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(-) Description

Title :  LIGANDED STEROL CARRIER PROTEIN TYPE 2 (SCP-2) LIKE DOMAIN OF HUMAN MULTIFUNCTIONAL ENZYME TYPE 2 (MFE-2)
 
Authors :  A. M. Haapalainen, D. M. F. Van Aalten, T. Glumoff
Date :  07 May 01  (Deposition) - 14 Nov 01  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym./Biol. Unit :  A
Keywords :  Alfa-Beta Fold, Protein-Triton X-100 Complex, Hydrophobic Tunnel, Exposed Peroxisomal Targeting Signal Type 1 (Pts1), Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. M. Haapalainen, D. M. Van Aalten, G. Merilainen, J. E. Jalonen, P. Pirila, R. K. Wierenga, J. K. Hiltunen, T. Glumoff
Crystal Structure Of The Liganded Scp-2-Like Domain Of Human Peroxisomal Multifunctional Enzyme Type 2 At 1. 75 A Resolution.
J. Mol. Biol. V. 313 1127 2001
PubMed-ID: 11700068  |  Reference-DOI: 10.1006/JMBI.2001.5084
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ESTRADIOL 17 BETA-DEHYDROGENASE 4
    ChainsA
    EC Number1.1.1.62
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET3D
    Expression System StrainBL21 (DE3) PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentC-TERMINAL DOMAIN, RESIDUES 618-736
    GeneHSD17B4
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHUMAN MULTIFUNCTIONAL ENZYME TYPE 2, MFE-2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1OXN1Ligand/IonOXTOXYNOL-10
2SO42Ligand/IonSULFATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:101 , GLY A:102 , HOH A:1048 , HOH A:1125BINDING SITE FOR RESIDUE SO4 A 121
2AC2SOFTWAREGLU A:14 , HOH A:1311BINDING SITE FOR RESIDUE SO4 A 122
3AC3SOFTWARETRP A:36 , PRO A:89 , GLN A:90 , PHE A:93 , MET A:105 , SER A:107 , GLN A:108 , GLN A:111 , LEU A:114BINDING SITE FOR RESIDUE OXN A 123

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1IKT)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_052314T687IDHB4_HUMANPolymorphism28943592AT71I
2UniProtVAR_052315M728VDHB4_HUMANPolymorphism28943594AM112V

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (3, 3)

Asymmetric/Biological Unit (3, 3)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000002562161aENSE00002062781chr5:118788138-118788328191DHB4_HUMAN1-20200--
1.2bENST000002562162bENSE00001715680chr5:118792010-11879206354DHB4_HUMAN20-38190--
1.4cENST000002562164cENSE00001645814chr5:118809603-118809710108DHB4_HUMAN38-74370--
1.5bENST000002562165bENSE00001703065chr5:118810096-11881015560DHB4_HUMAN74-94210--
1.6bENST000002562166bENSE00001607423chr5:118811401-11881142222DHB4_HUMAN94-10180--
1.7aENST000002562167aENSE00001705604chr5:118811519-11881156547DHB4_HUMAN101-117170--
1.10cENST0000025621610cENSE00001647277chr5:118813112-11881319685DHB4_HUMAN117-145290--
1.12fENST0000025621612fENSE00001790487chr5:118814529-118814716188DHB4_HUMAN145-208640--
1.13ENST0000025621613ENSE00000972272chr5:118824887-11882497892DHB4_HUMAN208-238310--
1.14ENST0000025621614ENSE00000998891chr5:118827795-11882781925DHB4_HUMAN239-24790--
1.15cENST0000025621615cENSE00001143969chr5:118829513-118829641129DHB4_HUMAN247-290440--
1.17cENST0000025621617cENSE00001143964chr5:118832238-118832341104DHB4_HUMAN290-324350--
1.18aENST0000025621618aENSE00001143958chr5:118835012-118835248237DHB4_HUMAN325-403790--
1.19bENST0000025621619bENSE00001143950chr5:118837736-11883778752DHB4_HUMAN404-421180--
1.20ENST0000025621620ENSE00001143943chr5:118842513-11884258472DHB4_HUMAN421-445250--
1.21ENST0000025621621ENSE00001143936chr5:118844836-118844939104DHB4_HUMAN445-479350--
1.23ENST0000025621623ENSE00001143927chr5:118850676-11885074166DHB4_HUMAN480-501220--
1.24aENST0000025621624aENSE00000972280chr5:118860911-11886098070DHB4_HUMAN502-525240--
1.25cENST0000025621625cENSE00000972281chr5:118861612-118861718107DHB4_HUMAN525-560360--
1.26aENST0000025621626aENSE00000972282chr5:118862828-11886291487DHB4_HUMAN561-589290--
1.27aENST0000025621627aENSE00000972283chr5:118865589-11886567587DHB4_HUMAN590-618290--
1.28ENST0000025621628ENSE00000972284chr5:118866961-118867099139DHB4_HUMAN619-665471A:6-4944
1.29bENST0000025621629bENSE00000972285chr5:118872118-118872245128DHB4_HUMAN665-707431A:49-9143
1.30iENST0000025621630iENSE00001833743chr5:118877600-118878028429DHB4_HUMAN708-736291A:92-12029

(-) 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:115
 aligned with DHB4_HUMAN | P51659 from UniProtKB/Swiss-Prot  Length:736

    Alignment length:115
                                   631       641       651       661       671       681       691       701       711       721       731     
           DHB4_HUMAN   622 LQSTFVFEEIGRRLKDIGPEVVKKVNAVFEWHITKGGNIGAKWTIDLKSGSGKVYQGPAKGAADTTIILSDEDFMEVVLGKLDPQKAFFSGRLKARGNIMLSQKLQMILKDYAKL 736
               SCOP domains d1ikta_ A: SCP2-like domain of MFE-2                                                                                SCOP domains
               CATH domains 1iktA00 A:6-120 Nonspecific Lipid-transfer Protein; Chain A                                                         CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhheeeeeeee....eeeeeeeee.....eeee........eeeeeehhhhhhhhh...hhhhhhhh...eeeehhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -----------------------------------------------------------------I----------------------------------------V-------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.28  PDB: A:6-49 UniProt: 619-665     ------------------------------------------Exon 1.30i  PDB: A:92-120     Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.29b  PDB: A:49-91 UniProt: 665-707  ----------------------------- Transcript 1 (2)
                 1ikt A   6 LQSTFVFEEIGRRLKDIGPEVVKKVNAVFEWHITKGGNIGAKWTIDLKSGSGKVYQGPAKGAADTTIILSDEDFMEVVLGKLDPQKAFFSGRLKARGNIMLSQKLQMILKDYAKL 120
                                    15        25        35        45        55        65        75        85        95       105       115     

   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  (0, 0)

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

(-) Gene Ontology  (30, 30)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (DHB4_HUMAN | P51659)
molecular function
    GO:0044594    17-beta-hydroxysteroid dehydrogenase (NAD+) activity    Catalysis of the reaction: a 17-beta-hydroxysteroid + NAD+ = a 17-oxosteroid + NADH + H+.
    GO:0003857    3-hydroxyacyl-CoA dehydrogenase activity    Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+).
    GO:0033989    3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA hydratase activity    Catalysis of the reaction: (24R,25R)-3alpha,7alpha,12alpha,24-tetrahydroxy-5beta-cholestanoyl-CoA = (24E)-3alpha,7alpha,12alpha-trihydroxy-5beta-cholest-24-enoyl-CoA + H2O.
    GO:0016853    isomerase activity    Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
    GO:0016508    long-chain-enoyl-CoA hydratase activity    Catalysis of the reaction: a long-chain (3S)-3-hydroxyacyl-CoA = a long-chain trans-2-enoyl-CoA + H2O. A long-chain acyl-CoA is an acyl-CoA thioester where the acyl chain contains 13 to 22 carbon atoms.
    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:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    GO:0016616    oxidoreductase activity, acting on the CH-OH group of donors, NAD or NADP as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which a CH-OH group acts as a hydrogen or electron donor and reduces NAD+ or NADP.
    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.
biological process
    GO:0060009    Sertoli cell development    The process whose specific outcome is the progression of a Sertoli cell over time, from its formation to the mature structure. Cell development does not include the steps involved in committing a cell to a Sertoli cell fate.
    GO:0036109    alpha-linolenic acid metabolic process    The chemical reactions and pathways involving alpha-linolenic acid, an unsaturated omega-6 fatty acid that has the molecular formula C18H32O2.
    GO:0008209    androgen metabolic process    The chemical reactions and pathways involving androgens, C19 steroid hormones that can stimulate the development of male sexual characteristics.
    GO:0006699    bile acid biosynthetic process    The chemical reactions and pathways resulting in the formation of bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0008210    estrogen metabolic process    The chemical reactions and pathways involving estrogens, C18 steroid hormones that can stimulate the development of female sexual characteristics. Also found in plants.
    GO:0006635    fatty acid beta-oxidation    A fatty acid oxidation process that results in the complete oxidation of a long-chain fatty acid. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and occurs by successive cycles of reactions during each of which the fatty acid is shortened by a two-carbon fragment removed as acetyl coenzyme A; the cycle continues until only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0033540    fatty acid beta-oxidation using acyl-CoA oxidase    A fatty acid beta-oxidation pathway in which the initial step, which converts an acyl-CoA to a trans-2-enoyl-CoA, is catalyzed by acyl-CoA oxidase; the electrons removed by oxidation pass directly to oxygen and produce hydrogen peroxide, which is cleaved by peroxisomal catalases. Fatty acid beta-oxidation begins with the addition of coenzyme A to a fatty acid, and ends when only two or three carbons remain (as acetyl-CoA or propionyl-CoA respectively).
    GO:0006631    fatty acid metabolic process    The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
    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:0036112    medium-chain fatty-acyl-CoA metabolic process    The chemical reactions and pathways involving medium-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a long-chain fatty-acyl group. A medium-chain fatty acid is a fatty acid with a chain length of between C6 and C12.
    GO:0001649    osteoblast differentiation    The process whereby a relatively unspecialized cell acquires the specialized features of an osteoblast, a mesodermal or neural crest cell that gives rise to bone.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0000038    very long-chain fatty acid metabolic process    The chemical reactions and pathways involving a fatty acid which has a chain length greater than C22.
    GO:0036111    very long-chain fatty-acyl-CoA metabolic process    The chemical reactions and pathways involving very long-chain fatty-acyl-CoAs, any derivative of coenzyme A in which the sulfhydryl group is in a thioester linkage with a medium-chain fatty-acyl group. A very long-chain fatty acid is a fatty acid which has a chain length greater than C22.
cellular component
    GO:0043231    intracellular membrane-bounded organelle    Organized structure of distinctive morphology and function, bounded by a single or double lipid bilayer membrane and occurring within the cell. Includes the nucleus, mitochondria, plastids, vacuoles, and vesicles. Excludes the plasma membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005782    peroxisomal matrix    The volume contained within the membranes of a peroxisome; in many cells the matrix contains a crystalloid core largely composed of urate oxidase.
    GO:0005778    peroxisomal membrane    The lipid bilayer surrounding a peroxisome.
    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
        DHB4_HUMAN | P516591s9c 1zbq

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