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(-) Description

Title :  STRUCTURE OF A TRYPTIC CORE FRAGMENT OF TIGAR FROM DANIO RERIO
 
Authors :  H. Li, G. Jogl
Date :  21 Aug 08  (Deposition) - 16 Dec 08  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Histidine Phosphatase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. Li, G. Jogl
Tigar (Tp53 Induced Glycolysis And Apoptosis Regulator) Is Fructose-2, 6- And Fructose-1, 6-Bisphosphatase
To Be Published
PubMed: search

(-) Compounds

Molecule 1
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET26B
    Expression System StrainBL21STAR
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentTRYPTIC CORE FRAGMENT
    Organism CommonLEOPARD DANIO,ZEBRA DANIO,ZEBRA FISH
    Organism ScientificDANIO RERIO
    Organism Taxid7955

 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  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1K2Ligand/IonPOTASSIUM ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1K-1Ligand/IonPOTASSIUM ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:202 , PRO A:203 , HOH A:282 , VAL B:195 , GLU B:196 , LEU B:198BINDING SITE FOR RESIDUE K A 266
2AC2SOFTWAREVAL A:195 , GLU A:196 , LEU A:198 , LEU B:202 , PRO B:203BINDING SITE FOR RESIDUE K A 267

(-) SS Bonds  (1, 1)

Asymmetric Unit
No.Residues
1A:201 -B:201

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Pro B:120 -Gly B:121

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3E9C)

(-) PROSITE Motifs  (1, 2)

Asymmetric Unit (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.TIGRB_DANRE8-17
 
  2A:8-14
B:8-14
Biological Unit 1 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.TIGRB_DANRE8-17
 
  1A:8-14
-
Biological Unit 2 (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PG_MUTASEPS00175 Phosphoglycerate mutase family phosphohistidine signature.TIGRB_DANRE8-17
 
  1-
B:8-14

(-) Exons   (0, 0)

(no "Exon" information available for 3E9C)

(-) 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:204
 aligned with TIGRB_DANRE | Q7ZVE3 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:250
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250
          TIGRB_DANRE     1 MLTFALTIVRHGETQYNRDKLLQGQGIDTPLSDTGHQQAAAAGRYLKDLHFTNVFVSNLQRAIQTAEIILGNNLHSSATEMILDPLLRERGFGVAEGRPKEHLKNMANAAGQSCRDYTPPGGETLEQVKTRFKMFLKSLFQRMLEEHGSALSSAPSEADQPVIAGLADDGAQNVPVHALMVSHGAFIRISVRHLVEDLQCCLPAGLKMNQVFSPCPNTGISRFIFTIHREESVLRATRIQGVFINRKDHL 250
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeee....-------------....hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh........eee.hhhh....-----------------------------..hhhhhhhhhhhhhhhhhhhhhhhhh.....----...................eeeeeehhhhhhhhhhhhhhh..eee....hhhhhh.......eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------PG_MUTASE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9c A   1 MLTFALTIVRHGET-------------DTPLSDTGHQQAAAAGRYLKDLHFTNVFVSNLQRAIQTAEIILGNNLHSSATEMILDPLLRERGF-----------------------------GETLEQVKTRFKMFLKSLFQRMFEEHGSALSS----ADQPVIAGLADDGAQNVPVHALMVSHGAFIRISVRHLVEDLQCCLPAGLKMNQVFSPCPNTGISRFIFTIHREESVLRATRIQGVFINRKDHL 250
                                    10   |     -       |30        40        50        60        70        80        90 |       -         -         - |     130       140       150  |    160       170       180       190       200       210       220       230       240       250
                                        14            28                                                              92                           122                            153  158                                                                                            

Chain B from PDB  Type:PROTEIN  Length:199
 aligned with TIGRB_DANRE | Q7ZVE3 from UniProtKB/Swiss-Prot  Length:257

    Alignment length:249
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241         
          TIGRB_DANRE     2 LTFALTIVRHGETQYNRDKLLQGQGIDTPLSDTGHQQAAAAGRYLKDLHFTNVFVSNLQRAIQTAEIILGNNLHSSATEMILDPLLRERGFGVAEGRPKEHLKNMANAAGQSCRDYTPPGGETLEQVKTRFKMFLKSLFQRMLEEHGSALSSAPSEADQPVIAGLADDGAQNVPVHALMVSHGAFIRISVRHLVEDLQCCLPAGLKMNQVFSPCPNTGISRFIFTIHREESVLRATRIQGVFINRKDHL 250
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....-------------....hhhhhhhhhhhhhhh......eeee..hhhhhhhhhhhhhh........eee.hhhh....--------------------------.....hhhhhhhhhhhhhhhhhhhhhhhhh-----------.................eeeeeehhhhhhhhhhhhhhh..eee....hhhhhh.......eeeeeeeeeee..eeeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------PG_MUTASE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3e9c B   2 LTFALTIVRHGET-------------DTPLSDTGHQQAAAAGRYLKDLHFTNVFVSNLQRAIQTAEIILGNNLHSSATEMILDPLLRERGF--------------------------PPGGETLEQVKTRFKMFLKSLFQRMFEEHG-----------QPVIAGLADDGAQNVPVHALMVSHGAFIRISVRHLVEDLQCCLPAGLKMNQVFSPCPNTGISRFIFTIHREESVLRATRIQGVFINRKDHL 250
                                    11  |      -      | 31        41        51        61        71        81        91|        -         -       121       131       141      |  -       161       171       181       191       201       211       221       231       241         
                                       14            28                                                              92                        119                          148         160                                                                                          

   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 3E9C)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3E9C)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3E9C)

(-) Gene Ontology  (15, 15)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (TIGRB_DANRE | Q7ZVE3)
molecular function
    GO:0004083    bisphosphoglycerate 2-phosphatase activity    Catalysis of the reaction: 2,3-bisphospho-D-glycerate + H(2)O = 3-phospho-D-glycerate + phosphate.
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004331    fructose-2,6-bisphosphate 2-phosphatase activity    Catalysis of the reaction: D-fructose 2,6-bisphosphate + H2O = D-fructose-6-phosphate + 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.
biological process
    GO:0006915    apoptotic process    A programmed cell death process which begins when a cell receives an internal (e.g. DNA damage) or external signal (e.g. an extracellular death ligand), and proceeds through a series of biochemical events (signaling pathway phase) which trigger an execution phase. The execution phase is the last step of an apoptotic process, and is typically characterized by rounding-up of the cell, retraction of pseudopodes, reduction of cellular volume (pyknosis), chromatin condensation, nuclear fragmentation (karyorrhexis), plasma membrane blebbing and fragmentation of the cell into apoptotic bodies. When the execution phase is completed, the cell has died.
    GO:0006914    autophagy    The process in which cells digest parts of their own cytoplasm; allows for both recycling of macromolecular constituents under conditions of cellular stress and remodeling the intracellular structure for cell differentiation.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0030388    fructose 1,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 1,6-bisphosphate, also known as FBP. The D enantiomer is a metabolic intermediate in glycolysis and gluconeogenesis.
    GO:0006003    fructose 2,6-bisphosphate metabolic process    The chemical reactions and pathways involving fructose 2,6-bisphosphate. The D enantiomer is an important regulator of the glycolytic and gluconeogenic pathways. It inhibits fructose 1,6-bisphosphatase and activates phosphofructokinase.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
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:0005741    mitochondrial outer membrane    The outer, i.e. cytoplasm-facing, lipid bilayer of the mitochondrial envelope.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    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
        TIGRB_DANRE | Q7ZVE33e9d 3e9e

(-) Related Entries Specified in the PDB File

3dcy CRYSTAL STRUCTURE A TP53-INDUCED GLYCOLYSIS AND APOPTOSIS REGULATOR PROTEIN FROM HOMO SAPIENS.
3e9d
3e9e