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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN CYTOSOLIC 5'(3')-DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THE INHIBITOR PB-PVU
 
Authors :  P. Pachl, P. Rezacova, J. Brynda
Date :  20 Nov 13  (Deposition) - 09 Sep 15  (Release) - 09 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.82
Chains :  Asym./Biol. Unit :  A,B
Keywords :  5'-Nucleotidase, Dephosphorylation, Phosphorylation, Had-Like, Mitochondria, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Pachl, O. Simak, P. Rezacova, M. Fabry, M. Budesinsky, I. Rosenberg J. Brynda
Structure-Based Design Of A Bisphosphonate 5'(3')-Deoxyribonucleotidase Inhibitor
Medchemcomm 2015
PubMed: search  |  Reference-DOI: 10.1039/C5MD00235D

(-) Compounds

Molecule 1 - 5'(3')-DEOXYRIBONUCLEOTIDASE, CYTOSOLIC TYPE
    Chains: A, B
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 1-195
    Gene: NT5C, DNT1, UMPH2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: CYTOSOLIC 5',3'-PYRIMIDINE NUCLEOTIDASE,DEOXY-5'- NUCLEOTIDASE 1,DNT-1

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
12O22Ligand/Ion1-{2-DEOXY-3,5-O-[PHENYL(PHOSPHONO)METHYLIDENE]-BETA-D-THREO-PENTOFURANOSYL}-5-[(E)-2-PHOSPHONOETHENYL]PYRIMIDINE-2,4(1H,3H)-DIONE
2GOL1Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:10 , ASP A:12 , ASP A:145 , PO4 A:202 , 2O2 A:203 , GOL A:204 , HOH A:369binding site for residue MG A 201
2AC2SOFTWAREASP A:10 , MET A:11 , ASP A:12 , THR A:99 , SER A:100 , LYS A:134 , MG A:201 , 2O2 A:203 , HOH A:369 , HOH A:370 , HOH A:388 , HOH A:389binding site for residue PO4 A 202
3AC3SOFTWAREASP A:12 , PHE A:18 , PHE A:44 , LEU A:45 , ALA A:46 , ARG A:47 , TYR A:65 , SER A:100 , LEU A:102 , LEU A:103 , ARG A:132 , MG A:201 , PO4 A:202 , GOL A:204 , HOH A:385 , HOH A:388 , HOH A:389binding site for residue 2O2 A 203
4AC4SOFTWAREASP A:12 , GLY A:13 , PHE A:18 , GLU A:19 , PHE A:44 , ASP A:145 , CYS A:165 , HIS A:167 , MG A:201 , 2O2 A:203 , HOH A:338binding site for residue GOL A 204
5AC5SOFTWAREASP B:10 , ASP B:12 , ASP B:145 , PO4 B:202 , 2O2 B:203 , HOH B:321binding site for residue MG B 201
6AC6SOFTWAREASP B:10 , MET B:11 , ASP B:12 , THR B:99 , SER B:100 , LYS B:112 , LYS B:134 , MG B:201 , 2O2 B:203 , HOH B:321 , HOH B:339binding site for residue PO4 B 202
7AC7SOFTWAREASP B:12 , PHE B:18 , PHE B:44 , LEU B:45 , ALA B:46 , ARG B:47 , TYR B:65 , LEU B:102 , LEU B:103 , ARG B:132 , MG B:201 , PO4 B:202 , HOH B:321 , HOH B:333 , HOH B:336binding site for residue 2O2 B 203

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YIH)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhh.eeee.hhhhh...eeee..............eeeee..............eee.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4yih A   4 SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLVLPPTRRRLLSWSDNWREILDSKR 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193  


Chain B from PDB  Type:PROTEIN  Length:187
                                                                                                                                                                                                                           
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee........hhhhhhhhhhhhhhhhhhh.eee..hhhhh...eeee..............eeeee.........eee.....hhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yih B   4 SVRVLVDMDGVLADFEAGLLRGFRRRFPEEPHVPLEQRRGFLAREQYRALRPDLADKVASVYEAPGFFLDLEPIPGALDAVREMNDLPDTQVFICTSPLLKYHHCVGEKYRWVEQHLGPQFVERIILTRDKTVVLGDLLIDDKDTVRGQEETPSWEHILFTCCHNRHLRRRLLSWSDNWREILDSKR 195
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       178       188       
                                                                                                                                                                                                 171|                  
                                                                                                                                                                                                  177
   Legend:   → Mismatch (orange background)
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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  (0, 0)

(no "SCOP Domain" information available for 4YIH)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (18, 18)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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UniProtKB/Swiss-Prot
        NT5C_HUMAN | Q8TCD5: 2i7d 4l57

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