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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN THYMIDINE PHOSPHORYLASE IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
 
Authors :  R. A. Norman, S. T. Barry, M. Bate, J. Breed, J. G. Colls, R. J. Ernill, R. W. A. Luke, C. A. Minshull, M. S. B. Mcalister, E. J. Mccall, H. H. J. Mcmiken, D. S. Paterson, D. Timms, J. A. Tucker, R. A. Pauptit
Date :  23 Sep 03  (Deposition) - 22 Jan 04  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.11
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Phosphorylase, Transferase, Glycosyltransferase, Chemotaxis, Angiogenesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  R. A. Norman, S. T. Barry, M. Bate, J. Breed, J. G. Colls, R. J. Ernill, R. W. A. Luke, C. A. Minshull, M. S. B. Mcalister, E. J. Mccall, H. H. J. Mcmicken, D. S. Paterson, D. Timms, J. A. Tucker, R. A. Pauptit
Crystal Structure Of Human Thymidine Phosphorylase In Complex With A Small Molecule Inhibitor
Structure V. 12 75 2004
PubMed-ID: 14725767  |  Reference-DOI: 10.1016/J.STR.2003.11.018

(-) Compounds

Molecule 1 - THYMIDINE PHOSPHORYLASE
    ChainsA
    EC Number2.4.2.4
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMOAL-10T
    Expression System Taxid562
    FragmentRESIDUES 12-408,411-482
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTDRPASE, TP, PLATELET-DERIVED ENDOTHELIAL CELL GROWTH FACTOR, PD-ECGF, GLIOSTATIN

 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, 1)

Asymmetric Unit (1, 1)
No.NameCountTypeFull Name
1CMU1Ligand/Ion5-CHLORO-6-(1-(2-IMINOPYRROLIDINYL) METHYL)URACIL
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CMU2Ligand/Ion5-CHLORO-6-(1-(2-IMINOPYRROLIDINYL) METHYL)URACIL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:116 , SER A:117 , THR A:118 , ARG A:146 , LEU A:148 , THR A:151 , GLY A:152 , TYR A:199 , ARG A:202 , ILE A:214 , SER A:217 , LYS A:221 , HOH A:2074BINDING SITE FOR RESIDUE CMU A1481

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1UOU)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (6, 6)

Asymmetric Unit (6, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016777R44QTYPH_HUMANDisease (MTDPS1)28931613AR44Q
2UniProtVAR_007643G145RTYPH_HUMANDisease (MTDPS1)121913037AG145R
3UniProtVAR_007644G153STYPH_HUMANDisease (MTDPS1)121913038AG153S
4UniProtVAR_007645K222RTYPH_HUMANDisease (MTDPS1)149977726AK222R
5UniProtVAR_007646E289ATYPH_HUMANDisease (MTDPS1)121913036AE289A
6UniProtVAR_007648S471LTYPH_HUMANPolymorphism11479AL471L

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (6, 12)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_016777R44QTYPH_HUMANDisease (MTDPS1)28931613AR44Q
2UniProtVAR_007643G145RTYPH_HUMANDisease (MTDPS1)121913037AG145R
3UniProtVAR_007644G153STYPH_HUMANDisease (MTDPS1)121913038AG153S
4UniProtVAR_007645K222RTYPH_HUMANDisease (MTDPS1)149977726AK222R
5UniProtVAR_007646E289ATYPH_HUMANDisease (MTDPS1)121913036AE289A
6UniProtVAR_007648S471LTYPH_HUMANPolymorphism11479AL471L

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

(-) PROSITE Motifs  (1, 1)

Asymmetric Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMID_PHOSPHORYLASEPS00647 Thymidine and pyrimidine-nucleoside phosphorylases signature.TYPH_HUMAN144-159  1A:144-159
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMID_PHOSPHORYLASEPS00647 Thymidine and pyrimidine-nucleoside phosphorylases signature.TYPH_HUMAN144-159  2A:144-159

(-) Exons   (9, 9)

Asymmetric Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1gENST000003956801gENSE00001522468chr22:50968428-5096833396TYPH_HUMAN-00--
1.1jENST000003956801jENSE00001522466chr22:50968183-50967925259TYPH_HUMAN1-72721A:33-7240
1.1oENST000003956801oENSE00000657761chr22:50967767-50967565203TYPH_HUMAN72-139681A:72-13968
1.1pENST000003956801pENSE00000657760chr22:50967039-5096694199TYPH_HUMAN140-172331A:140-17233
1.2aENST000003956802aENSE00000657759chr22:50966146-50966017130TYPH_HUMAN173-216441A:173-21644
1.3ENST000003956803ENSE00000878932chr22:50965712-50965594119TYPH_HUMAN216-255401A:216-255 (gaps)40
1.4ENST000003956804ENSE00000657757chr22:50965167-50965005163TYPH_HUMAN256-310551A:256-31055
1.5aENST000003956805aENSE00000657756chr22:50964905-50964675231TYPH_HUMAN310-387781A:310-38778
1.5dENST000003956805dENSE00000657754chr22:50964570-50964430141TYPH_HUMAN387-434481A:387-434 (gaps)48
1.6eENST000003956806eENSE00000878931chr22:50964347-50964181167TYPH_HUMAN434-482491A:434-48047

(-) 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:438
 aligned with TYPH_HUMAN | P19971 from UniProtKB/Swiss-Prot  Length:482

    Alignment length:448
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472        
           TYPH_HUMAN    33 PKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFGGAAVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGAGRSRAGEPLRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPSPFAELVLPP 480
               SCOP domains d1uoua1 A:33-100 Thymidine phosphorylase                            d1uoua2 A:101-373 Thymidine phosphorylase                                                                                                                                                                                                                                        d1uoua3 A:374-480 Thymidine phosp        horylase                                                           SCOP domains
               CATH domains 1uouA01 A:33-100                                                    1uouA02 A:101-371,A:469-480 Pyrimidine Nucleoside Phosphorylase; Chain A, domain 2                                                                                                                                                                                             1uouA03 A:372-468  [code=3.90.1170.        30, no name defined]                                  1uouA02      CATH domains
               Pfam domains --Glycos_trans_3N-1uouA02 A:35-100                                  --------Glycos_transf_3-1uouA03 A:109-362                                                                                                                                                                                                                             -------------------------PYNP_C-1uouA01 A:38        8-462                                           ------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhh....hhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhh.......hhhhhhh.eeeee......hhhhhhhhhhhh....eeee.........hhhhhhh.........hhhhhhhhhhhhheeee......hhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh...eeeeeeee.--....hhhhhhhhhhhhhhhhhhh...eeeeeee.......ee.hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhh....eeeeee....eeeeeehhhhhhhhhhhhhh--------.....eeee......ee....eeeeeee.....hhhhhhhhhhheeee............eee... Sec.struct. author
                 SAPs(SNPs) -----------Q----------------------------------------------------------------------------------------------------R-------S--------------------------------------------------------------------R------------------------------------------------------------------A-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------L--------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------THYMID_PHOSPHORY--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1j  PDB: A:33-72 UniProt: 1-72   -------------------------------------------------------------------Exon 1.1p  PDB: A:140-172        Exon 1.2a  PDB: A:173-216 UniProt: 173-216  ---------------------------------------Exon 1.4  PDB: A:256-310 UniProt: 256-310              ----------------------------------------------------------------------------Exon 1.5d  PDB: A:387-434 (gaps)                ---------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------Exon 1.1o  PDB: A:72-139 UniProt: 72-139                            ----------------------------------------------------------------------------Exon 1.3  PDB: A:216-255 (gaps)         ------------------------------------------------------Exon 1.5a  PDB: A:310-387 UniProt: 310-387                                    ----------------------------------------------Exon 1.6e  PDB: A:434-480 UniProt: 434-482      Transcript 1 (2)
                 1uou A  33 PKQLPELIRMKRDGGRLSEADIRGFVAAVVNGSAQGAQIGAMLMAIRLRGMDLEETSVLTQALAQSGQQLEWPEAWRQQLVDKHSTGGVGDKVSLVLAPALAACGCKVPMISGRGLGHTGGTLDKLESIPGFNVIQSPEQMQVLLDQAGCCIVGQSEQLVPADGILYAARDVTATVDSLPLITASILSKKLVEGLSALVVDVKFG--AVFPNQEQARELAKTLVGVGASLGLRVAAALTAMDKPLGRCVGHALEVEEALLCMDGAGPPDLRDLVTTLGGALLWLSGHAGTQAQGAARVAAALDDGSALGRFERMLAAQGVDPGLARALCSGSPAERRQLLPRAREQEELLAPADGTVELVRALPLALVLHELGA--------LRLGVGAELLVDVGQRLRRGTPWLRVHRDGPALSGPQSRALQEALVLSDRAPFAAPLPFAELVLPP 480
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    |  242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402   |     -  |    422       432       442       452       462       472        
                                                                                                                                                                                                                                      237  |                                                                                                                                                                   406      415                                                                 
                                                                                                                                                                                                                                         240                                                                                                                                                                                                                                                

   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  (3, 3)

Asymmetric Unit

(-) CATH Domains  (3, 3)

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

(-) Pfam Domains  (3, 3)

Asymmetric Unit
(-)
Clan: Hybrid (58)

(-) Gene Ontology  (21, 21)

Asymmetric Unit(hide GO term definitions)
Chain A   (TYPH_HUMAN | P19971)
molecular function
    GO:0008083    growth factor activity    The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
    GO:0004645    phosphorylase activity    Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase.
    GO:0005161    platelet-derived growth factor receptor binding    Interacting selectively and non-covalently with the platelet-derived growth factor receptor.
    GO:0016154    pyrimidine-nucleoside phosphorylase activity    Catalysis of the reaction: pyrimidine nucleoside + phosphate = pyrimidine + alpha-D-ribose 1-phosphate.
    GO:0009032    thymidine phosphorylase activity    Catalysis of the reaction: thymidine + phosphate = thymine + 2-deoxy-D-ribose 1-phosphate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0016763    transferase activity, transferring pentosyl groups    Catalysis of the transfer of a pentosyl group from one compound (donor) to another (acceptor).
biological process
    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:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0006935    chemotaxis    The directed movement of a motile cell or organism, or the directed growth of a cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
    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.
    GO:0000002    mitochondrial genome maintenance    The maintenance of the structure and integrity of the mitochondrial genome; includes replication and segregation of the mitochondrial chromosome.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0046135    pyrimidine nucleoside catabolic process    The chemical reactions and pathways resulting in the breakdown of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0006213    pyrimidine nucleoside metabolic process    The chemical reactions and pathways involving any pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0043097    pyrimidine nucleoside salvage    Any process that generates a pyrimidine nucleoside, one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose, from derivatives of it, without de novo synthesis.
    GO:0006220    pyrimidine nucleotide metabolic process    The chemical reactions and pathways involving a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
cellular component
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

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 Related Entries

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

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        TYPH_HUMAN | P199712j0f 2wk5 2wk6

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