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 :  KLEBSIELLA PNEUMONIAE DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND 6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
 
Authors :  K. M. Lamb, A. C. Anderson
Date :  11 Feb 14  (Deposition) - 03 Dec 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.76
Chains :  Asym./Biol. Unit :  A
Keywords :  5, 6, 7, 8-Tetrahydrofolate; 7, 8-Dihydrofolate, Hydride Shift, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. M. Lamb, M. N. Lombardo, J. Alverson, N. D. Priestley, D. L. Wright, A. C. Anderson
Crystal Structures Of Klebsiella Pneumoniae Dihydrofolate Reductase Bound To Propargyl-Linked Antifolates Reveal Features For Potency And Selectivity.
Antimicrob. Agents Chemother. V. 58 7484 2014
PubMed-ID: 25288083  |  Reference-DOI: 10.1128/AAC.03555-14

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    ChainsA
    EC Number1.5.1.3
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneFOLA, D364_00170
    Organism ScientificKLEBSIELLA PNEUMONIAE CG43
    Organism Taxid1244085

 Structural Features

(-) Chains, Units

  1
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
125U1Ligand/Ion6-ETHYL-5-{3-[3-(PYRIMIDIN-5-YL)PHENYL]PROP-1-YN-1-YL}PYRIMIDINE-2,4-DIAMINE
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:6 , ALA A:7 , ILE A:14 , GLY A:15 , MET A:16 , ASN A:18 , ALA A:19 , MET A:20 , TRP A:22 , GLY A:43 , ARG A:44 , LEU A:45 , THR A:46 , ILE A:62 , SER A:63 , SER A:64 , SER A:76 , ILE A:94 , GLY A:96 , GLY A:97 , ARG A:98 , VAL A:99 , TYR A:100 , GLN A:102 , 25U A:202 , HOH A:305 , HOH A:313 , HOH A:326 , HOH A:327 , HOH A:341 , HOH A:352 , HOH A:380 , HOH A:408 , HOH A:409 , HOH A:429 , HOH A:433 , HOH A:446BINDING SITE FOR RESIDUE NAP A 201
2AC2SOFTWAREILE A:5 , ALA A:6 , MET A:20 , ASP A:27 , LEU A:28 , PHE A:31 , SER A:49 , ILE A:50 , ARG A:52 , LEU A:54 , ILE A:94 , TYR A:100 , THR A:113 , NAP A:201 , HOH A:301BINDING SITE FOR RESIDUE 25U A 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4OR7)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:95 -Gly A:96

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4OR7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4OR7)

(-) Exons   (0, 0)

(no "Exon" information available for 4OR7)

(-) 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:165
                                                                                                                                                                                                     
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeehhh.eee........hhhhhhhhhhhhh...eeeehhhhhhhh.......eeee..........eee.hhhhhhhhhh....eeeeehhhhhhhhhhhh.eeeeeee.......ee....hhh.eeeeeeeee.........eeeeeeee....... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4or7 A   1 MISLIAALAVDRVIGMENAMPWNLPADLAWFKRNTLNKPVVMGRLTWESIGRPLPGRKNIVISSKPGSDDRVQWVSSVEEAIAACGDVEEIMVIGGGRVYEQFLPKAQKLYLTHIDAEVEGDTHFPDYDPDEWESVFSEFHDADAQNSHSYCFEILERRHHHHHH 165
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160     

   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 4OR7)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4OR7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4OR7)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 4OR7)

 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
    25U  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:95 - Gly A:96   [ RasMol ]  
 

(-) Still Images

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

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4or7
    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
  (no 'UniProt ID/Accession number' available) |
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProt
 
Access by Enzyme Classificator   (EC Number)
  1.5.1.3
    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
  (no 'UniProt ID/Accession number' available) |
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 4OR7)

(-) Related Entries Specified in the PDB File

4osg