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(-) Description

Title :  STRUCTURE OF CDC14B PHOSPHATASE WITH A PEPTIDE LIGAND
 
Authors :  C. H. Gray, V. M. Good, N. K. Tonks, D. Barford
Date :  24 May 03  (Deposition) - 24 Jul 03  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Protein Phosphatase, Cell Cycle, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. H. Gray, V. M. Good, N. K. Tonks, D. Barford
The Structure Of The Cell Cycle Protein Cdc14 Reveals A Proline-Directed Protein Phosphatase
Embo J. V. 22 3524 2003
PubMed-ID: 12853468  |  Reference-DOI: 10.1093/EMBOJ/CDG348

(-) Compounds

Molecule 1 - CDC14B2 PHOSPHATASE
    ChainsA
    EngineeredYES
    Expression SystemBACULOVIRUS/INSECT CELL
    Expression System Vector TypeBACULOVIRUS
    FragmentCORE DOMAIN, RESIDUES 39-386
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCDC14B
 
Molecule 2 - PEPTIDE LIGAND
    ChainsB
    Organism ScientificESCHERICHIA COLI
    Organism Taxid562
    Other DetailsSUBSTRATE
    SyntheticNON-BIOLOGICAL SEQUENCE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1ACE1Mod. Amino AcidACETYL GROUP
2SEP1Mod. Amino AcidPHOSPHOSERINE

(-) Sites  (0, 0)

(no "Site" information available for 1OHE)

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1OHE)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Gly A:90 -Pro A:91

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_019959I302TCC14B_HUMANPolymorphism16911114AI302T
2UniProtVAR_019960I341TCC14B_HUMANPolymorphism16911075AI341T

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

(-) PROSITE Motifs  (2, 2)

Asymmetric/Biological Unit (2, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1TYR_PHOSPHATASE_2PS50056 Tyrosine specific protein phosphatases family profile.CC14B_HUMAN297-359  1A:297-359
2TYR_PHOSPHATASE_1PS00383 Tyrosine specific protein phosphatases active site.CC14B_HUMAN312-322  1A:312-322

(-) Exons   (11, 11)

Asymmetric/Biological Unit (11, 11)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003752411aENSE00001151891chr9:99382112-99381501612CC14B_HUMAN1-54541A:42-5413
1.4bENST000003752414bENSE00000983159chr9:99327765-9932767591CC14B_HUMAN54-84311A:54-8431
1.5aENST000003752415aENSE00000713115chr9:99327134-9932705976CC14B_HUMAN84-109261A:84-10926
1.6aENST000003752416aENSE00000713113chr9:99325067-9932497593CC14B_HUMAN110-140311A:110-14031
1.7bENST000003752417bENSE00000713110chr9:99314154-9931407877CC14B_HUMAN141-166261A:141-16626
1.8ENST000003752418ENSE00000713107chr9:99304174-9930410867CC14B_HUMAN166-188231A:166-18823
1.9aENST000003752419aENSE00000804941chr9:99301422-9930136063CC14B_HUMAN189-209211A:189-20921
1.11ENST0000037524111ENSE00000983160chr9:99296824-9929673788CC14B_HUMAN210-239301A:210-23930
1.12cENST0000037524112cENSE00002188249chr9:99296439-99296209231CC14B_HUMAN239-316781A:239-31678
1.13ENST0000037524113ENSE00001732055chr9:99286007-99285869139CC14B_HUMAN316-362471A:316-36247
1.14ENST0000037524114ENSE00001608556chr9:99285702-99285543160CC14B_HUMAN362-415541A:362-38019
1.15ENST0000037524115ENSE00001686535chr9:99284885-9928478898CC14B_HUMAN416-448330--
1.18ENST0000037524118ENSE00001669587chr9:99272071-99271955117CC14B_HUMAN448-487400--
1.19dENST0000037524119dENSE00001689039chr9:99266071-992623953677CC14B_HUMAN487-498120--

(-) 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:339
 aligned with CC14B_HUMAN | O60729 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:339
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         
          CC14B_HUMAN    42 RDPQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDHHDLFFADGSTPTDAIVKEFLDICENAEGAIAVHCKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGPQQQFLVMKQTNLWLEGDYFRQKLKG 380
               SCOP domains d1ohea1 A:42-198 Proline directed phosphatase CDC14b2                                                                                                        d1ohea2 A:199-380 Proline directed phosphatase CDC14b2                                                                                                                                 SCOP domains
               CATH domains 1oheA01 A:42-190 Protein tyrosine phosphatase superfamily                                                                                            --------------------1oheA02 A:211-379 Protein tyrosine phosphatase superfamily                                                                                                               - CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DSPc-1oheA01 A:239-366                                                                                                          -------------- Pfam domains
         Sec.struct. author .hhhhheeee....eeeee..........eeeee.................hhhhhhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.....................hhhhhhhhhhhhhhh........hhhhhhhhhhhhhh.eeeee...eeee.................hhhhhhhhhhh.eeeeee.......hhhhhh...eeee.........hhhhhhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh.hhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------T--------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHATASE_2  PDB: A:297-359 UniProt: 297-359             --------------------- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------TYR_PHOSPHA---------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.1a    -----------------------------Exon 1.5a  PDB: A:84-109  Exon 1.6a  PDB: A:110-140      Exon 1.7b  PDB: A:141-166 ----------------------Exon 1.9a            Exon 1.11  PDB: A:210-239     ----------------------------------------------------------------------------Exon 1.13  PDB: A:316-362 UniProt: 316-362     ------------------ Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.4b  PDB: A:54-84        ---------------------------------------------------------------------------------Exon 1.8  PDB: A:166-18--------------------------------------------------Exon 1.12c  PDB: A:239-316 UniProt: 239-316                                   ---------------------------------------------Exon 1.14           Transcript 1 (2)
                 1ohe A  42 RDPQDDVYLDITDRLCFAILYSRPKSASNVHYFSIDNELEYENFYADFGPLNLAMVYRYCCKINKKLKSITMLRKKIVHFTGSDQRKQANAAFLVGCYMVIYLGRTPEEAYRILIFGETSYIPFRDAAYGSCNFYITLLDCFHAVKKAMQYGFLNFNSFNLDEYEHYEKAENGDLNWIIPDRFIAFCGPHSRARLESGYHQHSPETYIQYFKNHNVTTIIRLNKRMYDAKRFTDAGFDHHDLFFADGSTPTDAIVKEFLDICENAEGAIAVHSKAGLGRTGTLIACYIMKHYRMTAAETIAWVRICRPGSVIGPQQQFLVMKQTNLWLEGDYFRQKLKG 380
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371         

Chain B from PDB  Type:PROTEIN  Length:4
                                    
               SCOP domains ---- SCOP domains
               CATH domains ---- CATH domains
               Pfam domains ---- Pfam domains
         Sec.struct. author .... Sec.struct. author
                 SAPs(SNPs) ---- SAPs(SNPs)
                    PROSITE ---- PROSITE
                 Transcript ---- Transcript
                 1ohe B   0 xAsP   3
                            | | 
                            0-ACE
                              2-SEP

   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/Biological Unit

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (19, 19)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CC14B_HUMAN | O60729)
molecular function
    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:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    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:0004722    protein serine/threonine phosphatase activity    Catalysis of the reaction: protein serine phosphate + H2O = protein serine + phosphate, and protein threonine phosphate + H2O = protein threonine + phosphate.
    GO:0004725    protein tyrosine phosphatase activity    Catalysis of the reaction: protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
    GO:0008138    protein tyrosine/serine/threonine phosphatase activity    Catalysis of the reactions: protein serine + H2O = protein serine + phosphate; protein threonine phosphate + H2O = protein threonine + phosphate; and protein tyrosine phosphate + H2O = protein tyrosine + phosphate.
biological process
    GO:0006281    DNA repair    The process of restoring DNA after damage. Genomes are subject to damage by chemical and physical agents in the environment (e.g. UV and ionizing radiations, chemical mutagens, fungal and bacterial toxins, etc.) and by free radicals or alkylating agents endogenously generated in metabolism. DNA is also damaged because of errors during its replication. A variety of different DNA repair pathways have been reported that include direct reversal, base excision repair, nucleotide excision repair, photoreactivation, bypass, double-strand break repair pathway, and mismatch repair pathway.
    GO:0031572    G2 DNA damage checkpoint    A cell cycle checkpoint that detects and negatively regulates progression from G2 to M phase in the cell cycle in response to DNA damage.
    GO:0006974    cellular response to DNA damage stimulus    Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a stimulus indicating damage to its DNA from environmental insults or errors during metabolism.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0035335    peptidyl-tyrosine dephosphorylation    The removal of phosphoric residues from peptidyl-O-phospho-tyrosine to form peptidyl-tyrosine.
    GO:1904668    positive regulation of ubiquitin protein ligase activity    Any process that activates or increases the frequency, rate or extent of ubiquitin protein ligase activity.
    GO:0006470    protein dephosphorylation    The process of removing one or more phosphoric residues from a protein.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        CC14B_HUMAN | O607291ohc 1ohd

(-) Related Entries Specified in the PDB File

1ohc STRUCTURE OF THE PROLINE DIRECTED PHOSPHATASE CDC14
1ohd STRUCTURE OF CDC14 IN COMPLEX WITH TUNGSTATE