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(-) Description

Title :  CRYSTAL STRUCTURE OF AKR1C1 IN COMPLEX WITH NADP AND 3,5-DICHLOROSALICYLIC ACID
 
Authors :  U. Dhagat, O. El-Kabbani
Date :  28 Jan 08  (Deposition) - 26 Aug 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Aldo-Keto Reductase, 20 Alpha Hydroxysteroid Dehydrogenase, Akr1C1, Cytoplasm, Nadp, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  U. Dhagat, S. Endo, R. Sumii, A. Hara, O. El-Kabbani
Selectivity Determinants Of Inhibitor Binding To Human 20Alpha-Hydroxysteroid Dehydrogenase: Crystal Structure Of The Enzyme In Ternary Complex With Coenzyme And The Potent Inhibitor 3, 5-Dichlorosalicylic Acid
J. Med. Chem. V. 51 4844 2008
PubMed-ID: 18620380  |  Reference-DOI: 10.1021/JM8003575
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - ALDO-KETO REDUCTASE FAMILY 1 MEMBER C1
    ChainsA
    EC Number1.1.1.149
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPKK223-3
    Expression System StrainPKKDD1
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAKR1C1, DDH, DDH1
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAKR1C1, 20-ALPHA-HYDROXYSTEROID DEHYDROGENASE, 20- ALPHA-HSD, TRANS-1,2-DIHYDROBENZENE-1,2-DIOL DEHYDROGENASE, HIGH-AFFINITY HEPATIC BILE ACID-BINDING PROTEIN, HBAB, CHLORDECONE REDUCTASE HOMOLOG HAKRC, DIHYDRODIOL DEHYDROGENASE 1/2, DD1/DD2

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 3)
No.NameCountTypeFull Name
1C2U1Ligand/Ion3,5-DICHLORO-2-HYDROXYBENZOIC ACID
2NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3ZN1Ligand/IonZINC ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:133 , HIS A:248 , GLU A:292 , HOH A:673BINDING SITE FOR RESIDUE ZN A 324
2AC2SOFTWAREGLY A:22 , THR A:23 , TYR A:24 , ASP A:50 , TYR A:55 , HIS A:117 , SER A:166 , ASN A:167 , GLN A:190 , TYR A:216 , SER A:217 , ALA A:218 , LEU A:219 , GLY A:220 , SER A:221 , HIS A:222 , LEU A:236 , ALA A:253 , LEU A:268 , LYS A:270 , SER A:271 , TYR A:272 , ARG A:276 , GLN A:279 , ASN A:280 , LEU A:306 , HOH A:364 , HOH A:424 , HOH A:428 , HOH A:436 , HOH A:483 , HOH A:678BINDING SITE FOR RESIDUE NAP A 350
3AC3SOFTWARETYR A:24 , LEU A:54 , TYR A:55 , TRP A:86 , HIS A:117 , HIS A:222 , TRP A:227 , LEU A:308BINDING SITE FOR RESIDUE C2U A 351

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3C3U)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Glu A:225 -Pro A:226

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_048214R170HAK1C1_HUMANPolymorphism139588200AR170H
2UniProtVAR_048215Q172LAK1C1_HUMANPolymorphism17354444AQ172L

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

(-) PROSITE Motifs  (3, 3)

Asymmetric/Biological Unit (3, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1ALDOKETO_REDUCTASE_1PS00798 Aldo/keto reductase family signature 1.AK1C1_HUMAN45-62  1A:45-62
2ALDOKETO_REDUCTASE_2PS00062 Aldo/keto reductase family signature 2.AK1C1_HUMAN151-168  1A:151-168
3ALDOKETO_REDUCTASE_3PS00063 Aldo/keto reductase family putative active site signature.AK1C1_HUMAN268-283  1A:268-283

(-) Exons   (9, 9)

Asymmetric/Biological Unit (9, 9)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2bENST000003808722bENSE00002191078chr10:5005445-5005720276AK1C1_HUMAN1-28281A:4-2825
1.4bENST000003808724bENSE00001707745chr10:5008106-5008273168AK1C1_HUMAN29-84561A:29-8456
1.5aENST000003808725aENSE00001605320chr10:5009119-5009235117AK1C1_HUMAN85-123391A:85-12339
1.5dENST000003808725dENSE00001782597chr10:5010501-501057878AK1C1_HUMAN124-149261A:124-14926
1.6ENST000003808726ENSE00001777306chr10:5011014-5011136123AK1C1_HUMAN150-190411A:150-19041
1.8ENST000003808728ENSE00001632630chr10:5014393-5014502110AK1C1_HUMAN191-227371A:191-22737
1.9bENST000003808729bENSE00001714957chr10:5014776-5014941166AK1C1_HUMAN227-282561A:227-28256
1.10ENST0000038087210ENSE00001803180chr10:5018043-501812583AK1C1_HUMAN283-310281A:283-31028
1.11cENST0000038087211cENSE00001822803chr10:5019892-50221592268AK1C1_HUMAN310-323141A:310-32314

(-) 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:320
 aligned with AK1C1_HUMAN | Q04828 from UniProtKB/Swiss-Prot  Length:323

    Alignment length:320
                                    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
          AK1C1_HUMAN     4 KYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY 323
               SCOP domains d3c3ua_ A: automated matches                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 3c3uA00 A:4-323 NADP-dependent oxidoreductase                                                                                                                                                                                                                                                                                    CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.....eee.eeee........hhhhhhhhhhhhhhh..eee.hhhhhhhhhhhhhhhhhhhh...hhhhheeeeeehhhhhhhhhhhhhhhhhhhhhh...eeeeee..........................hhhhhhhhhhhhhhh..eeeeeee..hhhhhhhhhh.........eeeee......hhhhhhhhhhh..eeeee.................hhhhhhhhhhhhhhh..hhhhhhhhhhhhh..eeeee..hhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhh........... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------H-L------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------ALDOKETO_REDUCTASE----------------------------------------------------------------------------------------ALDOKETO_REDUCTASE---------------------------------------------------------------------------------------------------ALDOKETO_REDUCTA---------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.2b  PDB: A:4-28   Exon 1.4b  PDB: A:29-84 UniProt: 29-84                  Exon 1.5a  PDB: A:85-123               Exon 1.5d  PDB: A:124-149 Exon 1.6  PDB: A:150-190 UniProt: 150-190Exon 1.8  PDB: A:191-227             -------------------------------------------------------Exon 1.10  PDB: A:283-310   ------------- Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Exon 1.9b  PDB: A:227-282 UniProt: 227-282              ---------------------------Exon 1.11c     Transcript 1 (2)
                 3c3u A   4 KYQCVKLNDGHFMPVLGFGTYAPAEVPKSKALEATKLAIEAGFRHIDSAHLYNNEEQVGLAIRSKIADGSVKREDIFYTSKLWCNSHRPELVRPALERSLKNLQLDYVDLYLIHFPVSVKPGEEVIPKDENGKILFDTVDLCATWEAVEKCKDAGLAKSIGVSNFNRRQLEMILNKPGLKYKPVCNQVECHPYFNQRKLLDFCKSKDIVLVAYSALGSHREEPWVDPNSPVLLEDPVLCALAKKHKRTPALIALRYQLQRGVVVLAKSYNEQRIRQNVQVFEFQLTSEEMKAIDGLNRNVRYLTLDIFAGPPNYPFSDEY 323
                                    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

   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 3C3U)

(-) Gene Ontology  (32, 32)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (AK1C1_HUMAN | Q04828)
molecular function
    GO:0047006    17-alpha,20-alpha-dihydroxypregn-4-en-3-one dehydrogenase activity    Catalysis of the reaction: NAD(P)+ + 17-alpha,20-alpha-dihydroxypregn-4-en-3-one = NAD(P)H + H+ + 17-alpha-hydroxyprogesterone.
    GO:0004032    alditol:NADP+ 1-oxidoreductase activity    Catalysis of the reaction: an alditol + NADP+ = an aldose + NADPH + H+.
    GO:0004033    aldo-keto reductase (NADP) activity    Catalysis of the reaction: an alcohol + NADP+ = an aldehyde or a ketone + NADPH + H+.
    GO:0047042    androsterone dehydrogenase (B-specific) activity    Catalysis of the reaction: NAD(P)+ + androsterone = NAD(P)H + H+ + 5-alpha-androstane-3,17-dione. The reaction is B-specific (i.e. the pro-S hydrogen is transferred from the 4-position of reduced nicotinamide cofactor) with respect to NAD(P)+.
    GO:0032052    bile acid binding    Interacting selectively and non-covalently with bile acids, any of a group of steroid carboxylic acids occurring in bile.
    GO:0031406    carboxylic acid binding    Interacting selectively and non-covalently with a carboxylic acid, any organic acid containing one or more carboxyl (COOH) groups or anions (COO-).
    GO:0047718    indanol dehydrogenase activity    Catalysis of the reaction: indan-1-ol + NAD(P)+ = indanone + NAD(P)H + H+.
    GO:0047086    ketosteroid monooxygenase activity    Catalysis of the reaction: O2 + NADPH + progesterone = H2O + NADP+ + testosterone acetate.
    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:0016655    oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor    Catalysis of an oxidation-reduction (redox) reaction in which NADH or NADPH acts as a hydrogen or electron donor and reduces a quinone or a similar acceptor molecule.
    GO:0018636    phenanthrene 9,10-monooxygenase activity    Catalysis of the reaction: phenanthrene + O2 + NADH + H+ = H2O + NAD+ + phenanthrene-9,10-oxide.
    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:0047115    trans-1,2-dihydrobenzene-1,2-diol dehydrogenase activity    Catalysis of the reaction: NADP+ + trans-1,2-dihydrobenzene-1,2-diol = NADPH + catechol.
biological process
    GO:0015721    bile acid and bile salt transport    The directed movement of bile acid and bile salts into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore.
    GO:0008206    bile acid metabolic process    The chemical reactions and pathways involving bile acids, any of a group of steroid carboxylic acids occurring in bile, where they are present as the sodium salts of their amides with glycine or taurine.
    GO:0071395    cellular response to jasmonic acid 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 jasmonic acid stimulus.
    GO:0042632    cholesterol homeostasis    Any process involved in the maintenance of an internal steady state of cholesterol within an organism or cell.
    GO:0044597    daunorubicin metabolic process    The chemical reactions and pathways involving daunorubicin, a chemotherapeutic of the anthracycline family that is given as a treatment for some types of cancer.
    GO:0007586    digestion    The whole of the physical, chemical, and biochemical processes carried out by multicellular organisms to break down ingested nutrients into components that may be easily absorbed and directed into metabolism.
    GO:0044598    doxorubicin metabolic process    The chemical reactions and pathways involving doxorubicin, an anthracycline antibiotic, used in cancer chemotherapy.
    GO:0030855    epithelial cell differentiation    The process in which a relatively unspecialized cell acquires specialized features of an epithelial cell, any of the cells making up an epithelium.
    GO:0030299    intestinal cholesterol absorption    Uptake of cholesterol into the blood by absorption from the small intestine.
    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:0042448    progesterone metabolic process    The chemical reactions and pathways involving progesterone, a steroid hormone produced in the ovary which prepares and maintains the uterus for pregnancy. Also found in plants.
    GO:0051260    protein homooligomerization    The process of creating protein oligomers, compounds composed of a small number, usually between three and ten, of identical component monomers. Oligomers may be formed by the polymerization of a number of monomers or the depolymerization of a large protein polymer.
    GO:0046683    response to organophosphorus    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 an organophosphorus stimulus. Organophosphorus is a compound containing phosphorus bound to an organic molecule; several organophosphorus compounds are used as insecticides, and they are highly toxic cholinesterase inhibitors.
    GO:0042574    retinal metabolic process    The chemical reactions and pathways involving retinal, a compound that plays an important role in the visual process in most vertebrates. In the retina, retinal combines with opsins to form visual pigments. Retinal is one of the forms of vitamin A.
    GO:0001523    retinoid metabolic process    The chemical reactions and pathways involving retinoids, any member of a class of isoprenoids that contain or are derived from four prenyl groups linked head-to-tail. Retinoids include retinol and retinal and structurally similar natural derivatives or synthetic compounds, but need not have vitamin A activity.
    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.

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 Related Entries

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

UniProtKB/Swiss-Prot
        AK1C1_HUMAN | Q048281mrq 3gug 3nty 4yvp

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3C3U)