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(-) Description

Title :  CRYSTAL STRUCTURE OF MURINE SOLUBLE EPOXIDE HYDROLASE COMPLEXED WITH CIU INHIBITOR
 
Authors :  M. A. Argiriadi, C. Morisseau, M. H. Goodrow, D. L. Dowdy, B. D. Hammock, D. W. Christianson
Date :  06 Mar 00  (Deposition) - 31 May 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Homodimer, Alpha/Beta Hydrolase Fold, Disubstituted Urea Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. A. Argiriadi, C. Morisseau, M. H. Goodrow, D. L. Dowdy, B. D. Hammock, D. W. Christianson
Binding Of Alkylurea Inhibitors To Epoxide Hydrolase Implicates Active Site Tyrosines In Substrate Activation.
J. Biol. Chem. V. 275 15265 2000
PubMed-ID: 10747889  |  Reference-DOI: 10.1074/JBC.M000278200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - EPOXIDE HYDROLASE
    ChainsA, B
    EC Number3.3.2.3
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System CommonFALL ARMYWORM
    Expression System Taxid7108
    Expression System VectorBACCULOVIRUS
    Expression System Vector TypeVIRUS
    Organism CommonHOUSE MOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1CIU2Ligand/IonN-CYCLOHEXYL-N'-(4-IODOPHENYL)UREA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:265 , ASP A:333 , TRP A:334 , VAL A:337 , MET A:361 , TYR A:381 , GLN A:382 , PHE A:406 , TYR A:465 , VAL A:497BINDING SITE FOR RESIDUE CIU A 1100
2AC2SOFTWAREPHE B:265 , ASP B:333 , TRP B:334 , VAL B:337 , MET B:361 , TYR B:381 , GLN B:382 , PHE B:406 , TYR B:465 , HIS B:523 , TRP B:524BINDING SITE FOR RESIDUE CIU B 1200

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1EK1)

(-) Cis Peptide Bonds  (10, 10)

Asymmetric/Biological Unit
No.Residues
1Leu A:16 -Pro A:17
2Lys A:160 -Pro A:161
3Asn A:231 -Pro A:232
4Gly A:256 -Pro A:257
5Phe A:265 -Pro A:266
6Leu B:16 -Pro B:17
7Lys B:160 -Pro B:161
8Asn B:231 -Pro B:232
9Gly B:256 -Pro B:257
10Phe B:265 -Pro B:266

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1EK1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1EK1)

(-) Exons   (0, 0)

(no "Exon" information available for 1EK1)

(-) 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:490
 aligned with HYES_MOUSE | P34914 from UniProtKB/Swiss-Prot  Length:554

    Alignment length:541
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543 
           HYES_MOUSE     4 RVAAFDLDGVLALPSIAGAFRRSEEALALPRDFLLGAYQTEFPEGPTEQLMKGKITFSQWVPLMDESYRKSSKACGANLPENFSISQIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNWLDDGDKRDSLAQMMCELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRELEKVTGTQFPEAPLPVPCNPNDVSHGYVTVKPGIRLHFVEMGSGPALCLCHGFPESWFSWRYQIPALAQAGFRVLAIDMKGYGDSSSPPEIEEYAMELLCKEMVTFLDKLGIPQAVFIGHDWAGVMVWNMALFYPERVRAVASLNTPFMPPDPDVSPMKVIRSIPVFNYQLYFQEPGVAEAELEKNMSRTFKSFFRASDETGFIAVHKATEIGGILVNTPEDPNLSKITTEEEIEFYIQQFKKTGFRGPLNWYRNTERNWKWSCKGLGRKILVPALMVTAEKDIVLRPEMSKNMEKWIPFLKRGHIEDCGHWTQIEKPTEVNQILIKWLQTE 544
               SCOP domains d1ek1a1 A:4-225                             Epoxide hydrolase,                        N-terminal domain                                                                                                                       d1ek1a2 A:226-544 Mammalian epoxide hydrolase, C-terminal domain                                                                                                                                                                                                                                                                SCOP domains
               CATH domains ----1ek1A01 A:8-                            218  [code=3.40.50.                       1000, no name defined]                                                                                                           ----------------1ek1A02 A:235-542  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                             -- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee......ee...----------------------------hhhhhhh............-----------------------..........eehhhhhhhhhhhhhhh..eeeee........hhhhhhhhhhhhhh...eeee..........hhhhhhhhhhhh.....ee.......hhhhhhhhh............hhhhhhh......................eee.....eeeeeee....eee.......hhhhhhhhhhhhhhhhheeeee.............hhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhh...........hhhhh..................hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..........eeeeee......hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ek1 A   4 RVAAFDLDGVLALPSI----------------------------GPTEQLMKGKITFSQWVPL-----------------------QIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNWLDDGDKRDSLAQMMCELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRELEKVTGTQFPEAPLPVPCNPNDVSHGYVTVKPGIRLHFVEMGSGPALCLCHGFPESWFSWRYQIPALAQAGFRVLAIDMKGYGDSSSPPEIEEYAMELLCKEMVTFLDKLGIPQAVFIGHDWAGVMVWNMALFYPERVRAVASLNTPFMPPDPDVSPMKVIRSIPVFNYQLYFQEPGVAEAELEKNMSRTFKSFFRASDETGFIAVHKATEIGGILVNTPEDPNLSKITTEEEIEFYIQQFKKTGFRGPLNWYRNTERNWKWSCKGLGRKILVPALMVTAEKDIVLRPEMSKNMEKWIPFLKRGHIEDCGHWTQIEKPTEVNQILIKWLQTE 544
                                    13     |   -         -         -    |   53        63  |      -         -      | 93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543 
                                          19                           48                66                      90                                                                                                                                                                                                                                                                                                                                                                                                                                                                      

Chain B from PDB  Type:PROTEIN  Length:541
 aligned with HYES_MOUSE | P34914 from UniProtKB/Swiss-Prot  Length:554

    Alignment length:541
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543 
           HYES_MOUSE     4 RVAAFDLDGVLALPSIAGAFRRSEEALALPRDFLLGAYQTEFPEGPTEQLMKGKITFSQWVPLMDESYRKSSKACGANLPENFSISQIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNWLDDGDKRDSLAQMMCELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRELEKVTGTQFPEAPLPVPCNPNDVSHGYVTVKPGIRLHFVEMGSGPALCLCHGFPESWFSWRYQIPALAQAGFRVLAIDMKGYGDSSSPPEIEEYAMELLCKEMVTFLDKLGIPQAVFIGHDWAGVMVWNMALFYPERVRAVASLNTPFMPPDPDVSPMKVIRSIPVFNYQLYFQEPGVAEAELEKNMSRTFKSFFRASDETGFIAVHKATEIGGILVNTPEDPNLSKITTEEEIEFYIQQFKKTGFRGPLNWYRNTERNWKWSCKGLGRKILVPALMVTAEKDIVLRPEMSKNMEKWIPFLKRGHIEDCGHWTQIEKPTEVNQILIKWLQTE 544
               SCOP domains d1ek1b1 B:4-225 Epoxide hydrolase, N-terminal domain                                                                                                                                                                          d1ek1b2 B:226-544 Mammalian epoxide hydrolase, C-terminal domain                                                                                                                                                                                                                                                                SCOP domains
               CATH domains 1ek1B01       1ek1B02 B:18-97 Putative phosphatase; domain 2                                  1ek1B01 B:4-17,B:98-218  [code=3.40.50.1000, no name defined]                                                            ----------------1ek1B03 B:235-544  [code=3.40.50.1820, no name defined]                                                                                                                                                                                                                                                                CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee.......ee..hhhhhhh...........hhhhh.......hhhhhhh......hhhhhhhhhhhhhh........................eehhhhhhhhhhhhhh..eeeeee........hhhhhhhhhhhhh....eeeehhhhh.....hhhhhhhhhhhh.....ee..........hhhhhh.........................................eee.....eeeeeee....eee.......hhhhhhhhhhhhhhhhheeeee.............hhhhhhhhhhhhhhhhhhhhh...eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh..........eeeeee......hhhhhhhhhhh....eeeee.....hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ek1 B   4 RVAAFDLDGVLALPSIAGAFRRSEEALALPRDFLLGAYQTEFPEGPTEQLMKGKITFSQWVPLMDESYRKSSKACGANLPENFSISQIFSQAMAARSINRPMLQAAIALKKKGFTTCIVTNNWLDDGDKRDSLAQMMCELSQHFDFLIESCQVGMIKPEPQIYNFLLDTLKAKPNEVVFLDDFGSNLKPARDMGMVTILVHNTASALRELEKVTGTQFPEAPLPVPCNPNDVSHGYVTVKPGIRLHFVEMGSGPALCLCHGFPESWFSWRYQIPALAQAGFRVLAIDMKGYGDSSSPPEIEEYAMELLCKEMVTFLDKLGIPQAVFIGHDWAGVMVWNMALFYPERVRAVASLNTPFMPPDPDVSPMKVIRSIPVFNYQLYFQEPGVAEAELEKNMSRTFKSFFRASDETGFIAVHKATEIGGILVNTPEDPNLSKITTEEEIEFYIQQFKKTGFRGPLNWYRNTERNWKWSCKGLGRKILVPALMVTAEKDIVLRPEMSKNMEKWIPFLKRGHIEDCGHWTQIEKPTEVNQILIKWLQTE 544
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543 

   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  (2, 4)

Asymmetric/Biological Unit

(-) CATH Domains  (3, 5)

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

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1EK1)

(-) Gene Ontology  (25, 25)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (HYES_MOUSE | P34914)
molecular function
    GO:0033885    10-hydroxy-9-(phosphonooxy)octadecanoate phosphatase activity    Catalysis of the reaction: (9S,10S)-10-hydroxy-9-(phosphonooxy)octadecanoate + H(2)O = (9S,10S)-9,10-dihydroxyoctadecanoate + 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:0004301    epoxide hydrolase activity    Catalysis of the reaction: an epoxide + H2O = a glycol.
    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:0042577    lipid phosphatase activity    Catalysis of the reaction: a phospholipid + H2O = a lipid + phosphate.
    GO:0000287    magnesium ion binding    Interacting selectively and non-covalently with magnesium (Mg) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0016791    phosphatase activity    Catalysis of the hydrolysis of phosphoric monoesters, releasing inorganic phosphate.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0015643    toxic substance binding    Interacting selectively and non-covalently with a toxic substance, a poisonous substance that causes damage to biological systems.
biological process
    GO:0019439    aromatic compound catabolic process    The chemical reactions and pathways resulting in the breakdown of aromatic compounds, any substance containing an aromatic carbon ring.
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0016311    dephosphorylation    The process of removing one or more phosphoric (ester or anhydride) residues from a molecule.
    GO:0006629    lipid metabolic process    The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
    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:0046839    phospholipid dephosphorylation    The process of removing one or more phosphate groups from a phosphorylated lipid, any member of a group of substances soluble in lipid solvents but only sparingly soluble in aqueous solvents.
    GO:0010628    positive regulation of gene expression    Any process that increases the frequency, rate or extent of gene expression. Gene expression is the process in which a gene's coding sequence is converted into a mature gene product or products (proteins or RNA). This includes the production of an RNA transcript as well as any processing to produce a mature RNA product or an mRNA or circRNA (for protein-coding genes) and the translation of that mRNA or circRNA into protein. Protein maturation is included when required to form an active form of a product from an inactive precursor form.
    GO:0090181    regulation of cholesterol metabolic process    Any process that modulates the rate, frequency, or extent of cholesterol metabolism, the chemical reactions and pathways involving cholesterol, cholest-5-en-3 beta-ol, the principal sterol of vertebrates and the precursor of many steroids, including bile acids and steroid hormones.
    GO:0009636    response to toxic substance    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 toxic stimulus.
    GO:0046272    stilbene catabolic process    The chemical reactions and pathways resulting in the breakdown of stilbenes, a class of polyketide compounds formed from cinnamic acid and three molecules of malonyl CoA.
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:0070062    extracellular exosome    A vesicle that is released into the extracellular region by fusion of the limiting endosomal membrane of a multivesicular body with the plasma membrane. Extracellular exosomes, also simply called exosomes, have a diameter of about 40-100 nm.
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HYES_MOUSE | P349141cqz 1cr6 1ek2

(-) Related Entries Specified in the PDB File

1cqz 1cr6 1ek2