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(-) Description

Title :  STRUCTURAL ANALYSIS OF PNEUMOCYSTIS CARINII AND HUMAN DHFR COMPLEXES WITH NADPH AND A SERIES OF POTENT 5-(OMEGA-CARBOXYL(ALKYLOXY) PYRIDO[2,-D]PYRIMIDINE DERIVATIVES
 
Authors :  V. Cody
Date :  16 Jul 10  (Deposition) - 29 Dec 10  (Release) - 20 Nov 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  X
Keywords :  Pneumocystius Carinii Dhfr Inhibitor Complexes, Oxidoreductase, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Cody, J. Pace
Structural Analysis Of Pneumocystis Carinii And Human Dhfr Complexes With Nadph And A Series Of Five Potent 6-[5'-([Omega]-Carboxyalkoxy)Benzyl]Pyrido[2, 3-D]Pyrimidine Derivatives
Acta Crystallogr. , Sect. D V. 67 1 2011
PubMed-ID: 21206056  |  Reference-DOI: 10.1107/S0907444910041004

(-) Compounds

Molecule 1 - DIHYDROFOLATE REDUCTASE
    Chains: X
    EC Number: 1.5.1.3
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: D3-157
    Expression System Taxid: 562
    Organism Scientific: PNEUMOCYSTIS CARINII
    Organism Taxid: 4754

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : X

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1D2N2Ligand/IonETHYL 6-{3-[(2,4-DIAMINO-5-METHYLPYRIDO[2,3-D]PYRIMIDIN-6-YL)METHYL]-4-METHOXYPHENOXY}HEXANOATE
2NDP1Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE X:10 , VAL X:11 , ALA X:12 , SER X:24 , LEU X:25 , GLU X:32 , PHE X:36 , PRO X:66 , ILE X:123 , TYR X:129 , NDP X:208 , HOH X:266BINDING SITE FOR RESIDUE D2N X 207
2AC2SOFTWAREVAL X:11 , ALA X:12 , ILE X:19 , GLY X:20 , SER X:24 , LEU X:25 , TRP X:27 , GLY X:58 , ARG X:59 , LYS X:60 , THR X:61 , SER X:64 , ILE X:80 , THR X:81 , ARG X:82 , LYS X:96 , ILE X:123 , GLY X:124 , GLY X:125 , ALA X:126 , GLN X:127 , LEU X:128 , TYR X:129 , ALA X:131 , D2N X:207 , D2N X:209 , HOH X:232BINDING SITE FOR RESIDUE NDP X 208
3AC3SOFTWAREILE X:10 , VAL X:11 , ALA X:12 , GLU X:32 , ILE X:33 , PHE X:36 , LYS X:37 , PRO X:66 , PHE X:69 , LYS X:73 , ILE X:123 , TYR X:129 , NDP X:208 , HOH X:219BINDING SITE FOR RESIDUE D2N X 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DYR_PNECA6-204  1X:6-204
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DYR_PNECA18-40  1X:18-40

(-) Exons   (0, 0)

(no "Exon" information available for 3NZB)

(-) 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 X from PDB  Type:PROTEIN  Length:206
 aligned with DYR_PNECA | P16184 from UniProtKB/Swiss-Prot  Length:206

    Alignment length:206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200      
            DYR_PNECA     1 MNQQKSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL 206
               SCOP domains d3nzbx_ X: Dihydrofolate reductases, eukaryotic type                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----DHFR_1-3nzbX01 X:6-204                                                                                                                                                                                 -- Pfam domains
         Sec.struct. author ......eeeeeeee...eee........hhhhhhhhhhhhhh...hhhh.eeeeeeeehhhhhhhhhhhh.....eeeee............eee.hhhhhhhhhhhhh......eeeeeee..hhhhhhhhhhh..eeeeeeeee.......ee......hhhhh...ee.hhhhhhhhhh.......eee..eeeeeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----DHFR_2  PDB: X:6-204 UniProt: 6-204                                                                                                                                                                    -- PROSITE (1)
                PROSITE (2) -----------------DHFR_1  PDB: X:18-40   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nzb X   1 MNQQKSLTLIVALTTSYGIGRSNSLPWKLKKEISYFKRVTSFVPTFDSFESMNVVLMGRKTWESIPLQFRPLKGRINVVITRNESLDLGNGIHSAKSLDHALELLYRTYGSESSVQINRIFVIGGAQLYKAAMDHPKLDRIMATIIYKDIHCDVFFPLKFRDKEWSSVWKKEKHSDLESWVGTKVPHGKINEDGFDYEFEMWTRDL 206
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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  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 3NZB)

(-) Pfam Domains  (1, 1)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain X   (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.

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  1.5.1.3
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 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 3nzc 3td8 4cd2 4g8z 4ixe 4ixf 4ixg 4qjz

(-) Related Entries Specified in the PDB File

2fzh 2fzi 2fzj 3nxo 3nxr 3nxt 3nxv 3nxx 3nxy 3nz6 3nz9 3nza 3nzc 3nzd