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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DNPH1 (RCL) WITH 6-NAPHTHYL-PURINE-RIBOSIDE-MONOPHOSPHATE
 
Authors :  A. Padilla, G. Labesse, P. A. Kaminski
Date :  16 Mar 14  (Deposition) - 20 Aug 14  (Release) - 20 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.35
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Rcl, Dnph1, Inhibitor, Rossmann Fold, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Amiable, J. Paoletti, A. Haouz, A. Padilla, G. Labesse, P. A. Kaminski, S. Pochet
6-(Hetero)Arylpurine Nucleotides As Inhibitors Of The Oncogenic Target Dnph1: Synthesis, Structural Studies And Cytotoxic Activities.
Eur. J. Med. Chem. V. 85C 418 2014
PubMed-ID: 25108359  |  Reference-DOI: 10.1016/J.EJMECH.2014.07.110
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1
    ChainsA, B
    EC Number3.2.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24A
    Expression System StrainBLI5
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneDNPH1, C6ORF108, RCL
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymC-MYC-RESPONSIVE PROTEIN RCL

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A (1x)B (1x)
Biological Unit 2 (1x)A (1x)B (1x)

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1CA1Ligand/IonCALCIUM ION
2N6P2Ligand/Ion6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-9H-PURINE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2N6P1Ligand/Ion6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-9H-PURINE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2N6P1Ligand/Ion6-(NAPHTHALEN-2-YL)-9-(5-O-PHOSPHONO-BETA-D-RIBOFURANOSYL)-9H-PURINE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:26 , GLY A:27 , SER A:28 , ILE A:29 , ARG A:30 , GLY A:31 , HIS A:56 , VAL A:57 , GLU A:67 , ILE A:76 , ASP A:80 , SER A:98 , GLY A:100 , GLU A:104 , HOH A:309 , HOH A:323 , HOH A:421 , SER B:128 , MET B:130binding site for residue N6P A 201
2AC2SOFTWARESER A:128 , MET A:130 , CYS B:26 , GLY B:27 , SER B:28 , ILE B:29 , ARG B:30 , GLY B:31 , ILE B:76 , ASP B:80 , SER B:98 , GLY B:100 , GLU B:104 , HOH B:317 , HOH B:336 , HOH B:348binding site for residue N6P B 201
3AC3SOFTWAREASP B:161 , PRO B:162 , GLU B:164 , HOH B:349 , HOH B:362binding site for residue CA B 202

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4P5E)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4P5E)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4P5E)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4P5E)

(-) Exons   (0, 0)

(no "Exon" information available for 4P5E)

(-) Sequences/Alignments

Asymmetric 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    
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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:140
                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee.hhhhhh......hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhh....eeeee.hhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5e A  20 RPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAGEEAAGGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLEH 165
                                    29        39        49        59|       75        85        95       105       115       125       135       145       155       165
                                                                  59|                                                                                                   
                                                                   66                                                                                                   

Chain B from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee...........hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhhhh....eeeee.hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4p5e B  20 RPALYFCGSIRGGREDRTLYERIVSRLRRFGTVLTEHVAAAELGDRLIHEQDLEWLQQADVVVAEVTQPSLGVGYELGRAVAFNKRILCLFRPQSGRVLSAMIRGAADGSRFQVWDYEEGEVEALLDRYFEADPLE 164
                                    29        39        49        59  ||    78        88        98       108       118       128       138       148       158      
                                                                     62|                                                                                            
                                                                      72                                                                                            

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  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 4P5E)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4P5E)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4P5E)

(-) Gene Ontology  (17, 17)

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4fyi 4p5d