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(-) Description

Title :  CRYSTAL STRUCTURE OF CELL DIVISION CYCLE 25C PROTEIN ISOFORM A FROM HOMO SAPIENS
 
Authors :  Y. Kim, A. Weger, C. Hatzos, P. Savitsky, C. Johansson, L. Ball, A. Barr, M. Vollmar, J. Muniz, J. Weigelt, C. H. Arrowsmith, A. Edwards, C. Boun O. Gileadi, F. Von Delft, S. Knapp, A. Joachimiak, Structural Genom Consortium (Sgc)
Date :  31 Aug 10  (Deposition) - 29 Sep 10  (Release) - 29 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.63
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Structural Genomics Consortium, Sgc, Alpha-Beta- Alpha Sandwich, Kinase, Cytosol, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, A. Weger, C. Hatzos, P. Savitsky, C. Johansson, L. Ball, A. Barr M. Vollmar, J. Muniz, J. Weigelt, C. H. Arrowsmith, A. Edwards, C. Bountra, O. Gileadi, F. Von Delft, S. Knapp, A. Joachimiak
Crystal Structure Of Cell Division Cycle 25C Protein Isofor A From Homo Sapiens
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - M-PHASE INDUCER PHOSPHATASE 3
    ChainsA
    EC Number3.1.3.48
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC28-BSA4
    Expression System StrainBL21(DE3)-R3-PRARE2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentUNP RESIDUES 270-462
    GeneCDC25C
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymDUAL SPECIFICITY PHOSPHATASE CDC25C

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
Biological Unit 1 (1, 8)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARESER A:349 , GLN A:350 , ARG A:386BINDING SITE FOR RESIDUE SO4 A 463
2AC2SOFTWAREARG A:392 , ARG A:396BINDING SITE FOR RESIDUE SO4 A 464
3AC3SOFTWARELYS A:324 , PHE A:325 , TYR A:326BINDING SITE FOR RESIDUE SO4 A 465
4AC4SOFTWARECYS A:377 , GLU A:378 , PHE A:379 , GLU A:382 , ARG A:383BINDING SITE FOR RESIDUE SO4 A 466

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3OP3)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:401 -Pro A:402
2Glu A:428 -Pro A:429

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (1, 1)

Asymmetric Unit (1, 1)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020146G297RMPIP3_HUMANPolymorphism11567997AG297R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (1, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_020146G297RMPIP3_HUMANPolymorphism11567997AG297R

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.MPIP3_HUMAN321-428  1A:321-428
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RHODANESE_3PS50206 Rhodanese domain profile.MPIP3_HUMAN321-428  2A:321-428

(-) Exons   (6, 6)

Asymmetric Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003237602bENSE00001853000chr5:137667524-137667284241MPIP3_HUMAN-00--
1.3aENST000003237603aENSE00001245545chr5:137666907-137666676232MPIP3_HUMAN1-65650--
1.4ENST000003237604ENSE00001086118chr5:137665336-13766524295MPIP3_HUMAN65-97330--
1.5bENST000003237605bENSE00001774532chr5:137664218-13766417346MPIP3_HUMAN97-112160--
1.6aENST000003237606aENSE00001086120chr5:137661743-13766171034MPIP3_HUMAN112-123120--
1.7ENST000003237607ENSE00002184468chr5:137661593-13766150490MPIP3_HUMAN124-153300--
1.8ENST000003237608ENSE00001245626chr5:137655063-137654908156MPIP3_HUMAN154-205520--
1.9bENST000003237609bENSE00001086111chr5:137627805-137627659147MPIP3_HUMAN206-254490--
1.10ENST0000032376010ENSE00001086104chr5:137626429-137626328102MPIP3_HUMAN255-288341A:280-2889
1.11aENST0000032376011aENSE00001086106chr5:137625252-13762519063MPIP3_HUMAN289-309211A:289-30921
1.12ENST0000032376012ENSE00001086119chr5:137622956-13762285899MPIP3_HUMAN310-342331A:310-34233
1.13ENST0000032376013ENSE00001086108chr5:137622319-137622186134MPIP3_HUMAN343-387451A:343-387 (gaps)45
1.14ENST0000032376014ENSE00001195280chr5:137621822-137621711112MPIP3_HUMAN387-424381A:387-42438
1.15fENST0000032376015fENSE00001853686chr5:137621530-137620954577MPIP3_HUMAN425-473491A:425-44824

(-) 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:167
 aligned with MPIP3_HUMAN | P30307 from UniProtKB/Swiss-Prot  Length:473

    Alignment length:169
                                   289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439         
          MPIP3_HUMAN   280 GHLIGDFSKVCALPTVSGKHQDLKYVNPETVAALLSGKFQGLIEKFYVIDCRYPYEYLGGHIQGALNLYSQEELFNFFLKKPIVPLDTQKRIIIVFHCEFSSERGPRMCRCLREEDRSLNQYPALYYPELYILKGGYRDFFPEYMELCEPQSYCPMHHQDHKTELLRCR 448
               SCOP domains d3op3a_ A: automated matches                                                                                                                                              SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -----------------------------------Rhodanese-3op3A01 A:315-422                                                                                 -------------------------- Pfam domains
         Sec.struct. author .......................eeehhhhhhhhhh......eeeeeeee..hhhhhhh.ee...ee..hhhhhhhhhh...........eeeeeee...--.hhhhhhhhhhhhhhhh..........eeee.hhhhhhh..hhh.ee.................... Sec.struct. author
                 SAPs(SNPs) -----------------R------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------RHODANESE_3  PDB: A:321-428 UniProt: 321-428                                                                -------------------- PROSITE
           Transcript 1 (1) Exon 1.10Exon 1.11a           Exon 1.12  PDB: A:310-342        Exon 1.13  PDB: A:343-387 (gaps)             -------------------------------------Exon 1.15f [INCOMPLETE]  Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------Exon 1.14  PDB: A:387-424             ------------------------ Transcript 1 (2)
                 3op3 A 280 GHLIGDFSKVCALPTVSGKHQDLKYVNPETVAALLSGKFQGLIEKFYVIDCRYPYEYLGGHIQGALNLYSQEELFNFFLKKPIVPLDTQKRIIIVFHCEF--ERGPRMCRCLREEDRSLNQYPALYYPELYILKGGYRDFFPEYMELCEPQSYCPMHHQDHKTELLRCR 448
                                   289       299       309       319       329       339       349       359       369       379  |    389       399       409       419       429       439         
                                                                                                                             379  |                                                                  
                                                                                                                                382                                                                  

   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, 1)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OP3)

(-) Pfam Domains  (1, 1)

Asymmetric Unit

(-) Gene Ontology  (25, 25)

Asymmetric Unit(hide GO term definitions)
Chain A   (MPIP3_HUMAN | P30307)
molecular function
    GO:0050699    WW domain binding    Interacting selectively and non-covalently with a WW domain of a protein, a small module composed of 40 amino acids and plays a role in mediating protein-protein interactions via proline-rich regions.
    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:0004721    phosphoprotein phosphatase activity    Catalysis of the reaction: a phosphoprotein + H2O = a protein + phosphate. Together with protein kinases, these enzymes control the state of phosphorylation of cell proteins and thereby provide an important mechanism for regulating cellular activity.
    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).
    GO:0019901    protein kinase binding    Interacting selectively and non-covalently with a protein kinase, any enzyme that catalyzes the transfer of a phosphate group, usually from ATP, to a protein substrate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0006977    DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest    A cascade of processes induced by the cell cycle regulator phosphoprotein p53, or an equivalent protein, in response to the detection of DNA damage and resulting in the stopping or reduction in rate of the cell cycle.
    GO:0006260    DNA replication    The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
    GO:0000086    G2/M transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G2 commits to M phase. The process begins when the kinase activity of M cyclin/CDK complex reaches a threshold high enough for the cell cycle to proceed. This is accomplished by activating a positive feedback loop that results in the accumulation of unphosphorylated and active M cyclin/CDK complex.
    GO:0007049    cell cycle    The progression of biochemical and morphological phases and events that occur in a cell during successive cell replication or nuclear replication events. Canonically, the cell cycle comprises the replication and segregation of genetic material followed by the division of the cell, but in endocycles or syncytial cells nuclear replication or nuclear division may not be followed by cell division.
    GO:0051301    cell division    The process resulting in division and partitioning of components of a cell to form more cells; may or may not be accompanied by the physical separation of a cell into distinct, individually membrane-bounded daughter cells.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
    GO:0051726    regulation of cell cycle    Any process that modulates the rate or extent of progression through the cell cycle.
    GO:0000079    regulation of cyclin-dependent protein serine/threonine kinase activity    Any process that modulates the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity.
    GO:0007088    regulation of mitotic nuclear division    Any process that modulates the frequency, rate or extent of mitosis.
    GO:0007283    spermatogenesis    The process of formation of spermatozoa, including spermatocytogenesis and spermiogenesis.
    GO:0016032    viral process    A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
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.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

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        MPIP3_HUMAN | P303072ojx 3bzi 5jit 5jiv

(-) Related Entries Specified in the PDB File

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