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(-) Description

Title :  CRYSTAL STRUCTURE ANALYSIS 0F THE TNF-A COVERTING ENZYME (TACE) IN COMPLEXED WITH ARYL-SULFONAMIDE
 
Authors :  Y. Wei, G. B. Rao, U. K. Bandarage
Date :  10 Jan 07  (Deposition) - 27 Nov 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A
Keywords :  Tnf-A Coverting Enzyme, Aryl-Sulfonamide, Tace Inhibitors, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. Govinda Rao, U. K. Bandarage, T. Wang, J. H. Come, E. Perola, Y. Wei, S. K. Tian, J. O. Saunders
Novel Thiol-Based Tace Inhibitors: Rational Design, Synthesis, And Sar Of Thiol-Containing Aryl Sulfonamides
Bioorg. Med. Chem. Lett. V. 17 2250 2007
PubMed-ID: 17289381  |  Reference-DOI: 10.1016/J.BMCL.2007.01.064
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TNF- A CONVERTING ENZYME (TACE)
    ChainsA
    EC Number3.4.24.86
    EngineeredYES
    Expression System CommonINSECT CELLS
    Expression System PlasmidPBEV11TOPO
    Expression System Vector TypeVIRUS
    FragmentTACE PROTEINASE DOMAIN (RESIDUES 216-477)
    GeneTACE
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymA DISINTEGRIN AND METALLOPROTEINASE DOMAIN 17, TNF-ALPHA-CONVERTING ENZYME, TNF-ALPHA CONVERTASE, SNAKE VENOM-LIKE PROTEASE, CD156B ANTIGEN

 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
12831Ligand/Ion(3S)-1-{[4-(BUT-2-YN-1-YLOXY)PHENYL]SULFONYL}PYRROLIDINE-3-THIOL
2ZN1Ligand/IonZINC ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARE283 A:1 , HIS A:405 , HIS A:409 , HIS A:415BINDING SITE FOR RESIDUE ZN A 2
2AC2SOFTWAREZN A:2 , THR A:347 , LEU A:348 , GLY A:349 , LEU A:401 , HIS A:405 , GLU A:406 , HIS A:409 , VAL A:434 , ALA A:439 , HOH A:500 , HOH A:600BINDING SITE FOR RESIDUE 283 A 1

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:225 -A:333
2A:365 -A:469
3A:423 -A:453

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Tyr A:304 -Pro A:305

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2OI0)

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ADAM_MEPROPS50215 ADAM type metalloprotease domain profile.ADA17_HUMAN223-474  1A:223-474
2ZINC_PROTEASEPS00142 Neutral zinc metallopeptidases, zinc-binding region signature.ADA17_HUMAN402-411  1A:402-411
3DISINTEGRIN_2PS50214 Disintegrin domain profile.ADA17_HUMAN475-563  1A:475-480

(-) Exons   (7, 7)

Asymmetric/Biological Unit (7, 7)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1bENST000003108231bENSE00001490067chr2:9695917-9695638280ADA17_HUMAN1-33330--
1.2ENST000003108232ENSE00001001245chr2:9683414-9683282133ADA17_HUMAN33-77450--
1.3ENST000003108233ENSE00001001246chr2:9676957-9676827131ADA17_HUMAN77-121450--
1.4ENST000003108234ENSE00001001240chr2:9676051-967596389ADA17_HUMAN121-150300--
1.5aENST000003108235aENSE00001070593chr2:9668083-9667915169ADA17_HUMAN151-207570--
1.6ENST000003108236ENSE00001070592chr2:9666373-9666240134ADA17_HUMAN207-251451A:216-25136
1.7ENST000003108237ENSE00001070603chr2:9663467-966337890ADA17_HUMAN252-281301A:252-28130
1.9ENST000003108239ENSE00001070599chr2:9661445-9661332114ADA17_HUMAN282-319381A:282-31938
1.10ENST0000031082310ENSE00001070595chr2:9658376-9658232145ADA17_HUMAN320-368491A:320-36849
1.11ENST0000031082311ENSE00001070597chr2:9658118-965803089ADA17_HUMAN368-397301A:368-39730
1.12ENST0000031082312ENSE00001001237chr2:9650260-9650108153ADA17_HUMAN398-448511A:398-44851
1.13ENST0000031082313ENSE00001001234chr2:9645494-9645295200ADA17_HUMAN449-515671A:449-481 (gaps)39
1.14ENST0000031082314ENSE00001001242chr2:9642405-9642302104ADA17_HUMAN515-550360--
1.15ENST0000031082315ENSE00001001233chr2:9637377-9637243135ADA17_HUMAN550-595460--
1.16ENST0000031082316ENSE00001001250chr2:9634896-9634766131ADA17_HUMAN595-638440--
1.17ENST0000031082317ENSE00001001241chr2:9633954-963387679ADA17_HUMAN639-665270--
1.18ENST0000031082318ENSE00001490117chr2:9633115-963302789ADA17_HUMAN665-694300--
1.19ENST0000031082319ENSE00001001249chr2:9631280-963123051ADA17_HUMAN695-711170--
1.20ENST0000031082320ENSE00001367317chr2:9630647-96286152033ADA17_HUMAN712-8241130--

(-) 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:266
 aligned with ADA17_HUMAN | P78536 from UniProtKB/Swiss-Prot  Length:824

    Alignment length:272
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485  
          ADA17_HUMAN   216 ADPDPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTSWDNAGFKGYGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCLAHLFTYQDFDMGTLGLAYVGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTILTKEADLVTTHELGHNFGAEHDPDGLAECAPNEDQGGKYVMYPIAVSGDHENNKMFSNCSKQSIYKTIESKAQECFQERSNKVCGNSRVDEGE 487
               SCOP domains d2oi0a_ A: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 2oi0A00 A:216-481 Collagenase (Catalytic Domain)                                                                                                                                                                                                                                 CATH domains
               Pfam domains -----Peptidase_M84-2oi0A01 A:221-451                                                                                                                                                                                                        ------------------------------------ Pfam domains
         Sec.struct. author ...hhhh.eeeeeeeehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh...........eeeeeeeee............................hhhhhhhhhhhhhhhhhh...eeeeee...hhhhh.eee.................eee....eee...eeeee.ee..ee.hhhhhhhhhhhhhhhhh..............hhhhh.............hhhhhh.hhhhhhhhhhhhhhhhhhhh........------... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------ADAM_MEPRO  PDB: A:223-474 UniProt: 223-474                                                                                                                                                                                                                 DISINTEGRIN_2 PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ZINC_PROTE---------------------------------------------------------------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.6  PDB: A:216-251            Exon 1.7  PDB: A:252-281      Exon 1.9  PDB: A:282-319              Exon 1.10  PDB: A:320-368 UniProt: 320-368       -----------------------------Exon 1.12  PDB: A:398-448 UniProt: 398-448         Exon 1.13  PDB: A:449-481 (gaps)        Transcript 1 (1)
           Transcript 1 (2) --------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.11  PDB: A:368-397     ------------------------------------------------------------------------------------------ Transcript 1 (2)
                 2oi0 A 216 ADPDPMKNTCKLLVVADHRFYRYMGRGEESTTTNYLIELIDRVDDIYRNTAWDNAGFKGYGIQIEQIRILKSPQEVKPGEKHYNMAKSYPNEEKDAWDVKMLLEQFSFDIAEEASKVCLAHLFTYQDFDMGTLGLAYVGSPRANSHGGVCPKAYYSPVGKKNIYLNSGLTSTKNYGKTILTKEADLVTTHELGHNFGAEHDPDGLAECAPNEDQGGKYVMYPIAVSGDHENNKMFSQCSKQSIYKTIESKAQECFQERSNKVI------EGR 481
                                   225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475  |    479  
                                                                                                                                                                                                                                                                                                478    479  

   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, 1)

Asymmetric/Biological Unit

(-) CATH Domains  (1, 1)

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

(-) Pfam Domains  (1, 1)

Asymmetric/Biological Unit

(-) Gene Ontology  (60, 60)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ADA17_HUMAN | P78536)
molecular function
    GO:0005112    Notch binding    Interacting selectively and non-covalently with the Notch (N) protein, a surface receptor.
    GO:0030165    PDZ domain binding    Interacting selectively and non-covalently with a PDZ domain of a protein, a domain found in diverse signaling proteins.
    GO:0017124    SH3 domain binding    Interacting selectively and non-covalently with a SH3 domain (Src homology 3) of a protein, small protein modules containing approximately 50 amino acid residues found in a great variety of intracellular or membrane-associated proteins.
    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:0005178    integrin binding    Interacting selectively and non-covalently with an integrin.
    GO:0005138    interleukin-6 receptor binding    Interacting selectively and non-covalently with the interleukin-6 receptor.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004222    metalloendopeptidase activity    Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008237    metallopeptidase activity    Catalysis of the hydrolysis of peptide bonds by a mechanism in which water acts as a nucleophile, one or two metal ions hold the water molecule in place, and charged amino acid side chains are ligands for the metal ions.
    GO:0008233    peptidase activity    Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
    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:0008270    zinc ion binding    Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
    GO:0030183    B cell differentiation    The process in which a precursor cell type acquires the specialized features of a B cell. A B cell is a lymphocyte of B lineage with the phenotype CD19-positive and capable of B cell mediated immunity.
    GO:0007220    Notch receptor processing    The series of successive proteolytic cleavages of the Notch protein, which result in an active form of the receptor.
    GO:0007219    Notch signaling pathway    A series of molecular signals initiated by the binding of an extracellular ligand to the receptor Notch on the surface of a target cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0051088    PMA-inducible membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain that occurs after induction by phorbol-12-myristate-13-acetate (PMA), a protein kinase C agonist.
    GO:0033077    T cell differentiation in thymus    The process in which a precursor cell type acquires the specialized features of a T cell via a differentiation pathway dependent upon transit through the thymus.
    GO:0007155    cell adhesion    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via cell adhesion molecules.
    GO:0033627    cell adhesion mediated by integrin    The attachment of a cell, either to another cell or to an underlying substrate such as the extracellular matrix, via an integrin, a heterodimeric adhesion receptor formed by the non-covalent association of particular alpha and beta subunits.
    GO:0048870    cell motility    Any process involved in the controlled self-propelled movement of a cell that results in translocation of the cell from one place to another.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0007173    epidermal growth factor receptor signaling pathway    A series of molecular signals initiated by binding of a ligand to the tyrosine kinase receptor EGFR (ERBB1) on the surface of a cell. The pathway ends with regulation of a downstream cellular process, e.g. transcription.
    GO:0035625    epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway    The process in which an epidermal growth factor-activated receptor is activated via signaling events from a G-protein coupled receptor. This is an example of cross-talk between the EGF and GPCR signaling pathways.
    GO:0002467    germinal center formation    The process in which germinal centers form. A germinal center is a specialized microenvironment formed when activated B cells enter lymphoid follicles. Germinal centers are the foci for B cell proliferation and somatic hypermutation.
    GO:0006509    membrane protein ectodomain proteolysis    The proteolytic cleavage of transmembrane proteins and release of their ectodomain (extracellular domain).
    GO:0031293    membrane protein intracellular domain proteolysis    The proteolytic cleavage of a transmembrane protein leading to the release of an intracellular domain.
    GO:0030512    negative regulation of transforming growth factor beta receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of any TGF-beta receptor signaling pathway.
    GO:0002446    neutrophil mediated immunity    Any process involved in the carrying out of an immune response by a neutrophil.
    GO:0010820    positive regulation of T cell chemotaxis    Any process that increases the rate, frequency or extent of T cell chemotaxis. T cell chemotaxis is the directed movement of a T cell in response to an external stimulus.
    GO:0030307    positive regulation of cell growth    Any process that activates or increases the frequency, rate, extent or direction of cell growth.
    GO:0030335    positive regulation of cell migration    Any process that activates or increases the frequency, rate or extent of cell migration.
    GO:0008284    positive regulation of cell proliferation    Any process that activates or increases the rate or extent of cell proliferation.
    GO:0051272    positive regulation of cellular component movement    Any process that activates or increases the frequency, rate or extent of the movement of a cellular component.
    GO:0032722    positive regulation of chemokine production    Any process that activates or increases the frequency, rate, or extent of chemokine production.
    GO:0031659    positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle    Any process that activates or increases the frequency, rate or extent of cyclin-dependent protein serine/threonine kinase activity contributing to the G1/S transition of the cell cycle.
    GO:0045741    positive regulation of epidermal growth factor-activated receptor activity    Any process that activates or increases the frequency, rate or extent of EGF-activated receptor activity.
    GO:0002690    positive regulation of leukocyte chemotaxis    Any process that activates or increases the frequency, rate, or extent of leukocyte chemotaxis.
    GO:0001934    positive regulation of protein phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to amino acids within a protein.
    GO:0030511    positive regulation of transforming growth factor beta receptor signaling pathway    Any process that activates or increases the frequency, rate or extent of TGF-beta receptor signaling pathway activity.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
    GO:0033025    regulation of mast cell apoptotic process    Any process that modulates the frequency, rate, or extent of mast cell apoptotic process.
    GO:0042493    response to drug    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 a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0055099    response to high density lipoprotein particle    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 a high density lipoprotein particle stimulus.
    GO:0001666    response to hypoxia    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 a stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0048536    spleen development    The process whose specific outcome is the progression of the spleen over time, from its formation to the mature structure. The spleen is a large vascular lymphatic organ composed of white and red pulp, involved both in hemopoietic and immune system functions.
    GO:0033209    tumor necrosis factor-mediated signaling pathway    A series of molecular signals initiated by the binding of a tumor necrosis factor to a receptor on the surface of a cell, and ending with regulation of a downstream cellular process, e.g. transcription.
    GO:0035313    wound healing, spreading of epidermal cells    The migration of an epidermal cell along or through a wound gap that contributes to the reestablishment of a continuous epidermis.
cellular component
    GO:0015629    actin cytoskeleton    The part of the cytoskeleton (the internal framework of a cell) composed of actin and associated proteins. Includes actin cytoskeleton-associated complexes.
    GO:0016324    apical plasma membrane    The region of the plasma membrane located at the apical end of the cell.
    GO:0009986    cell surface    The external part of the cell wall and/or plasma membrane.
    GO:0005911    cell-cell junction    A cell junction that forms a connection between two or more cells in a multicellular organism; excludes direct cytoplasmic junctions such as ring canals.
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005925    focal adhesion    Small region on the surface of a cell that anchors the cell to the extracellular matrix and that forms a point of termination of actin filaments.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0005887    integral component of plasma membrane    The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0045121    membrane raft    Any of the small (10-200 nm), heterogeneous, highly dynamic, sterol- and sphingolipid-enriched membrane domains that compartmentalize cellular processes. Small rafts can sometimes be stabilized to form larger platforms through protein-protein and protein-lipid interactions.
    GO:0005886    plasma membrane    The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.
    GO:0032587    ruffle membrane    The portion of the plasma membrane surrounding a ruffle.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ADA17_HUMAN | P785361bkc 1zxc 2a8h 2ddf 2fv5 2fv9 2i47 2m2f 3b92 3cki 3e8r 3edz 3ewj 3g42 3kmc 3kme 3l0t 3l0v 3le9 3lea 3lgp 3o64

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2OI0)