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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN BIFUNCTIONAL EPOXIDE HYDROXYLASE 2 COMPLEXED WITH A8
 
Authors :  J. Pilger, A. Mazur, P. Monecke, H. Schreuder, B. Elshorst, T. Langer, A. Schiffer, I. Krimm, M. Wegstroth, D. Lee, G. Hessler, K. -U. Wendt, S C. Griesinger
Date :  09 Sep 13  (Deposition) - 01 Oct 14  (Release) - 10 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.06
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Hydrolase, Drug Design, Multiple Binding Modes (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Pilger, A. Mazur, P. Monecke, H. Schreuder, B. Elshorst, S. Bartoschek, T. Langer, A. Schiffer, I. Krimm, M. Wegstroth, D. Lee, G. Hessler, K. Wendt, S. Becker, C. Griesinger
A Combination Of Spin Diffusion Methods For The Determination Of Protein-Ligand Complex Structural Ensembles.
Angew. Chem. Int. Ed. Engl. V. 54 6511 2015
PubMed-ID: 25877959  |  Reference-DOI: 10.1002/ANIE.201500671

(-) Compounds

Molecule 1 - BIFUNCTIONAL EPOXIDE HYDROLASE 2
    ChainsA, B
    EC Number3.3.2.10, 3.1.3.76
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System VectorPET16B
    Expression System Vector TypePLASMID
    FragmentEPOXIDE HYDROXYLASE DOMAIN RESIDUES 230-555
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymBIFUNCTIONAL EPOXIDE HYDROXYLASE 2, CYTOSOLIC EPOXIDE HYDROLASE 2, CEH, EPOXIDE HYDRATASE, SOLUBLE EPOXIDE HYDROLASE, SEH, LIPID-PHOSPHATE PHOSPHATASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1W9L2Ligand/Ion1-ETHYL-3-NAPHTHALEN-1-YLUREA
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1W9L1Ligand/Ion1-ETHYL-3-NAPHTHALEN-1-YLUREA
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1W9L1Ligand/Ion1-ETHYL-3-NAPHTHALEN-1-YLUREA

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPHE A:267 , ASP A:335 , TYR A:383 , LEU A:408 , MET A:419 , TYR A:466 , VAL A:498 , HIS A:524BINDING SITE FOR RESIDUE W9L A1548
2AC2SOFTWAREPHE B:267 , ASP B:335 , TYR B:383 , MET B:419 , TYR B:466 , VAL B:498 , HIS B:524BINDING SITE FOR RESIDUE W9L B1548

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4C4Z)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Phe A:267 -Pro A:268
2Phe B:267 -Pro B:268

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (3, 6)

Asymmetric Unit (3, 6)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014852R287QHYES_HUMANPolymorphism751141A/BR287Q
2UniProtVAR_055396M369VHYES_HUMANPolymorphism72475894A/BM369V
3UniProtVAR_055397E470GHYES_HUMANPolymorphism68053459A/BE470G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 1 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014852R287QHYES_HUMANPolymorphism751141AR287Q
2UniProtVAR_055396M369VHYES_HUMANPolymorphism72475894AM369V
3UniProtVAR_055397E470GHYES_HUMANPolymorphism68053459AE470G

  SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)
Biological Unit 2 (3, 3)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_014852R287QHYES_HUMANPolymorphism751141BR287Q
2UniProtVAR_055396M369VHYES_HUMANPolymorphism72475894BM369V
3UniProtVAR_055397E470GHYES_HUMANPolymorphism68053459BE470G

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4C4Z)

(-) Exons   (0, 0)

(no "Exon" information available for 4C4Z)

(-) 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:318
 aligned with HYES_HUMAN | P34913 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:318
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539        
           HYES_HUMAN   230 TSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR 547
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhheeeeeeee..eeeeeeee....eeeee.....hhhhhhhhhhhhhhh..eeeeee............hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhh...hhhhhhh..hhhhhhhhhh..........eeeeee......hhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------Q---------------------------------------------------------------------------------V----------------------------------------------------------------------------------------------------G----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c4z A 230 TSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR 547
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539        

Chain B from PDB  Type:PROTEIN  Length:318
 aligned with HYES_HUMAN | P34913 from UniProtKB/Swiss-Prot  Length:555

    Alignment length:318
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539        
           HYES_HUMAN   230 TSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR 547
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhheeeeeeee..eeeeeeee....eeeee.....hhhhhhhhhhhhhhhh.eeeee.............hhhhhhhhhhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhh...eeeeeee...........hhhhhhhhh..hhhhhhh...hhhhhhhhhhhhhhhhhhh.................................hhhhhhhhhhhh....hhhhhh...hhhhhhhhhh..........eeeeee......hhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------Q---------------------------------------------------------------------------------V----------------------------------------------------------------------------------------------------G----------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4c4z B 230 TSCNPSDMSHGYVTVKPRVRLHFVELGSGPAVCLCHGFPESWYSWRYQIPALAQAGYRVLAMDMKGYGESSAPPEIEEYCMEVLCKEMVTFLDKLGLSQAVFIGHDWGGMLVWYMALFYPERVRAVASLNTPFIPANPNMSPLESIKANPVFDYQLYFQEPGVAEAELEQNLSRTFKSLFRASDESVLSMHKVCEAGGLFVNSPEEPSLSRMVTEEEIQFYVQQFKKSGFRGPLNWYRNMERNWKWACKSLGRKILIPALMVTAEKDFVLVPQMSQHMEDWIPHLKRGHIEDCGHWTQMDKPTEVNQILIKWLDSDAR 547
                                   239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539        

   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 4C4Z)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4C4Z)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4C4Z)

(-) Gene Ontology  (32, 32)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (HYES_HUMAN | P34913)
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:0006874    cellular calcium ion homeostasis    Any process involved in the maintenance of an internal steady state of calcium ions at the level of a cell.
    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:0017144    drug metabolic process    The chemical reactions and pathways involving a drug, a substance used in the diagnosis, treatment or prevention of a disease; as used here antibiotic substances (see antibiotic metabolism) are considered to be drugs, even if not used in medical or veterinary practice.
    GO:0019373    epoxygenase P450 pathway    The chemical reactions and pathways by which arachidonic acid is converted to other compounds including epoxyeicosatrienoic acids and dihydroxyeicosatrienoic acids.
    GO:0006954    inflammatory response    The immediate defensive reaction (by vertebrate tissue) to infection or injury caused by chemical or physical agents. The process is characterized by local vasodilation, extravasation of plasma into intercellular spaces and accumulation of white blood cells and macrophages.
    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:0072593    reactive oxygen species metabolic process    The chemical reactions and pathways involving a reactive oxygen species, any molecules or ions formed by the incomplete one-electron reduction of oxygen. They contribute to the microbicidal activity of phagocytes, regulation of signal transduction and gene expression, and the oxidative damage to biopolymers.
    GO:0008217    regulation of blood pressure    Any process that modulates the force with which blood travels through the circulatory system. The process is controlled by a balance of processes that increase pressure and decrease pressure.
    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.
    GO:0006805    xenobiotic metabolic process    The chemical reactions and pathways involving a xenobiotic compound, a compound foreign to living organisms. Used of chemical compounds, e.g. a xenobiotic chemical, such as a pesticide.
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_HUMAN | P349131s8o 1vj5 1zd2 1zd3 1zd4 1zd5 3ans 3ant 3i1y 3i28 3koo 3otq 3pdc 3wk4 3wk5 3wk6 3wk7 3wk8 3wk9 3wka 3wkb 3wkc 3wkd 3wke 4c4x 4c4y 4hai 4j03 4jnc 4ocz 4od0 4x6x 4x6y 4y2j 4y2p 4y2q 4y2r 4y2s 4y2t 4y2u 4y2v 4y2x 4y2y 5ahx 5ai0 5ai4 5ai5 5ai6 5ai8 5ai9 5aia 5aib 5aic 5ak3 5ak4 5ak5 5ak6 5ake 5akg 5akh 5aki 5akj 5akk 5akl 5akx 5aky 5akz 5ald 5ale 5alf 5alg 5alh 5ali 5alj 5alk 5all 5alm 5aln 5alo 5alp 5alq 5alr 5als 5alt 5alu 5alv 5alw 5alx 5aly 5alz 5am0 5am1 5am2 5am3 5am4 5am5 5fp0

(-) Related Entries Specified in the PDB File

4c4x CRYSTAL STRUCTURE OF HUMAN BIFUNCTIONAL EPOXIDE HYDROXYLASE 2 COMPLEXED WITH C9
4c4y CRYSTAL STRUCTURE OF HUMAN BIFUNCTIONAL EPOXIDE HYDROXYLASE 2 COMPLEXED WITH A4