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(-) Description

Title :  MURINE ANGIOGENIN, SULPHATE COMPLEX
 
Authors :  D. E. Holloway, G. B. Chavali, M. C. Hares, V. Subramanian, K. R. Acharya
Date :  15 Jul 05  (Deposition) - 30 Nov 05  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.50
Chains :  Asym./Biol. Unit :  A
Keywords :  Ribonuclease, Angiogenesis, Cancer, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  D. E. Holloway, G. B. Chavali, M. C. Hares, V. Subramanian, K. R. Acharya
Structure Of Murine Angiogenin: Features Of The Substrate- And Cell-Binding Regions And Prospects For Inhibitor-Binding Studies.
Acta Crystallogr. , Sect. D V. 61 1568 2005
PubMed-ID: 16301790  |  Reference-DOI: 10.1107/S0907444905029616

(-) Compounds

Molecule 1 - ANGIOGENIN
    ChainsA
    EC Number3.1.27.5
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMANG
    Expression System StrainW3110
    Expression System Taxid562
    Expression System VectorPUC
    Organism CommonMOUSE
    Organism ScientificMUS MUSCULUS
    Organism Taxid10090
    StrainBALB/C
    SynonymRIBONUCLEASE 5, RNASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric/Biological Unit (1, 2)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:12 , HIS A:13 , LYS A:40 , HIS A:113 , PHE A:114 , HOH A:2009 , HOH A:2105 , HOH A:2106BINDING SITE FOR RESIDUE SO4 A1121
2AC2SOFTWARETYR A:6 , LYS A:50 , LYS A:54 , ARG A:65 , HOH A:2107 , HOH A:2108BINDING SITE FOR RESIDUE SO4 A1122

(-) SS Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1A:26 -A:80
2A:39 -A:91
3A:57 -A:106

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:37 -Pro A:38
2Pro A:89 -Pro A:90

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BWK)

(-) PROSITE Motifs  (1, 1)

Asymmetric/Biological Unit (1, 1)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1RNASE_PANCREATICPS00127 Pancreatic ribonuclease family signature.ANGI_MOUSE63-69  1A:39-45

(-) Exons   (1, 1)

Asymmetric/Biological Unit (1, 1)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.2ENSMUST000000690112ENSMUSE00000887157chr14:51715675-51716148474ANGI_MOUSE-00--
1.3ENSMUST000000690113ENSMUSE00000481648chr14:51721061-51721682622ANGI_MOUSE1-1511511A:3-120118

(-) 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:118
 aligned with ANGI_MOUSE | P21570 from UniProtKB/Swiss-Prot  Length:145

    Alignment length:118
                                    36        46        56        66        76        86        96       106       116       126       136        
           ANGI_MOUSE    27 DSRYTKFLTQHHDAKPKGRDDRYCERMMKRRSLTSPCKDVNTFIHGNKSNIKAICGANGSPYRENLRMSKSPFQVTTCKHTGGSPRPPCQYRASAGFRHVVIACENGLPVHFDESFFS 144
               SCOP domains d2bwka_ A: automated matches                                                                                           SCOP domains
               CATH domains 2bwkA00 A:3-120 P-30 Protein                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhh.......hhhhhhhhhhhh........eeeee..hhhhhhhhhh..eeee...eeee...eeeeeeeee........eeeeeeeee..eeeee..eeeee.hhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------RNASE_P--------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.3  PDB: A:3-120 UniProt: 1-151 [INCOMPLETE]                                                                     Transcript 1
                 2bwk A   3 DSRYTKFLTQHHDAKPKGRDDRYCERMMKRRSLTSPCKDVNTFIHGNKSNIKAICGANGSPYRENLRMSKSPFQVTTCKHTGGSPRPPCQYRASAGFRHVVIACENGLPVHFDESFFS 120
                                    12        22        32        42        52        62        72        82        92       102       112        

   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 2BWK)

(-) Gene Ontology  (48, 48)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (ANGI_MOUSE | P21570)
molecular function
    GO:0003677    DNA binding    Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0003779    actin binding    Interacting selectively and non-covalently with monomeric or multimeric forms of actin, including actin filaments.
    GO:0005507    copper ion binding    Interacting selectively and non-covalently with copper (Cu) ions.
    GO:0004519    endonuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids by creating internal breaks.
    GO:0008201    heparin binding    Interacting selectively and non-covalently with heparin, any member of a group of glycosaminoglycans found mainly as an intracellular component of mast cells and which consist predominantly of alternating alpha-(1->4)-linked D-galactose and N-acetyl-D-glucosamine-6-sulfate residues.
    GO:0016787    hydrolase activity    Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
    GO:0004518    nuclease activity    Catalysis of the hydrolysis of ester linkages within nucleic acids.
    GO:0003676    nucleic acid binding    Interacting selectively and non-covalently with any nucleic acid.
    GO:0042277    peptide binding    Interacting selectively and non-covalently with peptides, any of a group of organic compounds comprising two or more amino acids linked by peptide bonds.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0005102    receptor binding    Interacting selectively and non-covalently with one or more specific sites on a receptor molecule, a macromolecule that undergoes combination with a hormone, neurotransmitter, drug or intracellular messenger to initiate a change in cell function.
    GO:0004540    ribonuclease activity    Catalysis of the hydrolysis of phosphodiester bonds in chains of RNA.
biological process
    GO:0090501    RNA phosphodiester bond hydrolysis    The RNA metabolic process in which the phosphodiester bonds between ribonucleotides are cleaved by hydrolysis.
    GO:0030041    actin filament polymerization    Assembly of actin filaments by the addition of actin monomers to a filament.
    GO:0032431    activation of phospholipase A2 activity    Any process that initiates the activity of the inactive enzyme phospholipase A2.
    GO:0007202    activation of phospholipase C activity    The initiation of the activity of the inactive enzyme phospolipase C as the result of a series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand.
    GO:0032148    activation of protein kinase B activity    Any process that initiates the activity of the inactive enzyme protein kinase B.
    GO:0001525    angiogenesis    Blood vessel formation when new vessels emerge from the proliferation of pre-existing blood vessels.
    GO:0019731    antibacterial humoral response    An immune response against bacteria mediated through a body fluid. Examples of this process are the antibacterial humoral responses in Mus musculus and Drosophila melanogaster.
    GO:0019732    antifungal humoral response    An immune response against a fungus mediated through a body fluid. An example of this process is the antifungal humoral response in Drosophila melanogaster.
    GO:0030154    cell differentiation    The process in which relatively unspecialized cells, e.g. embryonic or regenerative cells, acquire specialized structural and/or functional features that characterize the cells, tissues, or organs of the mature organism or some other relatively stable phase of the organism's life history. Differentiation includes the processes involved in commitment of a cell to a specific fate and its subsequent development to the mature state.
    GO:0016477    cell migration    The controlled self-propelled movement of a cell from one site to a destination guided by molecular cues. Cell migration is a central process in the development and maintenance of multicellular organisms.
    GO:0007417    central nervous system development    The process whose specific outcome is the progression of the central nervous system over time, from its formation to the mature structure. The central nervous system is the core nervous system that serves an integrating and coordinating function. In vertebrates it consists of the brain and spinal cord. In those invertebrates with a central nervous system it typically consists of a brain, cerebral ganglia and a nerve cord.
    GO:0050830    defense response to Gram-positive bacterium    Reactions triggered in response to the presence of a Gram-positive bacterium that act to protect the cell or organism.
    GO:0006651    diacylglycerol biosynthetic process    The chemical reactions and pathways resulting in the formation of diacylglycerol, a glyceride in which any two of the R groups (positions not specified) are acyl groups while the remaining R group can be either H or an alkyl group.
    GO:0045087    innate immune response    Innate immune responses are defense responses mediated by germline encoded components that directly recognize components of potential pathogens.
    GO:0050900    leukocyte migration    The movement of a leukocyte within or between different tissues and organs of the body.
    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: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:0017148    negative regulation of translation    Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of proteins by the translation of mRNA or circRNA.
    GO:0001938    positive regulation of endothelial cell proliferation    Any process that activates or increases the rate or extent of endothelial cell proliferation.
    GO:0042327    positive regulation of phosphorylation    Any process that activates or increases the frequency, rate or extent of addition of phosphate groups to a molecule.
    GO:0050714    positive regulation of protein secretion    Any process that activates or increases the frequency, rate or extent of the controlled release of a protein from a cell.
    GO:0009303    rRNA transcription    The synthesis of ribosomal RNA (rRNA), any RNA that forms part of the ribosomal structure, from a DNA template.
    GO:0009725    response to hormone    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 hormone stimulus.
    GO:0001666    response to hypoxia    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 stimulus indicating lowered oxygen tension. Hypoxia, defined as a decline in O2 levels below normoxic levels of 20.8 - 20.95%, results in metabolic adaptation at both the cellular and organismal level.
    GO:0001878    response to yeast    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 stimulus from a yeast species.
cellular component
    GO:0032311    angiogenin-PRI complex    A stable heterodimer of angiogenin and placental ribonuclease inhibitor; interaction between angiogenin and PRI prevents angiogenin binding to its receptor to stimulate angiogenesis.
    GO:0005605    basal lamina    A thin sheet of proteoglycans and glycoproteins, especially laminin, secreted by cells as an extracellular matrix.
    GO:0031410    cytoplasmic vesicle    A vesicle found in the cytoplasm of a cell.
    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:0030426    growth cone    The migrating motile tip of a growing nerve cell axon or dendrite.
    GO:0043025    neuronal cell body    The portion of a neuron that includes the nucleus, but excludes cell projections such as axons and dendrites.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

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 Related Entries

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

UniProtKB/Swiss-Prot
        ANGI_MOUSE | P215702bwl

(-) Related Entries Specified in the PDB File

2bwl MURINE ANGIOGENIN, PHOSPHATE COMPLEX