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 :  STRUCTURAL ANALYSIS OF PNEUMOCYSTIS CARINII DIHYDROFOLATE REDUCTASE COMPLEX WITH NADPH AND 2,4-DIAMINO-5-METHYL-6-[2'-(4-CARBOXY-1-PENTYNYL)-5'-METHOXYBENZYL]PYRIDO[2,3-D]PYRIMIDINE
 
Authors :  V. Cody, J. Pace, E. Stewart
Date :  10 Aug 11  (Deposition) - 11 Apr 12  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Dihydrofolate Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Cody, J. Pace, E. Stewart
Structural Analysis Of Pneumocystis Cariniidihydrofolate Reductase Complexed With Nadph And 2, 4-Diamino-6-[2-(5-Carboxypent-1-Yn-1-Yl)-5-Methoxybenzyl] 5-Methylpyrido[2, 3-D]Pyrimidine.
Acta Crystallogr. , Sect. F V. 68 418 2012
PubMed-ID: 22505410  |  Reference-DOI: 10.1107/S1744309112008688

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET-SUMO
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PETSUMO
    Organism Scientific: PNEUMOCYSTIS CARINII
    Organism Taxid: 4754

 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
1D2R1Ligand/Ion6-{2-[(2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDIN-6-YL)METHYL]-4-METHOXYPHENYL}HEX-5-YNOIC ACID
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREVAL A:11 , ALA A:12 , ILE A:19 , GLY A:20 , 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 , LYS A:96 , ILE A:123 , GLY A:125 , ALA A:126 , GLN A:127 , LEU A:128 , TYR A:129 , ALA A:131 , VAL A:154 , D2R A:302 , HOH A:435 , HOH A:439BINDING SITE FOR RESIDUE NDP A 301
2AC2SOFTWAREILE A:10 , VAL A:11 , ALA A:12 , SER A:24 , LEU A:25 , GLU A:32 , ILE A:33 , PHE A:36 , SER A:64 , PRO A:66 , LEU A:72 , ARG A:75 , ILE A:123 , TYR A:129 , NDP A:301BINDING SITE FOR RESIDUE D2R A 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3TD8)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:70 -Pro A:71
2Gly A:124 -Gly A:125

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TD8)

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
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 3TD8)

(-) 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:194
 aligned with DYR_PNECA | P16184 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:202
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204  
            DYR_PNECA     5 KSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL 206
               SCOP domains d3td8a_ A: Dihydrofolate reductases, eukaryotic type                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eee........hhhhhhhhhhhhh..hhhhh..eeeeeeeehhhhhhhhhhhh.....eeeee...--------.eee.hhhhhhhhhhhhh......eeeeeee..hhhhhhhhhh...eeeeeeeee.......ee......hhhhh..eee.hhhhhhhhhh.......eee..eeeeeeeeee.. 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
                 3td8 A   5 KSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRN--------IHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL 206
                                    14        24        34        44        54        64        74        |-       |94       104       114       124       134       144       154       164       174       184       194       204  
                                                                                                         83       92
   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
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TD8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TD8)

(-) 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.

 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
    D2R  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:70 - Pro A:71   [ RasMol ]  
    Gly A:124 - Gly A:125   [ RasMol ]  
 

(-) 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
  3td8
    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
  DYR_PNECA | P16184
    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)
  1.5.1.3
    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
  DYR_PNECA | P16184
    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
        DYR_PNECA | P16184: 1cd2 1daj 1dyr 1e26 1klk 1ly3 1ly4 1s3y 1vj3 2cd2 2fzh 2fzi 3cd2 3nz6 3nz9 3nza 3nzb 3nzc 4cd2 4g8z 4ixe 4ixf 4ixg 4qjz

(-) Related Entries Specified in the PDB File

3cd2