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 :  MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND TRIMETHOPRIM
 
Authors :  A. K. W. Leung, R. C. Reynolds, D. W. Borhani
Date :  16 Nov 08  (Deposition) - 17 Nov 09  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.89
Chains :  Asym./Biol. Unit :  A
Keywords :  Nonclassical Antifolates, One-Carbon Metabolism, Lipophilic Antifolates, Nadp, Reductase, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. K. W. Leung, L. J. Ross, S. Zywno-Van Ginkel, R. C. Reynolds, L. E. Seitz, V. Pathak, W. W. Barrow, E. L. White, W. J. Suling, J. R. Piper, D. W. Borhani
Structural Basis For Selective Inhibition Of Mycobacterium Avium Dihydrofolate Reductase By A Lipophilic Antifolate
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: A
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET11A-MACDHFR-DEL
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector: PET11A
    Fragment: RESIDUES 1-167
    Organism Scientific: MYCOBACTERIUM AVIUM
    Organism Taxid: 1764
    Other Details: STRAIN OBTAINED FROM THE AIDS RESEARCH AND REFERENCE REAGENT PROGRAM, DIVISION OF AIDS, NIAID, NIH, CATALOG NUMBER 1786.

 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
1NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
2TOP1Ligand/IonTRIMETHOPRIM

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:10 , ALA A:11 , ILE A:18 , GLY A:22 , GLY A:47 , ARG A:48 , ARG A:49 , THR A:50 , SER A:53 , VAL A:69 , SER A:70 , ARG A:71 , ARG A:72 , GLY A:84 , ILE A:102 , GLY A:104 , ALA A:105 , GLN A:106 , ILE A:107 , TYR A:108 , LEU A:110 , ALA A:134 , TOP A:1169 , HOH A:2078 , HOH A:2079 , HOH A:2155 , HOH A:2156 , HOH A:2157 , HOH A:2158 , HOH A:2159 , HOH A:2160BINDING SITE FOR RESIDUE NDP A1168
2AC2SOFTWAREVAL A:9 , TRP A:10 , ALA A:11 , ASP A:31 , PHE A:35 , SER A:53 , LEU A:54 , ILE A:102 , TYR A:108 , NDP A:1168BINDING SITE FOR RESIDUE TOP A1169

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W3V)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Arg A:59 -Pro A:60
2Gly A:103 -Gly A:104

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W3V)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W3V)

(-) Exons   (0, 0)

(no "Exon" information available for 2W3V)

(-) 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
 aligned with O30463_MYCAV | O30463 from UniProtKB/TrEMBL  Length:181

    Alignment length:165
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162     
         O30463_MYCAV     3 RAEVGLVWAQSTSGVIGRGGDIPWSVPEDLTRFKEVTMGHTVIMGRRTWESLPAKVRPLPGRRNVVVSRRPDFVAEGARVAGSLEAALAYAGSDPAPWVIGGAQIYLLALPHATRCEVTEIEIDLRRDDDDALAPALDDSWVGETGEWLASRSGLRYRFHSYRRD 167
               SCOP domains d2w3va_ A: automated matches                                                                                                                                          SCOP domains
               CATH domains 2w3vA00 A:3-167 Dihydrofolate Reductase, subunit A                                                                                                                    CATH domains
               Pfam domains --DHFR_1-2w3vA01 A:5-166                                                                                                                                            - Pfam domains
         Sec.struct. author ...eeeeeeee...eee........hhhhhhhhhhhhh..eeeeehhhhhhh..........eeeee...........eee.hhhhhhhhh......ee..hhhhhhhhh..eeeeeeeeee.........ee........eeee...ee.....eeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2w3v A   3 RAEVGLVWAQSTSGVIGRGGDIPWSVPEDLTRFKEVTMGHTVIMGRRTWESLPAKVRPLPGRRNVVVSRRPDFVAEGARVAGSLEAALAYAGSDPAPWVIGGAQIYLLALPHATRCEVTEIEIDLRRDDDDALAPALDDSWVGETGEWLASRSGLRYRFHSYRRD 167
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162
   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  (1, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Clan: DHFred (95)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (O30463_MYCAV | O30463)
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:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
    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
    NDP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TOP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Arg A:59 - Pro A:60   [ RasMol ]  
    Gly A:103 - Gly A:104   [ 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
  2w3v
    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
  O30463_MYCAV | O30463
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
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
  O30463_MYCAV | O30463
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        O30463_MYCAV | O30463: 2w3w

(-) Related Entries Specified in the PDB File

2w3w MYCOBACTERIUM AVIUM DIHYDROFOLATE REDUCTASE COMPLEXED WITH NADPH AND A LIPOPHILIC ANTIFOLATE SELECTIVE FOR M. AVIUM DHFR, 6 -((2,5-DIETHOXYPHENYL)AMINOMETHYL)-2,4- DIAMINO-5-METHYLPYRIDO(2,3-D)PYRIMIDINE ( SRI-8686)