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(-) Description

Title :  CRYSTAL STRUCTURE OF DNPH1 (RCL) WITH 6-CYCLOPENTYL-AMP
 
Authors :  A. Padilla, G. Labesse, P. A. Kaminski
Date :  27 May 13  (Deposition) - 05 Feb 14  (Release) - 05 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.69
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Deoxyribonucleoside 5'-Monophosphate N-Glycosidase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  C. Amiable, S. Pochet, A. Padilla, G. Labesse, P. A. Kaminski
N (6)-Substituted Amps Inhibit Mammalian Deoxynucleotide N-Hydrolase Dnph1.
Plos One V. 8 80755 2013
PubMed-ID: 24260472  |  Reference-DOI: 10.1371/JOURNAL.PONE.0080755
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - 2'-DEOXYNUCLEOSIDE 5'-PHOSPHATE N-HYDROLASE 1
    Chains: A, B, C, D
    EC Number: 3.2.2.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: BLI5
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 11-151
    Gene: DNPH1, RCL
    Mutation: YES
    Organism Common: BROWN RAT,RAT,RATS
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: DEOXYRIBONUCLEOSIDE 5'-MONOPHOSPHATE N-GLYCOSIDASE, C-MYC- RESPONSIVE PROTEIN RCL

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
16C64Ligand/IonN-CYCLOPENTYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
16C62Ligand/IonN-CYCLOPENTYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2SO4-1Ligand/IonSULFATE ION
Biological Unit 2 (2, 4)
No.NameCountTypeFull Name
16C62Ligand/IonN-CYCLOPENTYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
2SO42Ligand/IonSULFATE ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:15 , GLY A:16 , SER A:17 , ILE A:18 , ARG A:19 , GLY A:20 , HIS A:45 , VAL A:46 , GLU A:57 , ILE A:65 , ASN A:69 , SER A:87 , GLY A:89 , GLU A:93 , HOH A:304 , HOH A:305 , HOH A:322 , SER B:117 , MET B:119BINDING SITE FOR RESIDUE 6C6 A 201
2AC2SOFTWARESER A:117 , MET A:119 , CYS B:15 , GLY B:16 , SER B:17 , ILE B:18 , ARG B:19 , GLY B:20 , ILE B:65 , ASN B:69 , SER B:87 , GLY B:89 , VAL B:90 , GLU B:93 , HOH B:304 , HOH B:322 , HOH B:359BINDING SITE FOR RESIDUE 6C6 B 201
3AC3SOFTWARECYS C:15 , GLY C:16 , SER C:17 , ILE C:18 , ARG C:19 , GLY C:20 , HIS C:45 , VAL C:46 , ILE C:65 , ASN C:69 , SER C:87 , GLY C:89 , GLU C:93 , HOH C:307 , HOH C:310 , HOH C:335 , HOH C:371 , SER D:117 , MET D:119BINDING SITE FOR RESIDUE 6C6 C 201
4AC4SOFTWAREARG C:34 , ARG C:37BINDING SITE FOR RESIDUE SO4 C 202
5AC5SOFTWARESER C:117 , MET C:119 , CYS D:15 , GLY D:16 , SER D:17 , ILE D:18 , ARG D:19 , GLY D:20 , HIS D:45 , VAL D:46 , GLU D:57 , ILE D:65 , ASN D:69 , SER D:87 , GLY D:89 , GLU D:93 , HOH D:301 , HOH D:304 , HOH D:338 , HOH D:403BINDING SITE FOR RESIDUE 6C6 D 201
6AC6SOFTWAREARG D:34 , ARG D:37BINDING SITE FOR RESIDUE SO4 D 202

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KXL)

(-) 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    
   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:135
                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee.hhhhh.hhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhh......eeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxl A   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVAEAAGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLV 152
                                    18        28        38        57        67        77        87        97       107       117       127       137       147     
                                                                 47|                                                                                               
                                                                  57                                                                                               


Chain B from PDB  Type:PROTEIN  Length:126
                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeee........hhhhhhhhhhhhh...ee....hhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4kxl B  10 RSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYL 151
                                    19        29        39    ||  65        75        85        95       105       115       125       135       145      
                                                             44|                                                                                          
                                                              61                                                                                          


Chain C from PDB  Type:PROTEIN  Length:134
                                                                                                                                                                      
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee.hhhhhh..hhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhhh..eeeeehhhhh...hhhhhhhhhhh.eeeee.hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxl C   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADAGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLV 152
                                    18        28        38        48||      68        78        88        98       108       118       128       138       148    
                                                                   49|                                                                                            
                                                                    60                                                                                            


Chain D from PDB  Type:PROTEIN  Length:136
                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee........hhhhhhhhhhhhh...ee........hhhhhhhhhhhhhhhhhhh.eeeee....hhhhhhhhhhhhhh...eeeeehhhhh...hhhhhh......eeeee....hhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4kxl D   9 RRSVYFCGSIRGGREDQALYARIVSRLRRYGKVLTEHVADEAAGGDQFIHEQNLNWLQQADVVVAEVTQPSLGVGYELGRAVALGKPILCLFRPQSGRVLSAMIRGAADGSRFQVWDYAEGEVETMLDRYFEAYLV 152
                                    18        28        38        48|       66        76        86        96       106       116       126       136       146      
                                                                  48|                                                                                               
                                                                   57
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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 4KXL)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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  4kxl
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  DNPH1_RAT | O35820
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 Related Entries

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

UniProtKB/Swiss-Prot
        DNPH1_RAT | O35820: 2khz 2klh 4fyh 4fyi 4fyk 4kxm 4kxn 4p5d

(-) Related Entries Specified in the PDB File

4fyi 4kxm 4kxn