Show PDB file:   
         Plain Text   HTML   (compressed file size)
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

Authors :  H. H. Soutter, J. R. Miller
Date :  23 Jan 09  (Deposition) - 24 Mar 09  (Release) - 20 Apr 11  (Revision)
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Oxidoreductase, One-Carbon Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  H. Heaslet, M. Harris, K. Fahnoe, R. Sarver, H. Putz, J. Chang, C. Subramanian, G. Barreiro, J. R. Miller
Structural Comparison Of Chromosomal And Exogenous Dihydrofolate Reductase From Staphylococcus Aureus In Complex With The Potent Inhibitor Trimethoprim.
Proteins V. 76 706 2009
PubMed-ID: 19280600  |  Reference-DOI: 10.1002/PROT.22383

(-) Compounds

    EC Number1.5.1.3
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST14
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPDEST
    Organism ScientificSTAPHYLOCOCCUS AUREUS
    Organism Taxid1280

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
1AC1SOFTWARELEU A:5 , VAL A:6 , ALA A:7 , ASP A:27 , LEU A:28 , VAL A:31 , SER A:49 , ILE A:50 , PHE A:92 , NDP A:1160 , HOH A:2030BINDING SITE FOR RESIDUE TOP A1159
2AC2SOFTWAREVAL A:6 , ALA A:7 , ILE A:14 , GLY A:15 , ASN A:18 , GLN A:19 , LEU A:20 , GLY A:43 , ARG A:44 , LYS A:45 , THR A:46 , LEU A:62 , THR A:63 , SER A:64 , PHE A:92 , GLY A:93 , GLY A:94 , GLN A:95 , THR A:96 , GLU A:100 , THR A:121 , TOP A:1159 , HOH A:2011 , HOH A:2059 , HOH A:2085BINDING SITE FOR RESIDUE NDP A1160

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W9G)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Gly A:93 -Gly A:94

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W9G)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_STAAU2-157  1A:1-156
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_STAAU14-36  1A:13-35

(-) Exons   (0, 0)

(no "Exon" information available for 2W9G)

(-) 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:158
 aligned with DYR_STAAU | P0A017 from UniProtKB/Swiss-Prot  Length:159

    Alignment length:158
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151        
               SCOP domains d2w9ga_ A: automated matches                                                                                                                                   SCOP domains
               CATH domains 2w9gA00 A:1-158 Dihydrofolate Reductase, subunit A                                                                                                             CATH domains
               Pfam domains DHFR_1-2w9gA01 A:1-156                                                                                                                                      -- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) DHFR_2  PDB: A:1-156 UniProt: 2-157                                                                                                                         -- PROSITE (1)
                PROSITE (2) ------------DHFR_1  PDB: A:13-35   --------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150        

   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  (1, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

Asymmetric/Biological Unit
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
Clan: DHFred (95)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DYR_STAAU | P0A017)
molecular function
    GO:0050661    NADP binding    Interacting selectively and non-covalently with nicotinamide-adenine dinucleotide phosphate, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NADP+, or the reduced form, NADPH.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
biological process
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.


(-) 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)
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
(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
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TOP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
  Cis Peptide Bonds
    Gly A:93 - Gly A:94   [ RasMol ]  

(-) Still Images

  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
Access by UniProt ID/Accession number
  DYR_STAAU | P0A017
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
Access by Enzyme Classificator   (EC Number)
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
Access by UniProt ID/Accession number
  DYR_STAAU | P0A017
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        DYR_STAAU | P0A0172w9h 3fra 3frb 3frd 3fre 3frf 3fy8 3fy9 3fyv 3fyw 3i8a 3lg4 3m08 3m09 3sgy 3sh2 3sqy 3sr5 3srq 3srr 3srs 3sru 3srw 4fgg 4fgh 4lae 4lag 4lah 4lek 4xe6 4xec 5hf0 5hf2 5isp 5isq 5ist 5jg0

(-) Related Entries Specified in the PDB File