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Crystal structure of human CYP7A1 in complex with 7-ketocholesterol
Biology and Chemistry Report
3V8D
  •   Structure Details   Hide

    Structure Keywords

    Keywords OXIDOREDUCTASE
    Text cytochrome, OXIDOREDUCTASE

    Polymeric Molecules

    Chain A,B
    Description Cholesterol 7-alpha-monooxygenase 
    Fragment UNP residues 25-503 
    Mutation T104L 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 56482.5 
    Source Method genetically manipulated  
    Entity Name CYPVII, Cholesterol 7-alpha-hydroxylase, Cytochrome P450 7A1 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    0GV  (3beta,8alpha,9beta)-3-hydroxycholest-5-en-7-one  C27 H44 O2   400.64  View 
    HEM  PROTOPORPHYRIN IX CONTAINING FE  C34 H32 Fe N4 O4   616.49  View 
    SO4  SULFATE ION  O4 S   96.06  View 
    UNX  UNKNOWN ATOM OR ION  X   0.00  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B CP7A1_HUMAN P22680     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  1.14.13.17      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    6629   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. 
    6699   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. 
    6707   Cholesterol Catabolic Process  The Chemical Reactions and Pathways Resulting in the Breakdown of Cholesterol Cholest 5 En 3 Beta Ol the Principal Sterol of Vertebrates and the Precursor of Many Steroids Including Bile Acids and Steroid Hormones. 
    8202   Steroid Metabolic Process  The Chemical Reactions and Pathways Involving Steroids Compounds with a 1 2 Cyclopentanoperhydrophenanthrene Nucleus. 
    8203   Cholesterol Metabolic Process  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. It Is a Component of the Plasma Membrane Lipid Bilayer and of Plasma Lipoproteins and Can Be Found in All Animal Tissues. 
    42632   Cholesterol Homeostasis  Any Process Involved in the Maintenance of an Internal Steady State of Cholesterol Within an Organism or Cell. 
    55114   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. 
    70857   Regulation of Bile Acid Biosynthetic Process  Any Process That Modulates the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of Bile Acids. 
    71397   Cellular Response to Cholesterol  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 Cholesterol Stimulus. 
    5783   Endoplasmic Reticulum  The Irregular Network of Unit Membranes Visible Only by Electron Microscopy That Occurs in the Cytoplasm of Many Eukaryotic Cells. the Membranes Form a Complex Meshwork of Tubular Channels Which Are Often Expanded Into Slitlike Cavities Called Cisternae. the Er Takes Two Forms Rough (or Granular) with Ribosomes Adhering to the Outer Surface and Smooth (with No Ribosomes Attached). 
    5789   Endoplasmic Reticulum Membrane  The Lipid Bilayer Surrounding the Endoplasmic Reticulum. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    31090   Organelle Membrane  A Membrane That Is One of the Two Lipid Bilayers of an Organelle Envelope or the Outermost Membrane of Single Membrane Bound Organelle. 
    43231   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. 
    4497   Monooxygenase Activity  Catalysis of the Incorporation of One Atom From Molecular Oxygen Into a Compound and the Reduction of the Other Atom of Oxygen to Water. 
    8123   Cholesterol 7 Alpha Monooxygenase Activity  Catalysis of the Reaction: Cholesterol + Nadph + H+ + O2 = 7 Alpha Hydroxycholesterol + Nadp+ + H2o. 
    16491   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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene cyp7a1, cyp7
    Host Scientific Name Escherichia coli  
    Host Strain Jm109
    Host Vector Type Plasmid
    Host Plasmid Name pCW


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    8 8q11-q12 1581     cytochrome P450, family 7, subfamily A, polypeptide 1 CYP7A1    

    Single Nucleotide Polymorphisms (from LS-SNP database)

    SNP ID LsSnp Link dbSNP Link Chain PDB position Amino acid changes Secondary structure Solvent Accessibility Chromosome Chromosome position Ligand
    rs200846540 LS-SNP   dbSNP   A 27 R - > M Coil 58% (Exposed) 8 59412578
    rs138113674 LS-SNP   dbSNP   A 36 N - > K Beta Ladder 49% (Exposed) 8 59411001
    rs180916341 LS-SNP   dbSNP   A 49 G - > D Turn 63% (Exposed) 8 59410963
    rs189424028 LS-SNP   dbSNP   A 53 L - > F Helix 10% (Intermediate) 8 59410952
    rs148278254 LS-SNP   dbSNP   A 54 E - > D Helix 39% (Exposed) 8 59410947
    rs113258453 LS-SNP   dbSNP   A 63 H - > Q Helix 32% (Intermediate) 8 59410920
    rs143198855 LS-SNP   dbSNP   A 68 T - > I Beta Ladder 1% (Buried) 8 59410906
    rs62621283 LS-SNP   dbSNP   A 86 H - > N Helix 49% (Exposed) 8 59410853 UNX
    rs200836103 LS-SNP   dbSNP   A 100 F - > C Helix 15% (Intermediate) 8 59410810
    rs201114135 LS-SNP   dbSNP   A 151 R - > G Helix 44% (Exposed) 8 59409620
    rs72647413 LS-SNP   dbSNP   A 193 T - > I Bend 74% (Exposed) 8 59409493
    rs201046553 LS-SNP   dbSNP   A 195 R - > Q 3/10 Helix 71% (Exposed) 8 59409487
    rs8192874 LS-SNP   dbSNP   A 233 N - > S Helix 52% (Exposed) 8 59409373
    rs141299456 LS-SNP   dbSNP   A 235 R - > Q Helix 8% (Buried) 8 59409367
    rs192455108 LS-SNP   dbSNP   A 239 A - > T Helix 0% (Buried) 8 59409356
    rs146594981 LS-SNP   dbSNP   A 241 S - > N Helix 22% (Intermediate) 8 59409349
    rs150039957 LS-SNP   dbSNP   A 250 R - > M Coil 14% (Intermediate) 8 59409322
    rs200100159 LS-SNP   dbSNP   A 257 I - > S Helix 0% (Buried) 8 59409301
    rs139396617 LS-SNP   dbSNP   A 260 R - > L Helix 5% (Buried) 8 59409292 0GV
    rs151320685 LS-SNP   dbSNP   A 264 N - > S Helix 0% (Buried) 8 59409280
    rs142476981 LS-SNP   dbSNP   A 303 R - > K Helix 42% (Exposed) 8 59409163
    rs140288234 LS-SNP   dbSNP   A 313 E - > K Helix 59% (Exposed) 8 59407167
    rs147153175 LS-SNP   dbSNP   A 315 V - > M Helix 3% (Buried) 8 59407161
    rs143476559 LS-SNP   dbSNP   A 330 G - > D Bend 69% (Exposed) 8 59407115
    rs201041588 LS-SNP   dbSNP   A 332 P - > L Coil 50% (Exposed) 8 59407109
    rs8192875 LS-SNP   dbSNP   A 347 D - > N Helix 14% (Intermediate) 8 59407065
    rs149291486 LS-SNP   dbSNP   A 364 R - > W Beta Ladder 2% (Buried) 8 59405037
    rs138607943 LS-SNP   dbSNP   A 367 K - > M Bend 50% (Exposed) 8 59405027
    rs117423932 LS-SNP   dbSNP   A 377 G - > S Coil 25% (Intermediate) 8 59404998
    rs142708991 LS-SNP   dbSNP   A 398 P - > A Turn 60% (Exposed) 8 59404935
    rs138787236 LS-SNP   dbSNP   A 402 P - > T Bend 57% (Exposed) 8 59404923
    rs144997923 LS-SNP   dbSNP   A 404 P - > S Turn 15% (Intermediate) 8 59404917
    rs201787113 LS-SNP   dbSNP   A 417 G - > R Bend 42% (Exposed) 8 59404300
    rs151122002 LS-SNP   dbSNP   A 431 K - > R Bend 77% (Exposed) 8 59404257 UNX
    rs201341987 LS-SNP   dbSNP   A 435 M - > T Coil 1% (Buried) 8 59404245
    rs199557345 LS-SNP   dbSNP   A 450 A - > V Helix 8% (Buried) 8 59404200 HEM
    rs148119788 LS-SNP   dbSNP   A 481 Q - > E 3/10 Helix 15% (Intermediate) 8 59404108
    rs201171633 LS-SNP   dbSNP   A 483 R - > Q 3/10 Helix 7% (Buried) 8 59404101
    rs143725488 LS-SNP   dbSNP   A 483 R - > W 3/10 Helix 7% (Buried) 8 59404102
    rs148977608 LS-SNP   dbSNP   A 490 P - > R Coil 10% (Intermediate) 8 59404080