Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MITOCHONDRIAL 5'(3')-DEOXYRIBONUCLEOTIDASE IN COMPLEX WITH THE INHIBITOR CPB-T
 
Authors :  P. Pachl, P. Rezacova, J. Brynda
Date :  25 Sep 13  (Deposition) - 10 Sep 14  (Release) - 08 Oct 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.67
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  5'-Nucleotidase, Protein Conformation, Dephosphorylation, Phosphorylation, Had-Like, Mitochondia, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. Simak, P. Pachl, M. Fabry, M. Budesinsky, T. Jandusik, A. Hnizda, R. Sklenickova, M. Petrova, V. Veverka, P. Rezacova, J. Brynda, I. Rosenberg
Conformationally Constrained Nucleoside Phosphonic Acids - Potent Inhibitors Of Human Mitochondrial And Cytosolic 5'(3')-Nucleotidases.
Org. Biomol. Chem. V. 12 7971 2014
PubMed-ID: 25178098  |  Reference-DOI: 10.1039/C4OB01332H

(-) Compounds

Molecule 1 - 5'(3')-DEOXYRIBONUCLEOTIDASE, MITOCHONDRIAL
    Chains: A
    EC Number: 3.1.3.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 32-227
    Gene: DNT1, DNT2, NT5C, NT5M, UMPH2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: 5',3'-NUCLEOTIDASE, MITOCHONDRIAL, DEOXY-5'-NUCLEOTIDASE 2, DNT-2

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (4, 7)
No.NameCountTypeFull Name
12E21Ligand/Ion1-{3,5-O-[(4-CARBOXYPHENYL)(PHOSPHONO)METHYLIDENE]-2-DEOXY-BETA-D-THREO-PENTOFURANOSYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
2GOL3Ligand/IonGLYCEROL
3K2Ligand/IonPOTASSIUM ION
4PO41Ligand/IonPHOSPHATE ION
Biological Unit 1 (3, 10)
No.NameCountTypeFull Name
12E22Ligand/Ion1-{3,5-O-[(4-CARBOXYPHENYL)(PHOSPHONO)METHYLIDENE]-2-DEOXY-BETA-D-THREO-PENTOFURANOSYL}-5-METHYLPYRIMIDINE-2,4(1H,3H)-DIONE
2GOL6Ligand/IonGLYCEROL
3K-1Ligand/IonPOTASSIUM ION
4PO42Ligand/IonPHOSPHATE ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:43 , PHE A:49 , PHE A:75 , TRP A:76 , VAL A:77 , SER A:78 , TRP A:96 , SER A:131 , PRO A:132 , ARG A:163 , K A:304 , GOL A:306 , GOL A:307 , HOH A:401 , HOH A:528 , HOH A:540 , HOH A:542 , HOH A:549 , HOH A:554 , HOH A:575 , HOH A:576 , HOH A:633 , HOH A:634BINDING SITE FOR RESIDUE 2E2 A 301
2AC2SOFTWAREASP A:41 , MET A:42 , ASP A:43 , THR A:130 , SER A:131 , LYS A:143 , LYS A:165 , K A:304 , HOH A:401 , HOH A:402 , HOH A:528 , HOH A:549BINDING SITE FOR RESIDUE PO4 A 302
3AC3SOFTWAREALA A:119 , LEU A:121 , THR A:124 , HOH A:532 , HOH A:534 , HOH A:548BINDING SITE FOR RESIDUE K A 303
4AC4SOFTWAREASP A:41 , ASP A:43 , ASP A:176 , 2E2 A:301 , PO4 A:302 , GOL A:306 , HOH A:402 , HOH A:575 , HOH A:576BINDING SITE FOR RESIDUE K A 304
5AC5SOFTWAREPRO A:65 , PHE A:66 , HOH A:482BINDING SITE FOR RESIDUE GOL A 305
6AC6SOFTWAREASP A:43 , GLU A:50 , ARG A:72 , PHE A:75 , VAL A:77 , ASP A:176 , HIS A:198 , 2E2 A:301 , K A:304 , HOH A:422 , HOH A:575 , HOH A:576 , HOH A:578 , HOH A:634BINDING SITE FOR RESIDUE GOL A 306
7AC7SOFTWAREARG A:163 , ARG A:177 , THR A:181 , 2E2 A:301 , HOH A:418 , HOH A:454 , HOH A:561BINDING SITE FOR RESIDUE GOL A 307

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro A:206 -Pro A:207

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MWO)

(-) 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:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.......hhhhhhhhhhhhhh......hhhhh...hhhhhhhhhh.hhhhhhhhhhh............hhhhhhhhhhhh..eeeeeee.......hhhhhhhhhhhhhhhhhhhh.eee..........eeee..............eeeee..............eee.....hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mwo A  35 ALRVLVDMDGVLADFEGGFLRKFRARFPDQPFIALEDRRGFWVSEQYGRLRPGLSEKAISIWESKNFFFELEPLPGAVEAVKEMASLQNTDVFICTSPIKMFKYCPYEKYAWVEKYFGPDFLEQIVLTRDKTVVSADLLIDDRPDITGAEPTPSWEHVLFTACHNQHLQLQPPRRRLHSWADDWKAILDSKRP 227
                                    44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224
   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  (0, 0)

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

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    2E2  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    K  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Pro A:206 - Pro A:207   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4mwo
    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
  NT5M_HUMAN | Q9NPB1
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.1.3.-
    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
  NT5M_HUMAN | Q9NPB1
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        NT5M_HUMAN | Q9NPB1: 1mh9 1q91 1q92 1z4i 1z4j 1z4k 1z4l 1z4m 1z4p 1z4q 2jau 2jaw 4l6a 4l6c 4mum 4nfl 4yik

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4MWO)