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

(-) Description

Authors :  V. Cody, N. Galitsky, J. R. Luft, W. Pangborn, A. Rosowsky, S. F. Queener
Date :  12 Dec 01  (Deposition) - 12 Dec 02  (Release) - 02 Feb 11  (Revision)
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Structure-Based Design, Antifolate, Aids, Protein-Inhibitor Complex, Oxidoreductase, Nadp, One-Carbon Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  V. Cody, N. Galitsky, J. R. Luft, W. Pangborn, A. Rosowsky, S. F. Queene
Structure-Based Enzyme Inhibitor Design: Modeling Studies And Crystal Structure Analysis Of Pneumocystis Carinii Dihydrofolate Reductase Ternary Complex With Pt653 And Nadph.
Acta Crystallogr. , Sect. D V. 58 946 2002
PubMed-ID: 12037296  |  Reference-DOI: 10.1107/S090744490200505X
(for further references see the PDB file header)

(-) Compounds

    EC Number1.5.1.3
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPT7-7
    Expression System Taxid562
    Expression System Vector TypePLASMID
    Organism ScientificPNEUMOCYSTIS CARINII
    Organism Taxid4754

 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)
1AC1SOFTWAREILE A:10 , VAL A:11 , SER A:24 , LEU A:25 , GLU A:32 , ILE A:33 , PHE A:36 , SER A:64 , PHE A:69 , ILE A:123 , TYR A:129 , NDP A:207BINDING SITE FOR RESIDUE PMD A 653
2AC2SOFTWAREVAL A:11 , ALA A:12 , ILE A:19 , ASN A:23 , SER A:24 , LEU A:25 , GLY A:58 , ARG A:59 , LYS A:60 , THR A:61 , ILE A:80 , THR A:81 , ARG A:82 , ASN A:83 , LYS A:96 , ILE A:123 , GLY A:124 , GLY A:125 , ALA A:126 , GLN A:127 , LEU A:128 , TYR A:129 , ALA A:131 , PMD A:653 , HOH A:662BINDING SITE FOR RESIDUE NDP A 207

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1KLK)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Arg A:70 -Pro A:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1KLK)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_PNECA6-204  1A:6-204
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_PNECA18-40  1A:18-40

(-) Exons   (0, 0)

(no "Exon" information available for 1KLK)

(-) 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:203
 aligned with DYR_PNECA | P16184 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:203
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   
               SCOP domains d1klka_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                                        SCOP domains
               CATH domains 1klkA00 A:4-206 Dihydrofolate Reductase, subunit A                                                                                                                                                          CATH domains
               Pfam domains --DHFR_1-1klkA01 A:6-204                                                                                                                                                                                 -- Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --DHFR_2  PDB: A:6-204 UniProt: 6-204                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) --------------DHFR_1  PDB: A:18-40   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203   

   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_PNECA | P16184)
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 ]
    PMD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
  Cis Peptide Bonds
    Arg A:70 - Pro A:71   [ 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_PNECA | P16184
    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_PNECA | P16184
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

        DYR_PNECA | P161841cd2 1daj 1dyr 1e26 1ly3 1ly4 1s3y 1vj3 2cd2 2fzh 2fzi 3cd2 3nz6 3nz9 3nza 3nzb 3nzc 3td8 4cd2 4g8z 4ixe 4ixf 4ixg 4qjz

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1KLK)