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(-) Description

Authors :  S. Doublie, V. Bandaru, J. P. Bond, S. S. Wallace
Date :  22 May 04  (Deposition) - 20 Jul 04  (Release) - 24 Feb 09  (Revision)
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Helix Two Turns Helix, Zinc-Less Finger, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
Reference :  S. Doublie, V. Bandaru, J. P. Bond, S. S. Wallace
The Crystal Structure Of Human Endonuclease Viii-Like 1 (Neil1) Reveals A Zincless Finger Motif Required For Glycosylase Activity.
Proc. Natl. Acad. Sci. Usa V. 101 10284 2004
PubMed-ID: 15232006  |  Reference-DOI: 10.1073/PNAS.0402051101
(for further references see the PDB file header)

(-) Compounds

    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
1AC1SOFTWAREPRO A:2 , LYS A:54 , ARG A:78 , GLY A:80 , HOH A:1015 , HOH A:1173 , HOH A:1188 , HOH A:1307 , HOH A:1310BINDING SITE FOR RESIDUE TRS A 2000

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
1Gln A:67 -Pro A:68

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (8, 8)

Asymmetric/Biological Unit (8, 8)
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
7UniProtVAR_065018K242RNEIL1_HUMANUnclassified  ---AR242R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
1FPG_CATPS51068 Formamidopyrimidine-DNA glycosylase catalytic domain profile.NEIL1_HUMAN2-121  1A:2-121

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength

(-) 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:284
 aligned with NEIL1_HUMAN | Q96FI4 from UniProtKB/Swiss-Prot  Length:390

    Alignment length:289
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281         
               SCOP domains d1tdha2 A:2-131 Endonuclease VIII-like 1 (NEIL1)                                                                                  d1tdha1 A:132-246 Endonuclease VIII-like 1 (NEIL1)                                                                 d1tdha3 A:247-290                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains Fapy_DNA_glyco-1tdhA02 A:2-124                                                                                             ---------H2TH-1tdhA01 A:134-221                                                                  ------------------------------Neil1-DNA_bind-1tdhA03 A:252-290        Pfam domains
         Sec.struct. author Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------CD----------------------------------------------------R----------------------Q---------------------KM-----------------------------------------------------------R---------N-------------------------------------- SAPs(SNPs)
                    PROSITE FPG_CAT  PDB: A:2-121 UniProt: 2-121                                                                                    ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2a  PDB: A:2-145 UniProt: 1-145 [INCOMPLETE]                                                                                             ---------------------------------------Exon 1.4 [INCOMPLETE] Exon 1.5  PDB: A:208-240          ------------------------------------------Exon 1.7 Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------------------------------------------------------------------------------------------Exon 1.3  PDB: A:145-185 UniProt: 145-185------------------------------------------------------Exon 1.6  PDB: A:240-282 UniProt: 240-282  -------- Transcript 1 (2)
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201|     |211       221       231       241       251       261       271       281         
                                                                                                                                                                                                                                  202   208                                                                                  

   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/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1TDH)

(-) Pfam Domains  (3, 3)

Asymmetric/Biological Unit
Clan: H2TH (43)

(-) Gene Ontology  (26, 26)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (NEIL1_HUMAN | Q96FI4)
molecular function
    GO:0019104    DNA N-glycosylase activity    Catalysis of the removal of damaged bases by cleaving the N-C1' glycosidic bond between the target damaged DNA base and the deoxyribose sugar. The reaction releases a free base and leaves an apurinic/apyrimidinic (AP) site.
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003906    DNA-(apurinic or apyrimidinic site) lyase activity    Catalysis of the cleavage of the C-O-P bond 3' to the apurinic or apyrimidinic site in DNA by a beta-elimination reaction, leaving a 3'-terminal unsaturated sugar and a product with a terminal 5'-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:0003684    damaged DNA binding    Interacting selectively and non-covalently with damaged DNA.
    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:0016798    hydrolase activity, acting on glycosyl bonds    Catalysis of the hydrolysis of any glycosyl bond.
    GO:0016799    hydrolase activity, hydrolyzing N-glycosyl compounds    Catalysis of the hydrolysis of any N-glycosyl bond.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0008022    protein C-terminus binding    Interacting selectively and non-covalently with a protein C-terminus, the end of any peptide chain at which the 1-carboxy function of a constituent amino acid is not attached in peptide linkage to another amino-acid residue.
    GO:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
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:0006284    base-excision repair    In base excision repair, an altered base is removed by a DNA glycosylase enzyme, followed by excision of the resulting sugar phosphate. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase.
    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:0045008    depyrimidination    The disruption of the bond between the sugar in the backbone and the C or T base, causing the base to be removed and leaving a depyrimidinated sugar.
    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:0032074    negative regulation of nuclease activity    Any process that stops or reduces the rate of nuclease activity, the hydrolysis of ester linkages within nucleic acids.
    GO:0006289    nucleotide-excision repair    A DNA repair process in which a small region of the strand surrounding the damage is removed from the DNA helix as an oligonucleotide. The small gap left in the DNA helix is filled in by the sequential action of DNA polymerase and DNA ligase. Nucleotide excision repair recognizes a wide range of substrates, including damage caused by UV irradiation (pyrimidine dimers and 6-4 photoproducts) and chemicals (intrastrand cross-links and bulky adducts).
    GO:0006979    response to oxidative stress    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
    GO:0005694    chromosome    A structure composed of a very long molecule of DNA and associated proteins (e.g. histones) that carries hereditary information.
    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:0005815    microtubule organizing center    An intracellular structure that can catalyze gamma-tubulin-dependent microtubule nucleation and that can anchor microtubules by interacting with their minus ends, plus ends or sides.
    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)

        NEIL1_HUMAN | Q96FI44nrv 5itq 5itr 5itt 5itu 5itx 5ity

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 1TDH)