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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN MICROSOMAL P450 1A2 IN COMPLEX WITH ALPHA-NAPHTHOFLAVONE
 
Authors :  S. Sansen, J. K. Yano, R. L. Reynald, G. S. Schoch, C. D. Stout, E. F. Johnson
Date :  29 Jun 06  (Deposition) - 20 Feb 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym./Biol. Unit :  A
Keywords :  Cyp1A2, P450 1A2, P450, Monooxygenase, Drug Metabolizing Enzyme, Alpha-Naphthoflavone, Benzo(H)Flavone, 7, 8- Benzoflavone, Oxidoreductase, Heme (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. Sansen, J. K. Yano, R. L. Reynald, G. A. Schoch, K. J. Griffin, C. D. Stout, E. F. Johnson
Adaptations For The Oxidation Of Polycyclic Aromatic Hydrocarbons Exhibited By The Structure Of Human P450 1A2.
J. Biol. Chem. V. 282 14348 2007
PubMed-ID: 17311915  |  Reference-DOI: 10.1074/JBC.M611692200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - CYTOCHROME P450 1A2
    ChainsA
    EC Number1.14.14.1
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPCWORI
    Expression System StrainDH5ALPHA
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentRESIDUES 26-514
    GeneCYP1A2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymCYPIA2, P450-P3, P3, 450, P450 4

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
1BHF1Ligand/Ion2-PHENYL-4H-BENZO[H]CHROMEN-4-ONE
2HEM1Ligand/IonPROTOPORPHYRIN IX CONTAINING FE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:108 , THR A:124 , TRP A:133 , ARG A:137 , LEU A:144 , ILE A:314 , ALA A:317 , GLY A:318 , THR A:321 , PHE A:376 , PHE A:381 , LEU A:382 , THR A:385 , ILE A:386 , HIS A:388 , GLN A:411 , LEU A:450 , PHE A:451 , ARG A:456 , CYS A:458 , ILE A:459 , ALA A:464 , HOH A:694BINDING SITE FOR RESIDUE HEM A 900
2AC2SOFTWARETHR A:118 , PHE A:226 , PHE A:260 , ASP A:313 , GLY A:316 , ALA A:317 , ASP A:320 , THR A:321 , LEU A:497 , HOH A:733BINDING SITE FOR RESIDUE BHF A 800

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2HI4)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2HI4)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (21, 21)

Asymmetric/Biological Unit (21, 21)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
01UniProtVAR_025182P42RCP1A2_HUMANPolymorphism  ---AP42R
02UniProtVAR_025183G73RCP1A2_HUMANPolymorphism45565238AG73R
03UniProtVAR_020848T83MCP1A2_HUMANPolymorphism  ---AT83M
04UniProtVAR_025184D104NCP1A2_HUMANPolymorphism34067076AD104N
05UniProtVAR_025185L111FCP1A2_HUMANPolymorphism45442197AL111F
06UniProtVAR_020849E168QCP1A2_HUMANPolymorphism  ---AE168Q
07UniProtVAR_020850F186LCP1A2_HUMANPolymorphism  ---AF186L
08UniProtVAR_025186F205VCP1A2_HUMANPolymorphism45540640AF205V
09UniProtVAR_020851S212CCP1A2_HUMANPolymorphism  ---AS212C
10UniProtVAR_025187R281WCP1A2_HUMANPolymorphism45468096AR281W
11UniProtVAR_024709S298RCP1A2_HUMANPolymorphism17861157AS298R
12UniProtVAR_020852G299SCP1A2_HUMANPolymorphism35796837AG299S
13UniProtVAR_024710I314VCP1A2_HUMANPolymorphism28399418AI314V
14UniProtVAR_020793D348NCP1A2_HUMANPolymorphism56276455AD348N
15UniProtVAR_025188R377QCP1A2_HUMANPolymorphism  ---AR377Q
16UniProtVAR_020794I386FCP1A2_HUMANPolymorphism  ---AI386F
17UniProtVAR_020795C406YCP1A2_HUMANPolymorphism55889066AC406Y
18UniProtVAR_020796R431WCP1A2_HUMANPolymorphism28399424AR431W
19UniProtVAR_020853T438ICP1A2_HUMANPolymorphism45486893AT438I
20UniProtVAR_025189R456HCP1A2_HUMANPolymorphism  ---AR456H
21UniProtVAR_055563R457WCP1A2_HUMANPolymorphism34151816AR457W

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1CYTOCHROME_P450PS00086 Cytochrome P450 cysteine heme-iron ligand signature.CP1A2_HUMAN451-460  1A:451-460

(-) Exons   (0, 0)

(no "Exon" information available for 2HI4)

(-) 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:480
 aligned with CP1A2_HUMAN | P05177 from UniProtKB/Swiss-Prot  Length:515

    Alignment length:480
                                    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
          CP1A2_HUMAN    34 RVPKGLKSPPEPWGWPLLGHVLTLGKNPHLALSRMSQRYGDVLQIRIGSTPVLVLSRLDTIRQALVRQGDDFKGRPDLYTSTLITDGQSLTFSTDSGPVWAARRRLAQNALNTFSIASDPASSSSCYLEEHVSKEAKALISRLQELMAGPGHFDPYNQVVVSVANVIGAMCFGQHFPESSDEMLSLVKNTHEFVETASSGNPLDFFPILRYLPNPALQRFKAFNQRFLWFLQKTVQEHYQDFDKNSVRDITGALFKHSKKGPRASGNLIPQEKIVNLVNDIFGAGFDTVTTAISWSLMYLVTKPEIQRKIQKELDTVIGRERRPRLSDRPQLPYLEAFILETFRHSSFLPFTIPHSTTRDTTLNGFYIPKKCCVFVNQWQVNHDPELWEDPSEFRPERFLTADGTAINKPLSEKMMLFGMGKRRCIGEVLAKWEIFLFLAILLQQLEFSVPPGVKVDLTPIYGLTMKHARCEHVQARRFS 513
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...................hhhhhh.hhhhhhhhhhhhhh.eeeeee..eeeeee.hhhhhhhhhh.hhhhh.....hhhhhh.............hhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.hhhhhh.....hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh.ee..ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhh..hhhhhhhhhhhhhhhh.......ee....eee..eee....eeeehhhhhhhh..........hhhhhh.......hhhhhh......hhhhh..hhhhhhhhhhhhhhhhhhhheee.........................eee... Sec.struct. author
                 SAPs(SNPs) --------R------------------------------R---------M--------------------N------F--------------------------------------------------------Q-----------------L------------------V------C--------------------------------------------------------------------W----------------RS--------------V---------------------------------N----------------------------Q--------F-------------------Y------------------------W------I-----------------HW-------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------CYTOCHROME----------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2hi4 A  34 RVPKGLKSPPEPWGWPLLGHVLTLGKNPHLALSRMSQRYGDVLQIRIGSTPVLVLSRLDTIRQALVRQGDDFKGRPDLYTSTLITDGQSLTFSTDSGPVWAARRRLAQNALNTFSIASDPASSSSCYLEEHVSKEAKALISRLQELMAGPGHFDPYNQVVVSVANVIGAMCFGQHFPESSDEMLSLVKNTHEFVETASSGNPLDFFPILRYLPNPALQRFKAFNQRFLWFLQKTVQEHYQDFDKNSVRDITGALFKHSKKGPRASGNLIPQEKIVNLVNDIFGAGFDTVTTAISWSLMYLVTKPEIQRKIQKELDTVIGRERRPRLSDRPQLPYLEAFILETFRHSSFLPFTIPHSTTRDTTLNGFYIPKKCCVFVNQWQVNHDPELWEDPSEFRPERFLTADGTAINKPLSEKMMLFGMGKRRCIGEVLAKWEIFLFLAILLQQLEFSVPPGVKVDLTPIYGLTMKHARCEHVQARRFS 513
                                    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

   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 2HI4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2HI4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2HI4)

(-) Gene Ontology  (52, 52)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (CP1A2_HUMAN | P05177)
molecular function
    GO:0070330    aromatase activity    Catalysis of the reduction of an aliphatic ring to yield an aromatic ring.
    GO:0034875    caffeine oxidase activity    Catalysis of the reaction: caffeine + O2 + 2 H+ + 2 e- = 1,3,7-trimethyluric acid + H2O.
    GO:0032451    demethylase activity    Catalysis of the removal of a methyl group from a substrate.
    GO:0009055    electron carrier activity    Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
    GO:0019899    enzyme binding    Interacting selectively and non-covalently with any enzyme.
    GO:0020037    heme binding    Interacting selectively and non-covalently with heme, any compound of iron complexed in a porphyrin (tetrapyrrole) ring.
    GO:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0004497    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.
    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:0016705    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from each of two donors, and molecular oxygen is reduced or incorporated into a donor.
    GO:0016712    oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, reduced flavin or flavoprotein as one donor, and incorporation of one atom of oxygen    Catalysis of an oxidation-reduction (redox) reaction in which hydrogen or electrons are transferred from reduced flavin or flavoprotein and one other donor, and one atom of oxygen is incorporated into one donor.
    GO:0019825    oxygen binding    Interacting selectively and non-covalently with oxygen (O2).
biological process
    GO:0009820    alkaloid metabolic process    The chemical reactions and pathways involving alkaloids, nitrogen containing natural products which are not otherwise classified as peptides, nonprotein amino acids, amines, cyanogenic glycosides, glucosinolates, cofactors, phytohormones or primary metabolites (such as purine or pyrimidine bases).
    GO:0006725    cellular aromatic compound metabolic process    The chemical reactions and pathways involving aromatic compounds, any organic compound characterized by one or more planar rings, each of which contains conjugated double bonds and delocalized pi electrons, as carried out by individual cells.
    GO:0045333    cellular respiration    The enzymatic release of energy from inorganic and organic compounds (especially carbohydrates and fats) which either requires oxygen (aerobic respiration) or does not (anaerobic respiration).
    GO:0071276    cellular response to cadmium ion    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 cadmium (Cd) ion stimulus.
    GO:0018894    dibenzo-p-dioxin metabolic process    The chemical reactions and pathways involving dibenzo-p-dioxin, a substance composed of two benzene rings linked by two ether bonds. Dibenzo-p-dioxins are generated as by-products in the manufacturing of herbicides, insecticides, fungicides, paper pulp bleaching, and in incineration, and can accumulate in milk and throughout the food chain, creating significant health concern.
    GO:0042737    drug catabolic process    The chemical reactions and pathways resulting in the breakdown of a drug, a substance used in the diagnosis, treatment or prevention of a disease.
    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:0042738    exogenous drug catabolic process    The chemical reactions and pathways resulting in the breakdown of a drug that has originated externally to the cell or organism.
    GO:0046483    heterocycle metabolic process    The chemical reactions and pathways involving heterocyclic compounds, those with a cyclic molecular structure and at least two different atoms in the ring (or rings).
    GO:0050665    hydrogen peroxide biosynthetic process    The chemical reactions and pathways resulting in the formation of hydrogen peroxide (H2O2), a potentially harmful byproduct of aerobic cellular respiration which can cause damage to DNA.
    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:0030324    lung development    The process whose specific outcome is the progression of the lung over time, from its formation to the mature structure. In all air-breathing vertebrates the lungs are developed from the ventral wall of the oesophagus as a pouch which divides into two sacs. In amphibians and many reptiles the lungs retain very nearly this primitive sac-like character, but in the higher forms the connection with the esophagus becomes elongated into the windpipe and the inner walls of the sacs become more and more divided, until, in the mammals, the air spaces become minutely divided into tubes ending in small air cells, in the walls of which the blood circulates in a fine network of capillaries. In mammals the lungs are more or less divided into lobes, and each lung occupies a separate cavity in the thorax.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0032787    monocarboxylic acid metabolic process    The chemical reactions and pathways involving monocarboxylic acids, any organic acid containing one carboxyl (COOH) group or anion (COO-).
    GO:0016098    monoterpenoid metabolic process    The chemical reactions and pathways involving monoterpenoid compounds, terpenoids having a C10 skeleton.
    GO:0097267    omega-hydroxylase P450 pathway    The chemical reactions and pathways by which arachidonic acid is converted to other compounds initially by omega-hydroxylation.
    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:0071615    oxidative deethylation    The process of removing one or more ethyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
    GO:0070989    oxidative demethylation    The process of removing one or more methyl groups from a molecule, involving the oxidation (i.e. electron loss) of one or more atoms in the substrate.
    GO:0006778    porphyrin-containing compound metabolic process    The chemical reactions and pathways involving any member of a large group of derivatives or analogs of porphyrin. Porphyrins consists of a ring of four pyrrole nuclei linked each to the next at their alpha positions through a methine group.
    GO:0009791    post-embryonic development    The process whose specific outcome is the progression of the organism over time, from the completion of embryonic development to the mature structure. See embryonic development.
    GO:0010468    regulation of gene expression    Any process that modulates 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:0042493    response to drug    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 drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0032355    response to estradiol    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 stimulus by estradiol, a C18 steroid hormone hydroxylated at C3 and C17 that acts as a potent estrogen.
    GO:0035902    response to immobilization stress    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 being rendered immobile.
    GO:0032496    response to lipopolysaccharide    Any process that results in a change in state or activity of an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a lipopolysaccharide stimulus; lipopolysaccharide is a major component of the cell wall of gram-negative bacteria.
    GO:0014070    response to organic cyclic compound    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 organic cyclic compound stimulus.
    GO:0010033    response to organic 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 an organic substance stimulus.
    GO:0006706    steroid catabolic process    The chemical reactions and pathways resulting in the breakdown of steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0008202    steroid metabolic process    The chemical reactions and pathways involving steroids, compounds with a 1,2,cyclopentanoperhydrophenanthrene nucleus.
    GO:0009403    toxin biosynthetic process    The chemical reactions and pathways resulting in the formation of toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
    GO:0009404    toxin metabolic process    The chemical reactions and pathways involving a toxin, a poisonous compound (typically a protein) that is produced by cells or organisms and that can cause disease when introduced into the body or tissues of an organism.
    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:0005783    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).
    GO:0005789    endoplasmic reticulum membrane    The lipid bilayer surrounding the endoplasmic reticulum.
    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:0031090    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.

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 Related Entries

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

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(-) Related Entries Specified in the PDB File

1pq2 HUMAN DRUG METABOLIZING FAMILY 2 P450 2C8
1r90 HUMAN DRUG METABOLIZING FAMILY 2 P450 2C9
1tqn HUMAN DRUG METABOLIZING FAMILY 3 P450 3A4
1z10 HUMAN MICROSOMAL P450 2A6 WITH COUMARIN BOUND, USED AS MR SEARCH PROBE