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Crystal structure of the complex between cnto888 fab and mcp-1 mutant p8a
Biology and Chemistry Report
4DN4
  •   Structure Details   Hide

    Structure Keywords

    Keywords IMMUNE SYSTEM
    Text antibody chemokine, IMMUNE SYSTEM

    Polymeric Molecules

    Chain L
    Description CNTO888 LIGHT CHAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 23625.4 
    Source Method genetically manipulated  
    Chain H
    Description CNTO888 HEAVY CHAIN 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24175.2 
    Source Method genetically manipulated  
    Chain M
    Description C-C motif chemokine 2 
    Mutation P8A 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 8673.1 
    Source Method synthetic  
    Entity Name HC11, Monocyte chemoattractant protein 1, Monocyte chemotactic and activating factor, MCAF, Monocyte chemotactic protein 1, MCP-1, Monocyte secretory protein JE, Small-inducible cytokine A2 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    ACT  ACETATE ION  C2 H3 O2   59.04  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    M CCL2_HUMAN B2R4V3     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    Immune Epitopes (B-cell and T-Cell)

    Immune Epitope Database (IEDB)
    Epitope ID 176786    
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain M
    GO ID   Ontology GO Term Definition
    165   Mapk Cascade  An Intracellular Protein Kinase Cascade Containing At Least a Mapk a Mapkk and a Map3k. the Cascade Can Also Contain Two Additional Tiers: the Upstream Map4k and the Downstream Map Kinase Activated Kinase (mapkapk). the Kinases in Each Tier Phosphorylate and Activate the Kinases in the Downstream Tier to Transmit a Signal Within a Cell. 
    1525   Angiogenesis  Blood Vessel Formation When New Vessels Emerge From the Proliferation of Pre Existing Blood Vessels. 
    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. 
    1938   Positive Regulation of Endothelial Cell Proliferation  Any Process That Activates or Increases the Rate or Extent of Endothelial Cell Proliferation. 
    2548   Monocyte Chemotaxis  The Movement of a Monocyte in Response to an External Stimulus. 
    6468   Protein Phosphorylation  The Process of Introducing a Phosphate Group On to a Protein. 
    6874   Cellular Calcium Ion Homeostasis  Any Process Involved in the Maintenance of an Internal Steady State of Calcium Ions At the Level of a Cell. 
    6935   Chemotaxis  The Directed Movement of a Motile Cell or Organism or the Directed Growth of a Cell Guided by a Specific Chemical Concentration Gradient. Movement May Be Towards a Higher Concentration (positive Chemotaxis) or Towards a Lower Concentration (negative Chemotaxis). 
    6954   Inflammatory Response  The Immediate Defensive Reaction (by Vertebrate Tissue) to Infection or Injury Caused by Chemical or Physical Agents. the Process Is Characterized by Local Vasodilation Extravasation of Plasma Into Intercellular Spaces and Accumulation of White Blood Cells and Macrophages. 
    6955   Immune Response  Any Immune System Process That Functions in the Calibrated Response of an Organism to a Potential Internal or Invasive Threat. 
    6959   Humoral Immune Response  An Immune Response Mediated Through a Body Fluid. 
    6987   Activation of Signaling Protein Activity Involved in Unfolded Protein Response  The Conversion of a Specific Protein Possessing Protein Kinase and Endoribonuclease Activities to an Active Form As a Result of Signaling Via the Unfolded Protein Response. 
    7010   Cytoskeleton Organization  A Process That Is Carried Out At the Cellular Level Which Results in the Assembly Arrangement of Constituent Parts or Disassembly of Cytoskeletal Structures. 
    7155   Cell Adhesion  The Attachment of a Cell Either to Another Cell or to an Underlying Substrate Such As the Extracellular Matrix Via Cell Adhesion Molecules. 
    7165   Signal Transduction  The Cellular Process in Which a Signal Is Conveyed to Trigger a Change in the Activity or State of a Cell. Signal Transduction Begins with Reception of a Signal (e.g. a Ligand Binding to a Receptor or Receptor Activation by a Stimulus Such As Light) or For Signal Transduction in the Absence of Ligand Signal Withdrawal or the Activity of a Constitutively Active Receptor. Signal Transduction Ends with Regulation of a Downstream Cellular Process E.g. Regulation of Transcription or Regulation of a Metabolic Process. Signal Transduction Covers Signaling From Receptors Located On the Surface of the Cell and Signaling Via Molecules Located Within the Cell. For Signaling Between Cells Signal Transduction Is Restricted to Events At and Within the Receiving Cell. 
    7166   Cell Surface Receptor Signaling Pathway  A Series of Molecular Signals Initiated by Activation of a Receptor On the Surface of a Cell. the Pathway Begins with Binding of an Extracellular Ligand to a Cell Surface Receptor or For Receptors That Signal in the Absence of a Ligand by Ligand Withdrawal or the Activity of a Constitutively Active Receptor. the Pathway Ends with Regulation of a Downstream Cellular Process E.g. Transcription. 
    7179   Transforming Growth Factor Beta Receptor Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of an Extracellular Ligand to a Transforming Growth Factor Beta Receptor On the Surface of a Target Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    7186   G Protein Coupled Receptor Signaling Pathway  A Series of Molecular Signals That Proceeds with an Activated Receptor Promoting the Exchange of GDP For GTP On the Alpha Subunit of an Associated Heterotrimeric G Protein Complex. the GTP Bound Activated Alpha G Protein Then Dissociates From the Beta and Gamma Subunits to Further Transmit the Signal Within the Cell. the Pathway Begins with Receptor Ligand Interaction or For Basal Gpcr Signaling the Pathway Begins with the Receptor Activating Its G Protein in the Absence of an Agonist and Ends with Regulation of a Downstream Cellular Process E.g. Transcription. 
    7187   G Protein Coupled Receptor Signaling Pathway Coupled to Cyclic Nucleotide Second Messenger  The Series of Molecular Signals Generated As a Consequence of a G Protein Coupled Receptor Binding to Its Physiological Ligand Where the Pathway Proceeds with Activation or Inhibition of a Nucleotide Cyclase Activity and a Subsequent Change in the Concentration of a Cyclic Nucleotide. 
    7259   Jak Stat Cascade  Any Process in Which Stat Proteins (signal Transducers and Activators of Transcription) and Jak (janus Activated Kinase) Proteins Convey a Signal to Trigger a Change in the Activity or State of a Cell. the Jak Stat Cascade Begins with Activation of Stat Proteins by Members of the Jak Family of Tyrosine Kinases Proceeds Through Dimerization and Subsequent Nuclear Translocation of Stat Proteins and Ends with Regulation of Target Gene Expression by Stat Proteins. 
    7568   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 (go:0016265) and May Succeed Developmental Maturation (go:0021700). 
    8360   Regulation of Cell Shape  Any Process That Modulates the Surface Configuration of a Cell. 
    9408   Response to Heat  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 Heat Stimulus a Temperature Stimulus Above the Optimal Temperature For That Organism. 
    9611   Response to Wounding  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 Damage to the Organism. 
    9612   Response to Mechanical Stimulus  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 Mechanical Stimulus. 
    9617   Response to Bacterium  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 Bacterium. 
    9887   Organ Morphogenesis  Morphogenesis of an Organ. an Organ Is Defined As a Tissue or Set of Tissues That Work Together to Perform a Specific Function or Functions. Morphogenesis Is the Process in Which Anatomical Structures Are Generated and Organized. Organs Are Commonly Observed As Visibly Distinct Structures But May Also Exist As Loosely Associated Clusters of Cells That Work Together to Perform a Specific Function or Functions. 
    10332   Response to Gamma Radiation  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 Gamma Radiation Stimulus. Gamma Radiation Is a Form of Electromagnetic Radiation (emr) or Light Emission of a Specific Frequency Produced From Sub Atomic Particle Interaction Such As Electron Positron Annihilation and Radioactive Decay. Gamma Rays Are Generally Characterized As Emr Having the Highest Frequency and Energy and Also the Shortest Wavelength Within the Electromagnetic Radiation Spectrum. 
    10574   Regulation of Vascular Endothelial Growth Factor Production  Any Process That Modulates the Frequency Rate or Extent of Production of Vascular Endothelial Growth Factor. 
    10759   Positive Regulation of Macrophage Chemotaxis  Any Process That Increases the Rate Frequency or Extent of Macrophage Chemotaxis. Macrophage Chemotaxis Is the Movement of a Macrophage in Response to an External Stimulus. 
    14823   Response to Activity  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 Activity Stimulus. 
    16525   Negative Regulation of Angiogenesis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Angiogenesis. 
    19079   Viral Genome Replication  Any Process Involved Directly in Viral Genome Replication Including Viral Nucleotide Metabolism. 
    19221   Cytokine Mediated Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Cytokine to a Receptor On the Surface of a Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    19725   Cellular Homeostasis  Any Process Involved in the Maintenance of an Internal Steady State At the Level of the Cell. 
    30593   Neutrophil Chemotaxis  The Directed Movement of a Neutrophil Cell the Most Numerous Polymorphonuclear Leukocyte Found in the Blood in Response to an External Stimulus Usually an Infection or Wounding. 
    30968   Endoplasmic Reticulum Unfolded Protein Response  The Series of Molecular Signals Generated As a Consequence of the Presence of Unfolded Proteins in the Endoplasmic Reticulum (er) or Other Er Related Stress; Results in Changes in the Regulation of Transcription and Translation. 
    31100   Organ Regeneration  The Regrowth of a Lost or Destroyed Organ. 
    31663   Lipopolysaccharide Mediated Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Lipopolysaccharide (lps) to a Receptor On the Surface of a Target Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. Lipopolysaccharides Are Major Components of the Outer Membrane of Gram Negative Bacteria Making Them Prime Targets For Recognition by the Immune System. 
    32496   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. 
    32570   Response to Progesterone  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 Progesterone Stimulus. 
    33552   Response to Vitamin B3  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 Vitamin B3 Stimulus. 
    34351   Negative Regulation of Glial Cell Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Glial Cell Apoptotic Process. 
    35684   Helper T Cell Extravasation  The Migration of a Helper T Cell From the Blood Vessels Into the Surrounding Tissue. a Helper T Cell Is an Effector T Cell That Provides Help in the Form of Secreted Cytokines to Other Immune Cells. 
    42493   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. 
    43200   Response to Amino Acid  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 Amino Acid Stimulus. an Amino Acid Is a Carboxylic Acids Containing One or More Amino Groups. 
    43491   Protein Kinase B Signaling  A Series of Reactions Mediated by the Intracellular Serine/threonine Kinase Protein Kinase B (also Called Akt) Which Occurs As a Result of a Single Trigger Reaction or Compound. 
    43524   Negative Regulation of Neuron Apoptotic Process  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Cell Death by Apoptotic Process in Neurons. 
    43615   Astrocyte Cell Migration  The Orderly Movement of an Astrocyte a Class of Large Neuroglial (macroglial) Cells in the Central Nervous System the Largest and Most Numerous Neuroglial Cells in the Brain and Spinal Cord. 
    44267   Cellular Protein Metabolic Process  The Chemical Reactions and Pathways Involving a Specific Protein Rather Than of Proteins in General Occurring At the Level of an Individual Cell. Includes Cellular Protein Modification. 
    44344   Cellular Response to Fibroblast Growth Factor 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 an Fibroblast Growth Factor Stimulus. 
    45471   Response to Ethanol  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 Ethanol Stimulus. 
    46677   Response to Antibiotic  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 Antibiotic Stimulus. an Antibiotic Is a Chemical Substance Produced by a Microorganism Which Has the Capacity to Inhibit the Growth of or to Kill Other Microorganisms. 
    48010   Vascular Endothelial Growth Factor Receptor Signaling Pathway  Any Series of Molecular Signals Initiated by the Binding of an Extracellular Ligand to a Vascular Endothelial Growth Factor Receptor (vegfr) Located On the Surface of the Receiving Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    48246   Macrophage Chemotaxis  The Movement of a Macrophage in Response to an External Stimulus. 
    48247   Lymphocyte Chemotaxis  The Directed Movement of a Lymphocyte in Response to an External Stimulus. 
    50806   Positive Regulation of Synaptic Transmission  Any Process That Activates or Increases the Frequency Rate or Extent of Synaptic Transmission the Process of Communication From a Neuron to a Target (neuron Muscle or Secretory Cell) Across a Synapse. 
    50870   Positive Regulation of T Cell Activation  Any Process That Activates or Increases the Frequency Rate or Extent of T Cell Activation. 
    51384   Response to Glucocorticoid  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 Glucocorticoid Stimulus. Glucocorticoids Are Hormonal C21 Corticosteroids Synthesized From Cholesterol with the Ability to Bind with the Cortisol Receptor and Trigger Similar Effects. Glucocorticoids Act Primarily On Carbohydrate and Protein Metabolism and Have Anti Inflammatory Effects. 
    51770   Positive Regulation of Nitric Oxide Synthase Biosynthetic Process  Any Process That Activates or Increases the Frequency Rate or Extent of the Chemical Reactions and Pathways Resulting in the Formation of a Nitric Oxide Synthase Enzyme. 
    60137   Maternal Process Involved in Parturition  A Reproductive Process Occurring in the Mother That Results in Birth. 
    70098   Chemokine Mediated Signaling Pathway  A Series of Molecular Signals Initiated by the Binding of a Chemokine to a Receptor On the Surface of a Cell and Ending with Regulation of a Downstream Cellular Process E.g. Transcription. 
    71222   Cellular Response to Lipopolysaccharide  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 Lipopolysaccharide Stimulus; Lipopolysaccharide Is a Major Component of the Cell Wall of Gram Negative Bacteria. 
    71346   Cellular Response to Interferon Gamma  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 an Interferon Gamma Stimulus. Interferon Gamma Is the Only Member of the Type Ii Interferon Found So Far. 
    71347   Cellular Response to Interleukin 1  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 an Interleukin 1 Stimulus. 
    71356   Cellular Response to Tumor Necrosis Factor  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 Tumor Necrosis Factor Stimulus. 
    71407   Cellular Response to Organic Cyclic Compound  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 an Organic Cyclic Compound Stimulus. 
    90265   Positive Regulation of Immune Complex Clearance by Monocytes and Macrophages  Any Process That Increases the Rate Frequency or Extent of the Process of Immune Complex Clearance by Monocytes or Macrophages. 
    90280   Positive Regulation of Calcium Ion Import  Any Process That Increases the Rate Frequency or Extent of the Directed Movement of Calcium Ions Into a Cell or Organelle. 
    2000427   Positive Regulation of Apoptotic Cell Clearance  Any Process That Activates or Increases the Frequency Rate or Extent of Apoptotic Cell Clearance. 
    2000502   Negative Regulation of Natural Killer Cell Chemotaxis  Any Process That Stops Prevents or Reduces the Frequency Rate or Extent of Natural Killer Cell Chemotaxis. 
    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. 
    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. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    43025   Neuronal Cell Body  The Portion of a Neuron That Includes the Nucleus But Excludes Cell Projections Such As Axons and Dendrites. 
    1664   G Protein Coupled Receptor Binding  Interacting Selectively and Non Covalently with a G Protein Coupled Receptor. 
    4672   Protein Kinase Activity  Catalysis of the Phosphorylation of an Amino Acid Residue in a Protein Usually According to the Reaction: a Protein + ATP = a Phosphoprotein + Adp. 
    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. 
    5125   Cytokine Activity  Functions to Control the Survival Growth Differentiation and Effector Function of Tissues and Cells. 
    8009   Chemokine Activity  The Function of a Family of Small Chemotactic Cytokines; Their Name Is Derived From Their Ability to Induce Directed Chemotaxis in Nearby Responsive Cells. All Chemokines Possess a Number of Conserved Cysteine Residues Involved in Intramolecular Disulfide Bond Formation. Some Chemokines Are Considered Pro Inflammatory and Can Be Induced During an Immune Response to Recruit Cells of the Immune System to a Site of Infection While Others Are Considered Homeostatic and Are Involved in Controlling the Migration of Cells During Normal Processes of Tissue Maintenance or Development. Chemokines Are Found in All Vertebrates Some Viruses and Some Bacteria. 
    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. 
    31727   Ccr2 Chemokine Receptor Binding  Interacting Selectively and Non Covalently with a Ccr2 Chemokine Receptor. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain H
    Common Name Human
    Scientific Name Homo sapiens  
    Gene ccl2, mcp1, scya2
    Host Common Name Human
    Host Scientific Name Homo sapiens  
    Host Cell Line (hek) 293


    Chain L
    Common Name Human
    Scientific Name Homo sapiens  
    Host Common Name Human
    Host Scientific Name Homo sapiens  
    Host Cell Line (hek) 293


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    17 17q11.2-q12 6347     chemokine (C-C motif) ligand 2 CCL2    

    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
    rs145056785 LS-SNP   dbSNP   M 18 R - > K Bend 17% (Intermediate) 17 32583286
    rs148937652 LS-SNP   dbSNP   M 26 A - > V Beta Ladder 48% (Exposed) 17 32583310
    rs148285031 LS-SNP   dbSNP   M 46 I - > V Turn 47% (Exposed) 17 32583751
    rs190996557 LS-SNP   dbSNP   M 48 A - > T Bend 57% (Exposed) 17 32583757