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(-) Description

Title :  2.85 A CRYSTAL STRUCTURE OF PEDF
 
Authors :  M. Simonovic, P. G. W. Gettins, K. Volz
Date :  11 May 01  (Deposition) - 26 Sep 01  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.85
Chains :  Asym./Biol. Unit :  A
Keywords :  Serpin, Pedf, Angiogenesis, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Simonovic, P. G. Gettins, K. Volz
Crystal Structure Of Human Pedf, A Potent Anti-Angiogenic And Neurite Growth-Promoting Factor.
Proc. Natl. Acad. Sci. Usa V. 98 11131 2001
PubMed-ID: 11562499  |  Reference-DOI: 10.1073/PNAS.211268598

(-) Compounds

Molecule 1 - PIGMENT EPITHELIUM-DERIVED FACTOR
    ChainsA
    EngineeredYES
    Expression SystemCRICETULUS GRISEUS
    Expression System Cell LineBHK
    Expression System CommonCHINESE HAMSTER
    Expression System PlasmidPMA
    Expression System Taxid10029
    Expression System Vector TypePLASMID
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymPEDF

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:265BINDING SITE FOR RESIDUE NAG A 401

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (2, 2)

Asymmetric/Biological Unit (2, 2)
  dbSNPPDB
No.SourceVariant IDVariantUniProt IDStatusIDChainVariant
1UniProtVAR_009126T72MPEDF_HUMANPolymorphism1136287AM52M
2UniProtVAR_025500P132RPEDF_HUMANPolymorphism1804145AP112R

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

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1SERPINPS00284 Serpins signature.PEDF_HUMAN388-398  1A:368-378

(-) Exons   (6, 6)

Asymmetric/Biological Unit (6, 6)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENST000002547221ENSE00001376201chr17:1665253-1665407155PEDF_HUMAN-00--
1.2ENST000002547222ENSE00001309249chr17:1670197-167028892PEDF_HUMAN1-28280--
1.3ENST000002547223ENSE00000904177chr17:1673146-1673344199PEDF_HUMAN29-95671A:16-7560
1.4ENST000002547224ENSE00000904178chr17:1674323-1674478156PEDF_HUMAN95-147531A:75-12753
1.5ENST000002547225ENSE00000904179chr17:1675166-1675369204PEDF_HUMAN147-215691A:127-19569
1.6ENST000002547226ENSE00000904180chr17:1678352-1678494143PEDF_HUMAN215-262481A:195-24248
1.7ENST000002547227ENSE00001132115chr17:1679826-1680036211PEDF_HUMAN263-333711A:243-31371
1.8ENST000002547228ENSE00001328594chr17:1680481-1680859379PEDF_HUMAN333-418861A:313-398 (gaps)86

(-) 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:375
 aligned with PEDF_HUMAN | P36955 from UniProtKB/Swiss-Prot  Length:418

    Alignment length:383
                                    45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415   
           PEDF_HUMAN    36 TGALVEEEDPFFKVPVNKLAAAVSNFGYDLYRVRSSTSPTTNVLLSPLSVATALSALSLGAEQRTESIIHRALYYDLISSPDIHGTYKELLDTVTAPQKNLKSASRIVFEKKLRIKSSFVAPLEKSYGTRPRVLTGNPRLDLQEINNWVQAQMKGKLARSTKEIPDEISILLLGVAHFKGQWVTKFDSRKTSLEDFYLDEERTVRVPMMSDPKAVLRYGLDSDLSCKIAQLPLTGSMSIIFFLPLKVTQNLTLIEESLTSEFIHDIDRELKTVQAVLTVPKLKLSYEGEVTKSLQEMKLQSLFDSPDFSKITGKPIKLTQVEHRAGFEWNEDGAGTTPSPGLQPAHLTFPLDYHLNQPFIFVLRDTDTGALLFIGKILDPRGP 418
               SCOP domains d1imva_ A: Pigment epithelium-derived factor, PEDF                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 1imvA01      1imvA02 A:29-192,A:300-341 Antithrombin, subunit I, domain 2                                                                                                        1imvA01 A:16-28,A:193-299,A:342-398 Alpha-1-antitrypsin, domain 1                                          1imvA02 A:29-192,A:300-341                1imvA01 A:1        6-28,A:193-299,A:342-398               CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.....eeeeeeeee......hhhhhhhhhhhhh...ee...hhhhhhhhhhhhhhhhh................eeeeeeeeee..eee..hhhhheeeeee.....eeeeeeeeeeeeeeeeeee....eeeeeeee...eeeeeeee......hhhhhh..hhhhhhhhhhhheeeeeeeeee.eeeeeeeehhhhhhh...hhhhhh............eeeeeeeeeeee...eee..--------......eee....eeeeeee.....eeeeeee...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------M-----------------------------------------------------------R---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------SERPIN     -------------------- PROSITE
           Transcript 1 (1) Exon 1.3  PDB: A:16-75 UniProt: 29-95 [INCOMPLETE]          ---------------------------------------------------Exon 1.5  PDB: A:127-195 UniProt: 147-215                            -----------------------------------------------Exon 1.7  PDB: A:243-313 UniProt: 263-333                              ------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------------------Exon 1.4  PDB: A:75-127 UniProt: 95-147              -------------------------------------------------------------------Exon 1.6  PDB: A:195-242 UniProt: 215-262       ----------------------------------------------------------------------Exon 1.8  PDB: A:313-398 (gaps) UniProt: 333-418                                       Transcript 1 (2)
                 1imv A  16 TGALVEEEDPFFKVPVNKLAAAVSNFGYDLYRVRSSMSPTTNVLLSPLSVATALSALSLGADERTESIIHRALYYDLISSPDIHGTYKELLDTVTAPQKNLKSASRIVFEKKLRIKSSFVAPLEKSYGTRPRVLTGNPRLDLQEINNWVQAQMKGKLARSTKEIPDEISILLLGVAHFKGQWVTKFDSRKTSLEDFYLDEERTVRVPMMSDPKAVLRYGLDSDLSCKIAQLPLTGSMSIIFFLPLKVTQNLTLIEESLTSEFIHDIDRELKTVQAVLTVPKLKLSYEGEVTKSLQEMKLQSLFDSPDFSKITGKPIKLTQVEHRAGFEWNEDGAGTT--------HLTFPLDYHLNQPFIFVLRDTDTGALLFIGKILDPRGP 398
                                    25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345      |  -     | 365       375       385       395   
                                                                                                                                                                                                                                                                                                                                                                          352      361                                     

   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  (2, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (34, 34)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (PEDF_HUMAN | P36955)
molecular function
    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:0004867    serine-type endopeptidase inhibitor activity    Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
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:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0071279    cellular response to cobalt 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 cobalt ion stimulus.
    GO:0071549    cellular response to dexamethasone 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 dexamethasone stimulus.
    GO:0071333    cellular response to glucose 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 glucose stimulus.
    GO:0071300    cellular response to retinoic acid    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 retinoic acid stimulus.
    GO:0001822    kidney development    The process whose specific outcome is the progression of the kidney over time, from its formation to the mature structure. The kidney is an organ that filters the blood and/or excretes the end products of body metabolism in the form of urine.
    GO:0007275    multicellular organism development    The biological process whose specific outcome is the progression of a multicellular organism over time from an initial condition (e.g. a zygote or a young adult) to a later condition (e.g. a multicellular animal or an aged adult).
    GO:0016525    negative regulation of angiogenesis    Any process that stops, prevents, or reduces the frequency, rate or extent of angiogenesis.
    GO:0010951    negative regulation of endopeptidase activity    Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
    GO:0010596    negative regulation of endothelial cell migration    Any process that decreases the rate, frequency, or extent of the orderly movement of an endothelial cell into the extracellular matrix to form an endothelium.
    GO:0060770    negative regulation of epithelial cell proliferation involved in prostate gland development    Any process that decreases the rate, frequency or extent of epithelial cell proliferation that contributes to the progression of the prostate gland over time.
    GO:0010629    negative regulation of gene expression    Any process that decreases 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:0050728    negative regulation of inflammatory response    Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
    GO:1901215    negative regulation of neuron death    Any process that stops, prevents or reduces the frequency, rate or extent of neuron death.
    GO:0042698    ovulation cycle    The type of sexual cycle seen in females, often with physiologic changes in the endometrium that recur at regular intervals during the reproductive years.
    GO:0050769    positive regulation of neurogenesis    Any process that activates or increases the frequency, rate or extent of neurogenesis, the origin and formation of neurons.
    GO:0010976    positive regulation of neuron projection development    Any process that increases the rate, frequency or extent of neuron projection development. Neuron projection development is the process whose specific outcome is the progression of a neuron projection over time, from its formation to the mature structure. A neuron projection is any process extending from a neural cell, such as axons or dendrites (collectively called neurites).
    GO:0010447    response to acidic pH    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 pH stimulus with pH < 7. pH is a measure of the acidity or basicity of an aqueous solution.
    GO:0046685    response to arsenic-containing 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 arsenic stimulus from compounds containing arsenic, including arsenates, arsenites, and arsenides.
    GO:0060041    retina development in camera-type eye    The process whose specific outcome is the progression of the retina over time, from its formation to the mature structure. The retina is the innermost layer or coating at the back of the eyeball, which is sensitive to light and in which the optic nerve terminates.
    GO:0007614    short-term memory    The memory process that deals with the storage, retrieval and modification of information received a short time (up to about 30 minutes) ago. This type of memory is typically dependent on direct, transient effects of second messenger activation.
cellular component
    GO:0030424    axon    The long process of a neuron that conducts nerve impulses, usually away from the cell body to the terminals and varicosities, which are sites of storage and release of neurotransmitter.
    GO:0043203    axon hillock    Portion of the neuronal cell soma from which the axon originates.
    GO:0005604    basement membrane    A thin layer of dense material found in various animal tissues interposed between the cells and the adjacent connective tissue. It consists of the basal lamina plus an associated layer of reticulin fibers.
    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:0031012    extracellular matrix    A structure lying external to one or more cells, which provides structural support for cells or tissues.
    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:0042470    melanosome    A tissue-specific, membrane-bounded cytoplasmic organelle within which melanin pigments are synthesized and stored. Melanosomes are synthesized in melanocyte cells.
    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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