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CRYSTAL STRUCTURE OF HUMAN ANGIOGENIN IN COMPLEX WITH FAB FRAGMENT OF ITS MONOCLONAL ANTIBODY MAB 26-2F
Biology and Chemistry Report
1H0D
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM/HYDROLASE
    Text IMMUNE SYSTEM/HYDROLASE, COMPLEX (ANTIBODY-HYDROLASE), RIBONUCLEASE, ANTIBODY, IMMUNE SYSTEM-HYDROLASE complex

    Polymeric Molecules

    Chain A
    Description ANTIBODY FAB FRAGMENT, LIGHT CHAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23584.2 
    Source Method genetically manipulated  
    Chain B
    Description ANTIBODY FAB FRAGMENT, HEAVY CHAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23658.7 
    Source Method genetically manipulated  
    Chain C
    Description ANGIOGENIN 
    Nonstandard Linkage no 
    Nonstandard Monomers yes 
    Polymer Type polypeptide(L) 
    Formula Weight 14152.1 
    Source Method genetically manipulated  
    Entity Name RIBONUCLEASE 5, RNASE 5 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    SO4  SULFATE ION  O4 S   96.06  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    C ANGI_HUMAN P03950     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc Catalytic Site(s)
    3.1.27        

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 77533    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain C
    GO ID   Ontology GO Term Definition
    1525   Angiogenesis  Blood Vessel Formation When New Vessels Emerge From the Proliferation of Pre Existing Blood Vessels. 
    1541   Ovarian Follicle Development  The Process Whose Specific Outcome Is the Progression of the Ovarian Follicle Over Time From Its Formation to the Mature Structure. 
    1556   Oocyte Maturation  A Developmental Process Independent of Morphogenetic (shape) Change That Is Required For an Oocyte to Attain Its Fully Functional State. Oocyte Maturation Commences After Reinitiation of Meiosis Commonly Starting with Germinal Vesicle Breakdown and Continues Up to the Second Meiotic Arrest Prior to Fertilization. 
    1666   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. 
    1890   Placenta Development  The Process Whose Specific Outcome Is the Progression of the Placenta Over Time From Its Formation to the Mature Structure. the Placenta Is an Organ of Metabolic Interchange Between Fetus and Mother Partly of Embryonic Origin and Partly of Maternal Origin. 
    1938   Positive Regulation of Endothelial Cell Proliferation  Any Process That Activates or Increases the Rate or Extent of Endothelial Cell Proliferation. 
    6651   Diacylglycerol Biosynthetic Process  The Chemical Reactions and Pathways Resulting in the Formation of Diacylglycerol a Glycerol Molecule Substituted On the 1 and 2 Hydroxyl Groups with Long Chain Fatty Acyl Residues. 
    6950   Response to 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 a Disturbance in Organismal or Cellular Homeostasis Usually But Not Necessarily Exogenous (e.g. Temperature Humidity Ionizing Radiation). 
    7154   Cell Communication  Any Process That Mediates Interactions Between a Cell and Its Surroundings. Encompasses Interactions Such As Signaling or Attachment Between One Cell and Another Cell Between a Cell and an Extracellular Matrix or Between a Cell and Any Other Aspect of Its Environment. 
    7202   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. 
    7275   Multicellular Organismal 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). 
    8219   Cell Death  Any Biological Process That Results in Permanent Cessation of All Vital Functions of a Cell. a Cell Should Be Considered Dead When Any One of the Following Molecular or Morphological Criteria Is Met: (1) the Cell Has Lost the Integrity of Its Plasma Membrane; (2) the Cell Including Its Nucleus Has Undergone Complete Fragmentation Into Discrete Bodies (frequently Referred to As "apoptotic Bodies"); And/or (3) Its Corpse (or Its Fragments) Have Been Engulfed by an Adjacent Cell in Vivo. 
    9303   RRNA Transcription  The Synthesis of Ribosomal RNA (rrna) Any RNA That Forms Part of the Ribosomal Structure From a DNA Template. 
    9725   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. 
    16477   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. 
    17148   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. 
    30041   Actin Filament Polymerization  Assembly of Actin Filaments by the Addition of Actin Monomers to a Filament. 
    30154   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. 
    32148   Activation of Protein Kinase B Activity  Any Process That Initiates the Activity of the Inactive Enzyme Protein Kinase B. 
    32431   Activation of Phospholipase A2 Activity  Any Process That Initiates the Activity of the Inactive Enzyme Phospholipase A2. 
    42327   Positive Regulation of Phosphorylation  Any Process That Activates or Increases the Frequency Rate or Extent of Addition of Phosphate Groups to a Molecule. 
    42592   Homeostatic Process  Any Biological Process Involved in the Maintenance of an Internal Steady State. 
    48662   Negative Regulation of Smooth Muscle Cell Proliferation  Any Process That Stops Prevents or Reduces the Rate or Extent of Smooth Muscle Cell Proliferation. 
    50714   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. 
    90305   Nucleic Acid Phosphodiester Bond Hydrolysis  The Nucleic Acid Metabolic Process in Which the Phosphodiester Bonds Between Nucleotides Are Cleaved by Hydrolysis. 
    90501   RNA Phosphodiester Bond Hydrolysis  The RNA Metabolic Process in Which the Phosphodiester Bonds Between Ribonucleotides Are Cleaved by Hydrolysis. 
    5576   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. 
    5578   Proteinaceous Extracellular Matrix  A Layer Consisting Mainly of Proteins (especially Collagen) and Glycosaminoglycans (mostly As Proteoglycans) That Forms a Sheet Underlying or Overlying Cells Such As Endothelial and Epithelial Cells. the Proteins Are Secreted by Cells in the Vicinity. an Example of This Component Is Found in Mus Musculus. 
    5604   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. 
    5605   Basal Lamina  A Thin Sheet of Proteoglycans and Glycoproteins Especially Laminin Secreted by Cells As an Extracellular Matrix. 
    5615   Extracellular Space  That Part of a Multicellular Organism Outside the Cells Proper Usually Taken to Be Outside the Plasma Membranes and Occupied by Fluid. 
    5634   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. 
    5730   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. 
    30426   Growth Cone  The Migrating Motile Tip of a Growing Nerve Cell Axon or Dendrite. 
    32311   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. 
    43025   Neuronal Cell Body  The Portion of a Neuron That Includes the Nucleus But Excludes Cell Projections Such As Axons and Dendrites. 
    70062   Extracellular Vesicular Exosome  A Membrane Bounded Vesicle That Is Released Into the Extracellular Region by Fusion of the Limiting Endosomal Membrane of a Multivesicular Body with the Plasma Membrane. 
    3676   Nucleic Acid Binding  Interacting Selectively and Non Covalently with Any Nucleic Acid. 
    3677   DNA Binding  Any Molecular Function by Which a Gene Product Interacts Selectively and Non Covalently with DNA (deoxyribonucleic Acid). 
    3779   Actin Binding  Interacting Selectively and Non Covalently with Monomeric or Multimeric Forms of Actin Including Actin Filaments. 
    4518   Nuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids. 
    4519   Endonuclease Activity  Catalysis of the Hydrolysis of Ester Linkages Within Nucleic Acids by Creating Internal Breaks. 
    4540   Ribonuclease Activity  Catalysis of the Hydrolysis of Phosphodiester Bonds in Chains of Rna. 
    5102   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. 
    5507   Copper Ion Binding  Interacting Selectively and Non Covalently with Copper (cu) Ions. 
    5515   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). 
    8201   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. 
    16787   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. 
    19843   RRNA Binding  Interacting Selectively and Non Covalently with Ribosomal Rna. 
    42277   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. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain C
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  


    Chain B
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  


    Chain A
    Common Name Human
    Scientific Name Homo sapiens  
    Host Scientific Name Escherichia coli  


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    14 14q11.1-q11.2 283     angiogenin, ribonuclease, RNase A family, 5 ANG    

    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
    rs121909535 LS-SNP   dbSNP   C 12 Q - > L Helix 40% (Exposed) 14 21161830
    rs121909536 LS-SNP   dbSNP   C 17 K - > I Coil 88% (Exposed) 14 21161845
    rs121909537 LS-SNP   dbSNP   C 17 K - > E Coil 88% (Exposed) 14 21161844
    rs121909542 LS-SNP   dbSNP   C 28 S - > N Helix 24% (Intermediate) 14 21161878
    rs121909538 LS-SNP   dbSNP   C 31 R - > K Helix 61% (Exposed) 14 21161887
    rs11541242 LS-SNP   dbSNP   C 35 L - > P Coil 5% (Buried) 14 21161899
    rs148905586 LS-SNP   dbSNP   C 38 P - > R Turn 0% (Buried) 14 21161908
    rs121909539 LS-SNP   dbSNP   C 39 C - > W Turn 0% (Buried) 14 21161912
    rs121909540 LS-SNP   dbSNP   C 40 K - > I Coil 13% (Intermediate) 14 21161914
    rs121909541 LS-SNP   dbSNP   C 46 I - > V Beta Ladder 0% (Buried) 14 21161931
    rs146485834 LS-SNP   dbSNP   C 51 R - > H Helix 72% (Exposed) 14 21161947
    rs141055235 LS-SNP   dbSNP   C 54 K - > E Helix 43% (Exposed) 14 21161955
    rs17560 LS-SNP   dbSNP   C 60 K - > E Bend 66% (Exposed) 14 21161973
    rs201135457 LS-SNP   dbSNP   C 95 R - > G Beta Ladder 52% (Exposed) 14 21162078
    rs141398857 LS-SNP   dbSNP   C 95 R - > L Beta Ladder 52% (Exposed) 14 21162079
    rs121909543 LS-SNP   dbSNP   C 112 P - > L Beta Ladder 0% (Buried) 14 21162130
    rs121909544 LS-SNP   dbSNP   C 113 V - > I Beta Ladder 14% (Intermediate) 14 21162132