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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN APOLIPOPROTEIN D (APOD) IN COMPLEX WITH PROGESTERONE
 
Authors :  A. Eichinger, A. Skerra
Date :  09 Aug 06  (Deposition) - 14 Aug 07  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Lipocalin, Beta Barrel, Bilin-Binding Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. Eichinger, A. Nasreen, H. J. Kim, A. Skerra
Structural Insight Into The Dual Ligand Specificity And Mode Of High Density Lipoprotein Association Of Apolipoprotein D.
J. Biol. Chem. V. 282 31068 2007
PubMed-ID: 17699160  |  Reference-DOI: 10.1074/JBC.M703552200
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - APOLIPOPROTEIN D
    ChainsA
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPAPOD27DELTA(QA)
    Expression System StrainKS272
    Expression System Taxid562
    Expression System Vector TypePLASMID
    GeneAPOD
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymAPO-D, APOD

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1MSE3Mod. Amino AcidSELENOMETHIONINE
2STR1Ligand/IonPROGESTERONE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:34 , ALA A:44 , TYR A:46 , ASN A:58 , PHE A:89 , TYR A:98 , LEU A:129 , HOH A:461BINDING SITE FOR RESIDUE STR A 300

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:8 -A:114
2A:41 -A:165

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_011932S115LAPOD_HUMANPolymorphism5954AS95L
2UniProtVAR_011933T178KAPOD_HUMANPolymorphism5955AT158K

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1LIPOCALINPS00213 Lipocalin signature.APOD_HUMAN36-49  1A:16-29

(-) Exons   (4, 4)

Asymmetric/Biological Unit (4, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003432671aENSE00001386414chr3:195311076-195310749328APOD_HUMAN-00--
1.4ENST000003432674ENSE00002187051chr3:195306366-195306210157APOD_HUMAN1-41411A:3-2119
1.6ENST000003432676ENSE00001662195chr3:195300842-195300721122APOD_HUMAN42-82411A:22-6241
1.7aENST000003432677aENSE00001686972chr3:195298236-19529814889APOD_HUMAN82-112311A:62-9231
1.8dENST000003432678dENSE00001373102chr3:195296006-195295573434APOD_HUMAN112-189781A:92-16877

(-) 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:166
 aligned with APOD_HUMAN | P05090 from UniProtKB/Swiss-Prot  Length:189

    Alignment length:166
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182      
           APOD_HUMAN    23 FHLGKCPNPPVQENFDVNKYLGRWYEIEKIPTTFENGRCIQANYSLMENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFMPSAPYWILATDYENYALVYSCTCIIQLFHVDFAWILARNPNLPPETVDSLKNILTSNNIDVKKMTVTDQVNCPKL 188
               SCOP domains d2hzqa_ A: automated matches                                                                                                                                           SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee............hhhhh.eeeeeeee........eeeeeeeee.....eeeeeeee.....eeeeeeeeee.......eeeee.......eeeeeeee....eeeeeeeee....eeeeeeeeee.....hhhhhhhhhhhhhhh.......ee......... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------L--------------------------------------------------------------K---------- SAPs(SNPs)
                    PROSITE -------------LIPOCALIN     ------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.4           Exon 1.6  PDB: A:22-62 UniProt: 42-82    -----------------------------Exon 1.8d  PDB: A:92-168 UniProt: 112-189 [INCOMPLETE]                        Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.7a  PDB: A:62-92        ---------------------------------------------------------------------------- Transcript 1 (2)
                 2hzq A   3 FHLGKCPNPPVQENFDVNKYPGRWYEIEKIPTTFENGRCIQANYSLmENGKIKVLNQELRADGTVNQIEGEATPVNLTEPAKLEVKFSWFmPSAPYHILATDYENYALVYSCTSISQSFHVDFAWILARNVALPPETVDSLKNILTSNNIDVKKmTVTDQVNCPKL 168
                                    12        22        32        42      | 52        62        72        82        92|      102       112       122       132       142       152    |  162      
                                                                         49-MSE                                      93-MSE                                                         157-MSE       

   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  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (36, 36)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (APOD_HUMAN | P05090)
molecular function
    GO:0015485    cholesterol binding    Interacting selectively and non-covalently with 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:0008289    lipid binding    Interacting selectively and non-covalently with a lipid.
    GO:0005319    lipid transporter activity    Enables the directed movement of lipids into, out of or within a cell, or between cells.
    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:0036094    small molecule binding    Interacting selectively and non-covalently with a small molecule, any low molecular weight, monomeric, non-encoded molecule.
    GO:0005215    transporter activity    Enables the directed movement of substances (such as macromolecules, small molecules, ions) into, out of or within a cell, or between cells.
biological process
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0007420    brain development    The process whose specific outcome is the progression of the brain over time, from its formation to the mature structure. Brain development begins with patterning events in the neural tube and ends with the mature structure that is the center of thought and emotion. The brain is responsible for the coordination and control of bodily activities and the interpretation of information from the senses (sight, hearing, smell, etc.).
    GO:0006006    glucose metabolic process    The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
    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:0006869    lipid transport    The directed movement of lipids into, out of or within a cell, or between cells, by means of some agent such as a transporter or pore. Lipids are compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent.
    GO:2000405    negative regulation of T cell migration    Any process that stops, prevents or reduces the frequency, rate or extent of T cell migration.
    GO:1900016    negative regulation of cytokine production involved in inflammatory response    Any process that stops, prevents or reduces the frequency, rate or extent of cytokine production involved in inflammatory response.
    GO:0051895    negative regulation of focal adhesion assembly    Any process that stops, prevents, or reduces the frequency, rate or extent of focal adhesion assembly, the establishment and maturation of focal adhesions.
    GO:0060588    negative regulation of lipoprotein lipid oxidation    Any process that decreases the rate, frequency or extent of lipoprotein lipid oxidation. Lipoprotein lipid oxidation is the modification of a lipoprotein by oxidation of the lipid group.
    GO:0071638    negative regulation of monocyte chemotactic protein-1 production    Any process that stops, prevents, or reduces the frequency, rate, or extent of production of monocyte chemotactic protein-1.
    GO:0010642    negative regulation of platelet-derived growth factor receptor signaling pathway    Any process that stops, prevents, or reduces the frequency, rate or extent of the platelet-derived growth factor receptor signaling pathway.
    GO:0042308    negative regulation of protein import into nucleus    Any process that stops, prevents, or reduces the frequency, rate or extent of the movement of proteins from the cytoplasm into the nucleus.
    GO:0048662    negative regulation of smooth muscle cell proliferation    Any process that stops, prevents or reduces the rate or extent of smooth muscle cell proliferation.
    GO:2000098    negative regulation of smooth muscle cell-matrix adhesion    Any process that stops, prevents, or reduces the frequency, rate or extent of smooth muscle cell-matrix adhesion.
    GO:0014012    peripheral nervous system axon regeneration    The regrowth of axons outside the central nervous system (outside the brain and spinal cord) following an axonal injury.
    GO:0048678    response to axon injury    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 axon injury stimulus.
    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:0000302    response to reactive oxygen species    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 reactive oxygen species stimulus. Reactive oxygen species include singlet oxygen, superoxide, and oxygen free radicals.
    GO:0042246    tissue regeneration    The regrowth of lost or destroyed tissues.
    GO:0006810    transport    The directed movement of substances (such as macromolecules, small molecules, ions) or cellular components (such as complexes and organelles) into, out of or within a cell, or between cells, or within a multicellular organism by means of some agent such as a transporter, pore or motor protein.
cellular component
    GO:0022626    cytosolic ribosome    A ribosome located in the cytosol.
    GO:0030425    dendrite    A neuron projection that has a short, tapering, often branched, morphology, receives and integrates signals from other neurons or from sensory stimuli, and conducts a nerve impulse towards the axon or the cell body. In most neurons, the impulse is conveyed from dendrites to axon via the cell body, but in some types of unipolar neuron, the impulse does not travel via the cell body.
    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: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:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
    GO:0005615    extracellular space    That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
    GO:0005622    intracellular    The living contents of a cell; the matter contained within (but not including) the plasma membrane, usually taken to exclude large vacuoles and masses of secretory or ingested material. In eukaryotes it includes the nucleus and cytoplasm.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0048471    perinuclear region of cytoplasm    Cytoplasm situated near, or occurring around, the nucleus.

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 Related Entries

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

UniProtKB/Swiss-Prot
        APOD_HUMAN | P050902apd 2hzr

(-) Related Entries Specified in the PDB File

2hzr