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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 3-ALPHA
 
Authors :  L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Wisniewska, P. Nordlund, Structural Genomics Consortium (Sgc)
Date :  29 Mar 10  (Deposition) - 07 Apr 10  (Release) - 07 Apr 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Dipp3A, Nudt10, Aps2, Nudix, Hydrolase, Diphosphoinositol Pentakisphosphate, Signal Transduction, Structural Genomics, Structural Genomics Consortium, Sgc, Sgc Stockholm, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Tresaugues, M. Welin, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, I. Johansson, T. Karlberg, S. Kol, T. Kotenyova, M. Moche, T. Nyman, C. Persson, H. Schuler, P. Schutz, M. I. Siponen, A. G. Thorsell, S. Van Der Berg, E. Wahlberg, J. Weigelt, M. Wisniewska, P. Nordlund
Crystal Structure Of Human Diphosphoinositol Polyphosphate Phosphohydrolase 3-Alpha
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DIPHOSPHOINOSITOL POLYPHOSPHATE PHOSPHOHYDROLASE 3-ALPHA
    Chains: A, B
    EC Number: 3.6.1.52, 3.6.1.-
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PNIC-CH2
    Expression System Strain: BL21 DE3 R3 PRARE
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 17 TO 144
    Gene: APS2, DIPP3A, NUDT10
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: DIPP-3-ALPHA, DIPP3-ALPHA, HDIPP3ALPHA, DIADENOSINE 5',5'''-P1,P6-HEXAPHOSPHATE HYDROLASE 3-ALPHA, NUCLEOSIDE DIPHOSPHATE-LINKED MOIETY X MOTIF 10, NUDIX MOTIF 10, HAPS2

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (2, 3)
No.NameCountTypeFull Name
1FLC2Ligand/IonCITRATE ANION
2GOL1Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1FLC1Ligand/IonCITRATE ANION
2GOL1Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:38 , SER A:39 , ARG A:40 , ILE A:46 , ARG A:115 , LYS A:133 , HOH A:190 , HOH A:209 , HOH A:228BINDING SITE FOR RESIDUE FLC A 0
2AC2SOFTWARESER B:38 , SER B:39 , ARG B:40 , ILE B:46 , ARG B:115 , LYS B:133 , HOH B:232BINDING SITE FOR RESIDUE FLC B 0
3AC3SOFTWAREARG A:78 , HOH A:213 , HOH A:240 , GLU B:57 , GLY B:59 , TYR B:96 , VAL B:111 , HOH B:172BINDING SITE FOR RESIDUE GOL B 1

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3MCF)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 4)

Asymmetric Unit (2, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUD10_HUMAN17-144
 		  2A:17-144
B:17-144
2NUDIX_BOXPS00893 Nudix box signature.NUD10_HUMAN50-71
 		  2A:50-71
B:50-71
Biological Unit 1 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUD10_HUMAN17-144
 		  1A:17-144
-
2NUDIX_BOXPS00893 Nudix box signature.NUD10_HUMAN50-71
 		  1A:50-71
-
Biological Unit 2 (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1NUDIXPS51462 Nudix hydrolase domain profile.NUD10_HUMAN17-144
 		  1-
B:17-144
2NUDIX_BOXPS00893 Nudix box signature.NUD10_HUMAN50-71
 		  1-
B:50-71

(-) Exons   (0, 0)

(no "Exon" information available for 3MCF)

(-) 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:130
 aligned with NUD10_HUMAN | Q8NFP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:136
                                    25        35        45        55        65        75        85        95       105       115       125       135       145      
          NUD10_HUMAN    16 FKKRAACLCFRSEREDEVLLVSSSRYPDRWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGVFEQNQDPKHRTYVYVLTVTELLEDWEDSVSIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLKLGGSPTN 151
               SCOP domains d3mcfa_ A: automated matches                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee......eeeeee.......ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee.------.eeeeeeeeeeee...hhhhhhhh..eeeeehhhhhhhhhh.hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NUDIX  PDB: A:17-144 UniProt: 17-144                                                                                            ------- PROSITE (1)
                PROSITE (2) ----------------------------------NUDIX_BOX  PDB: A:50-7-------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcf A  16 MKKRAACLCFRSEREDEVLLVSSSRYPDRWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGVFE------HRTYVYVLTVTELLEDWEDSVSIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLKAHHHHHH 151
                                    25        35        45        55        65        75        |-     |  95       105       115       125       135       145      
                                                                                               84     91                                                            


Chain B from PDB  Type:PROTEIN  Length:123
 aligned with NUD10_HUMAN | Q8NFP7 from UniProtKB/Swiss-Prot  Length:164

    Alignment length:129
                                    25        35        45        55        65        75        85        95       105       115       125       135         
          NUD10_HUMAN    16 FKKRAACLCFRSEREDEVLLVSSSRYPDRWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGVFEQNQDPKHRTYVYVLTVTELLEDWEDSVSIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLK 144
               SCOP domains d3mcfb_ B: automated matches                                                                                                      SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -NUDIX-3mcfB01 B:17-143                                                                                                         - Pfam domains (1)
           Pfam domains (2) -NUDIX-3mcfB02 B:17-143                                                                                                         - Pfam domains (2)
         Sec.struct. author ..eeeeeeee......eeeeee.......ee..eee.....hhhhhhhhhhhhhhheeeeeeeeeeee.------.eeeeeeeeeeee...hhhhhhhh..eeeeehhhhhhhhhh.hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -NUDIX  PDB: B:17-144 UniProt: 17-144                                                                                             PROSITE (1)
                PROSITE (2) ----------------------------------NUDIX_BOX  PDB: B:50-7------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcf B  16 MKKRAACLCFRSEREDEVLLVSSSRYPDRWIVPGGGMEPEEEPGGAAVREVYEEAGVKGKLGRLLGVFE------HRTYVYVLTVTELLEDWEDSVSIGRKREWFKVEDAIKVLQCHKPVHAEYLEKLK 144
                                    25        35        45        55        65        75        |-     |  95       105       115       125       135         
                                                                                               84     91
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3MCF)

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Clan: NUDIX (85)

(-) Gene Ontology  (16, 16)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (NUD10_HUMAN | Q8NFP7)
molecular function
    GO:0008486    diphosphoinositol-polyphosphate diphosphatase activity    Catalysis of the reaction: diphospho-myo-inositol polyphosphate + H2O = myo-inositol polyphosphate + phosphate.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0052841    inositol bisdiphosphate tetrakisphosphate diphosphatase activity    Catalysis of the reaction: inositol bisdiphosphate tetrakisphosphate + H2O = inositol diphosphate pentakisphosphate + phosphate.
    GO:0052842    inositol diphosphate pentakisphosphate diphosphatase activity    Catalysis of the reaction: inositol diphosphate pentakisphosphate + H2O = inositol hexakisphosphate + phosphate.
    GO:0052840    inositol diphosphate tetrakisphosphate diphosphatase activity    Catalysis of the reaction: inositol diphosphate tetrakisphosphate + H2O = inositol 1,3,4,5,6-pentakisphosphate + phosphate.
    GO:0052846    inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 1-diphosphatase activity    Catalysis of the reaction: 1,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 1,2,3,4,6-pentakisphosphate + phosphate + H+.
    GO:0052847    inositol-1,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity    Catalysis of the reaction: 1,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 1-diphospho-1D-myo-inositol 2,3,4,5,6-pentakisphosphate + phosphate + H+.
    GO:0052843    inositol-1-diphosphate-2,3,4,5,6-pentakisphosphate diphosphatase activity    Catalysis of the reaction: inositol 1-diphosphate 2,3,4,5,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+.
    GO:0052848    inositol-3,5-bisdiphosphate-2,3,4,6-tetrakisphosphate 5-diphosphatase activity    Catalysis of the reaction: 3,5-bisdiphosphoinositol-1D-myo-inositol 2,3,4,6-tetrakisphosphate + H2O = 3-diphospho-1D-myo-inositol 1,2,4,5,6-pentakisphosphate + phosphate + H+.
    GO:0052844    inositol-3-diphosphate-1,2,4,5,6-pentakisphosphate diphosphatase activity    Catalysis of the reaction: inositol 3-diphosphate 1,2,4,5,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+.
    GO:0052845    inositol-5-diphosphate-1,2,3,4,6-pentakisphosphate diphosphatase activity    Catalysis of the reaction: inositol 5-diphosphate 1,2,3,4,6-pentakisphosphate + H2O = inositol 1,2,3,4,5,6-hexakisphosphate + phosphate + 2 H+.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0005515    protein binding    Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
    GO:0043647    inositol phosphate metabolic process    The chemical reactions and pathways involving inositol phosphate, 1,2,3,4,5,6-cyclohexanehexol, with one or more phosphate groups attached.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

 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
    FLC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mcf)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  3mcf
    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
  NUD10_HUMAN | Q8NFP7
    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)
  3.6.1.-
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  3.6.1.52
    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
  NUD10_HUMAN | Q8NFP7
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 3MCF)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3MCF)