUCTURE OF HEAT SHOCK-RELATED 70KDA PROTEIN 2 WITH SMALL-MOLECULE LIGAND 3,5-DIMETHYL-1H-PYRAZOLE-4- CARBOXYLIC ACID (AT9084) IN AN ALTERNATE BINDING SITE.
5fpo STRUCTURE OF BACTERIAL DNA LIGASE WITH SMALL-MOLECULE LIGAND 1H-INDAZOL-7-AMINE (AT4213) IN AN ALTERNATE BINDING SITE.
5fps STRUCTURE OF HEPATITIS C VIRUS (HCV) FULL-LENGTH NS3 COMPLEX WITH SMALL-MOLECULE LIGAND 3-AMINOBENZENE-1,2 -DICARBOXYLIC ACID (AT1246) IN AN ALTERNATE BINDING SITE.
5fpt STRUCTURE OF HEPATITIS C VIRUS (HCV) FULL-LENGTH NS3 COMPLEX WITH SMALL-MOLECULE LIGAND 2-(1-METHYL-1H- INDOL-3-YL)ACETIC ACID (AT3437) IN AN ALTERNATE BINDING SITE.
5fpy STRUCTURE OF HEPATITIS C VIRUS (HCV) FULL-LENGTH NS3 COMPLEX WITH SMALL-MOLECULE LIGAND 5-BROMO-1-METHYL- 1H-INDOLE-2-CARBOXYLIC ACID (AT21457) IN AN ALTERNATE BINDING SITE.