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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN TANKYRASE 1- CATALYTIC PARP DOMAIN
 
Authors :  L. Lehtio, T. Karlberg, C. H. Arrowsmith, H. Berglund, R. Busam, R. Coll L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Ham M. D. Herman, L. Holmberg-Schiavone, I. Johansson, A. Kallas, T. Kote M. Moche, P. Nordlund, T. Nyman, C. Persson, J. Sagemark, M. Sundstrom A. G. Thorsell, L. Tresaugues, S. Van Den Berg, M. Welin, J. Weigelt, Structural Genomics Consortium (Sgc)
Date :  28 Sep 07  (Deposition) - 09 Oct 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym./Biol. Unit :  A
Keywords :  Catalytic Fragment, Parp, Structural Genomics, Structural Genomics Consortium, Sgc, Adp-Ribosylation, Ank Repeat, Chromosomal Protein, Glycosyltransferase, Golgi Apparatus, Membrane, Mrna Transport, Nad, Nuclear Pore Complex, Nucleus, Phosphorylation, Protein Transport, Telomere, Transferase, Translocation, Transport (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Lehtio, R. Collins, S. Van Den Berg, A. Johansson, L. G. Dahlgren, M. Hammarstrom, T. Helleday, L. Holmberg-Schiavone, T. Karlberg, J. Weigelt
Zinc Binding Catalytic Domain Of Human Tankyrase 1.
J. Mol. Biol. V. 379 136 2008
PubMed-ID: 18436240  |  Reference-DOI: 10.1016/J.JMB.2008.03.058

(-) Compounds

Molecule 1 - TANKYRASE-1
    ChainsA
    EC Number2.4.2.30
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPNIC-BSA4
    Expression System StrainBL21(DE3)ROSETTA2
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentPARP CATALYTIC DOMAIN: RESIDUES 1091-1325
    GeneTNKS, PARP5A, PARPL, TIN1, TINF1, TNKS1
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTANK1, TANKYRASE I, TNKS-1, TRF1- INTERACTING ANKYRIN- RELATED ADP-RIBOSE POLYMERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1234 , HIS A:1237 , CYS A:1242 , CYS A:1245BINDING SITE FOR RESIDUE ZN A 1
2AC2SOFTWAREHIS A:1184 , SER A:1186 , PHE A:1188 , ILE A:1192 , PHE A:1197 , ASP A:1198 , HIS A:1201 , TYR A:1203 , HOH A:1412BINDING SITE FOR RESIDUE GOL A 1326

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2RF5)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2RF5)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2RF5)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PARP_CATALYTICPS51059 PARP catalytic domain profile.TNKS1_HUMAN1112-1317  1A:1112-1314

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003104301aENSE00001184319chr8:9413424-9414122699TNKS1_HUMAN1-2252250--
1.6bENST000003104306bENSE00001184302chr8:9437669-9437893225TNKS1_HUMAN225-300760--
1.8ENST000003104308ENSE00001184295chr8:9473092-947318796TNKS1_HUMAN300-332330--
1.14bENST0000031043014bENSE00001184291chr8:9537461-953749737TNKS1_HUMAN332-344130--
1.15aENST0000031043015aENSE00001658888chr8:9538235-953831076TNKS1_HUMAN344-369260--
1.16ENST0000031043016ENSE00001184284chr8:9562173-956226795TNKS1_HUMAN370-401320--
1.17ENST0000031043017ENSE00001184280chr8:9563697-956376367TNKS1_HUMAN401-423230--
1.18aENST0000031043018aENSE00001217818chr8:9564321-9564507187TNKS1_HUMAN424-486630--
1.19bENST0000031043019bENSE00001184276chr8:9565881-9566002122TNKS1_HUMAN486-526410--
1.20ENST0000031043020ENSE00001184274chr8:9567465-956755692TNKS1_HUMAN527-557310--
1.21aENST0000031043021aENSE00001184272chr8:9567652-956773079TNKS1_HUMAN557-583270--
1.22aENST0000031043022aENSE00001217782chr8:9577884-9578055172TNKS1_HUMAN584-641580--
1.24ENST0000031043024ENSE00001184264chr8:9584151-958423080TNKS1_HUMAN641-667270--
1.25bENST0000031043025bENSE00001184259chr8:9588400-9588545146TNKS1_HUMAN668-716490--
1.26ENST0000031043026ENSE00001184256chr8:9590789-9590954166TNKS1_HUMAN716-771560--
1.27aENST0000031043027aENSE00001621845chr8:9592375-9592594220TNKS1_HUMAN772-845740--
1.28ENST0000031043028ENSE00001184247chr8:9592887-9592996110TNKS1_HUMAN845-881370--
1.31aENST0000031043031aENSE00001217850chr8:9605534-9605722189TNKS1_HUMAN882-944630--
1.32bENST0000031043032bENSE00001184239chr8:9609119-9609356238TNKS1_HUMAN945-1024800--
1.33ENST0000031043033ENSE00001184236chr8:9610054-961013683TNKS1_HUMAN1024-1051280--
1.34ENST0000031043034ENSE00001184234chr8:9619026-9619146121TNKS1_HUMAN1052-1092410--
1.35ENST0000031043035ENSE00001184232chr8:9620657-962075498TNKS1_HUMAN1092-1124331A:1104-112421
1.36ENST0000031043036ENSE00001184230chr8:9622226-962230075TNKS1_HUMAN1125-1149251A:1125-114925
1.37ENST0000031043037ENSE00001184227chr8:9623202-9623307106TNKS1_HUMAN1150-1185361A:1150-118536
1.38ENST0000031043038ENSE00001184225chr8:9623749-9623935187TNKS1_HUMAN1185-1247631A:1185-124763
1.39aENST0000031043039aENSE00001184221chr8:9627616-9627772157TNKS1_HUMAN1247-1299531A:1247-1299 (gaps)53
1.41cENST0000031043041cENSE00001326665chr8:9634160-96398565697TNKS1_HUMAN1300-1327281A:1300-131415

(-) 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:207
 aligned with TNKS1_HUMAN | O95271 from UniProtKB/Swiss-Prot  Length:1327

    Alignment length:211
                                  1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273      1283      1293      1303      1313 
         TNKS1_HUMAN   1104 QGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTMKMAHAPPGHHSVIGRPSVNGLAYAEYVIYRGEQAYPEYLITYQIMKPE 1314
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains 2rf5A00 A:1104-1314  [code=3.90.228.10, no name defined]                                                                                                                                                            CATH domains
               Pfam domains -PARP-2rf5A01 A:1105-1282                                                                                                                                                          -------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh................eeeeeeeeeehhhhhhhhhhhhhhhhhhh.....eeeeee...hhhhhhhhh...............eeee.hhhhhhh...hhhhh...............eeeeeeeee...eeee..............eeee..----....eeee.hhh.eeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------PARP_CATALYTIC  PDB: A:1112-1314 UniProt: 1112-1317                                                                                                                                                         PROSITE
           Transcript 1 (1) Exon 1.35            Exon 1.36                Exon 1.37  PDB: A:1150-1185         -------------------------------------------------------------Exon 1.39a  PDB: A:1247-1299 (gaps)                  Exon 1.41c      Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------------------------------Exon 1.38  PDB: A:1185-1247 UniProt: 1185-1247                 ------------------------------------------------------------------- Transcript 1 (2)
                2rf5 A 1104 QGTILLDLAPEDKEYQSVEEEMQSTIREHRDGGNAGGIFNRYNVIRIQKVVNKKLRERFCHRQKEVSEENHNHHNERMLFHGSPFINAIIHKGFDERHAYIGGMFGAGIYFAENSSKSNQYVYGIGGGTGCPTHKDRSCYICHRQMLFCRVTLGKSFLQFSTIKMAHAPPGHHSVIGRP----LAYAEYVIYRGEQAYPEYLITYQIMKPE 1314
                                  1113      1123      1133      1143      1153      1163      1173      1183      1193      1203      1213      1223      1233      1243      1253      1263      1273        |-   |  1293      1303      1313 
                                                                                                                                                                                                           1282 1287                           

   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 2RF5)

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit
(-)
Family: PARP (21)

(-) Gene Ontology  (46, 46)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (TNKS1_HUMAN | O95271)
molecular function
    GO:0003950    NAD+ ADP-ribosyltransferase activity    Catalysis of the reaction: NAD+ + (ADP-D-ribosyl)(n)-acceptor = nicotinamide + (ADP-D-ribosyl)(n+1)-acceptor.
    GO:0042393    histone binding    Interacting selectively and non-covalently with a histone, any of a group of water-soluble proteins found in association with the DNA of eukaroytic chromosomes. They are involved in the condensation and coiling of chromosomes during cell division and have also been implicated in nonspecific suppression of gene activity.
    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).
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0016055    Wnt signaling pathway    The series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell and ending with a change in cell state.
    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:0051028    mRNA transport    The directed movement of mRNA, messenger ribonucleic acid, into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0007052    mitotic spindle organization    A process that is carried out at the cellular level which results in the assembly, arrangement of constituent parts, or disassembly of the microtubule spindle during a mitotic cell cycle.
    GO:1904908    negative regulation of maintenance of mitotic sister chromatid cohesion, telomeric    Any process that stops, prevents or reduces the frequency, rate or extent of maintenance of mitotic sister chromatid cohesion, telomeric.
    GO:1904357    negative regulation of telomere maintenance via telomere lengthening    Any process that stops, prevents or reduces the frequency, rate or extent of telomere maintenance via telomere lengthening.
    GO:1904743    negative regulation of telomeric DNA binding    Any process that stops, prevents or reduces the frequency, rate or extent of telomeric DNA binding.
    GO:0018105    peptidyl-serine phosphorylation    The phosphorylation of peptidyl-serine to form peptidyl-O-phospho-L-serine.
    GO:0018107    peptidyl-threonine phosphorylation    The phosphorylation of peptidyl-threonine to form peptidyl-O-phospho-L-threonine.
    GO:0090263    positive regulation of canonical Wnt signaling pathway    Any process that increases the rate, frequency, or extent of the Wnt signaling pathway through beta-catenin, the series of molecular signals initiated by binding of a Wnt protein to a frizzled family receptor on the surface of the target cell, followed by propagation of the signal via beta-catenin, and ending with a change in transcription of target genes.
    GO:0051973    positive regulation of telomerase activity    Any process that activates or increases the frequency, rate or extent of telomerase activity, the catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1).
    GO:1904355    positive regulation of telomere capping    Any process that activates or increases the frequency, rate or extent of telomere capping.
    GO:0032212    positive regulation of telomere maintenance via telomerase    Any process that activates or increases the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0045944    positive regulation of transcription from RNA polymerase II promoter    Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
    GO:0006471    protein ADP-ribosylation    The transfer, from NAD, of ADP-ribose to protein amino acids.
    GO:0070213    protein auto-ADP-ribosylation    The ADP-ribosylation by a protein of one or more of its own amino acid residues, or residues on an identical protein.
    GO:0070198    protein localization to chromosome, telomeric region    Any process in which a protein is transported to, or maintained at, the telomeric region of a chromosome.
    GO:0070212    protein poly-ADP-ribosylation    The transfer of multiple ADP-ribose residues from NAD to a protein amino acid, forming a poly(ADP-ribose) chain.
    GO:0000209    protein polyubiquitination    Addition of multiple ubiquitin groups to a protein, forming a ubiquitin chain.
    GO:0015031    protein transport    The directed movement of proteins into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0032210    regulation of telomere maintenance via telomerase    Any process that modulates the frequency, rate or extent of the addition of telomeric repeats by telomerase.
    GO:0051225    spindle assembly    The aggregation, arrangement and bonding together of a set of components to form the spindle, the array of microtubules and associated molecules that serves to move duplicated chromosomes apart.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0005794    Golgi apparatus    A compound membranous cytoplasmic organelle of eukaryotic cells, consisting of flattened, ribosome-free vesicles arranged in a more or less regular stack. The Golgi apparatus differs from the endoplasmic reticulum in often having slightly thicker membranes, appearing in sections as a characteristic shallow semicircle so that the convex side (cis or entry face) abuts the endoplasmic reticulum, secretory vesicles emerging from the concave side (trans or exit face). In vertebrate cells there is usually one such organelle, while in invertebrates and plants, where they are known usually as dictyosomes, there may be several scattered in the cytoplasm. The Golgi apparatus processes proteins produced on the ribosomes of the rough endoplasmic reticulum; such processing includes modification of the core oligosaccharides of glycoproteins, and the sorting and packaging of proteins for transport to a variety of cellular locations. Three different regions of the Golgi are now recognized both in terms of structure and function: cis, in the vicinity of the cis face, trans, in the vicinity of the trans face, and medial, lying between the cis and trans regions.
    GO:0000139    Golgi membrane    The lipid bilayer surrounding any of the compartments of the Golgi apparatus.
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    GO:0000775    chromosome, centromeric region    The region of a chromosome that includes the centromeric DNA and associated proteins. In monocentric chromosomes, this region corresponds to a single area of the chromosome, whereas in holocentric chromosomes, it is evenly distributed along the chromosome.
    GO:0000781    chromosome, telomeric region    The terminal region of a linear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005856    cytoskeleton    Any of the various filamentous elements that form the internal framework of cells, and typically remain after treatment of the cells with mild detergent to remove membrane constituents and soluble components of the cytoplasm. The term embraces intermediate filaments, microfilaments, microtubules, the microtrabecular lattice, and other structures characterized by a polymeric filamentous nature and long-range order within the cell. The various elements of the cytoskeleton not only serve in the maintenance of cellular shape but also have roles in other cellular functions, including cellular movement, cell division, endocytosis, and movement of organelles.
    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:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0000784    nuclear chromosome, telomeric region    The terminal region of a linear nuclear chromosome that includes the telomeric DNA repeats and associated proteins.
    GO:0031965    nuclear membrane    Either of the lipid bilayers that surround the nucleus and form the nuclear envelope; excludes the intermembrane space.
    GO:0005643    nuclear pore    Any of the numerous similar discrete openings in the nuclear envelope of a eukaryotic cell, where the inner and outer nuclear membranes are joined.
    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:0000242    pericentriolar material    A network of small fibers that surrounds the centrioles in cells; contains the microtubule nucleating activity of the centrosome.
    GO:0000922    spindle pole    Either of the ends of a spindle, where spindle microtubules are organized; usually contains a microtubule organizing center and accessory molecules, spindle microtubules and astral microtubules.

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 Related Entries

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

UniProtKB/Swiss-Prot
        TNKS1_HUMAN | O952713udd 3uh2 3uh4 4dvi 4i9i 4k4e 4k4f 4krs 4li6 4li7 4li8 4msg 4msk 4mt9 4n3r 4n4v 4oa7 4tor 4tos 4u6a 4uuh 4uw1 4w5s 4w6e 5ebt 5ece 5ety 5gp7 5jhq 5jti 5ju5 5kni

(-) Related Entries Specified in the PDB File

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