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Crystal Structure of Complement C3b in complex with Factors B and D
Biology and Chemistry Report
2XWB
  •   Structure Details   Hide

    Structure Keywords

    Keywords HYDROLASE
    Text IMMUNE SYSTEM, PRO-CONVERTASE, HYDROLASE, SERINE PROTEASE, CONFORMATIONAL CHANGES, ALTERNATIVE PATHWAY

    Polymeric Molecules

    Chain A,C
    Description COMPLEMENT C3B BETA CHAIN 
    Fragment RESIDUES 23-664 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 71154.9 
    Source Method natural source  
    Chain B,D
    Description COMPLEMENT C3B ALPHA' CHAIN 
    Fragment RESIDUES 752-1663 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 103761.0 
    Source Method natural source  
    Chain F,H
    Description COMPLEMENT FACTOR B 
    Fragment RESIDUES 35-764 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 82157.4 
    Source Method genetically manipulated  
    Entity Name C3/C5 CONVERTASE, GLYCINE-RICH BETA GLYCOPROTEIN, GBG, PBF2, PROPERDIN FACTOR B 
    Chain I,J
    Description COMPLEMENT FACTOR D 
    Mutation YES 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 24423.0 
    Source Method genetically manipulated  

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    BMA  BETA-D-MANNOSE  C6 H12 O6   180.16  View 
    GOL  GLYCEROL  C3 H8 O3   92.09  View 
    MG  MAGNESIUM ION  Mg   24.31  View 
    NAG  N-ACETYL-D-GLUCOSAMINE  C8 H15 N O6   221.21  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C CO3_HUMAN P01024     
    B,D CO3_HUMAN P01024     
    F,H CFAB_HUMAN P00751     
    I,J CFAD_HUMAN P00746     

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    F H  3.4.21.47      
    I J  3.4.21.46      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    4866   Endopeptidase Inhibitor Activity  Stops Prevents or Reduces the Activity of an Endopeptidase Any Enzyme That Hydrolyzes Nonterminal Peptide Bonds in Polypeptides. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    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. 
    4866   Endopeptidase Inhibitor Activity  Stops Prevents or Reduces the Activity of an Endopeptidase Any Enzyme That Hydrolyzes Nonterminal Peptide Bonds in Polypeptides. 
    Chain F,H
    GO ID   Ontology GO Term Definition
    2376   Immune System Process  Any Process Involved in the Development or Functioning of the Immune System an Organismal System For Calibrated Responses to Potential Internal or Invasive Threats. 
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    6956   Complement Activation  Any Process Involved in the Activation of Any of the Steps of the Complement Cascade Which Allows For the Direct Killing of Microbes the Disposal of Immune Complexes and the Regulation of Other Immune Processes; the Initial Steps of Complement Activation Involve One of Three Pathways the Classical Pathway the Alternative Pathway and the Lectin Pathway All of Which Lead to the Terminal Complement Pathway. 
    6957   Complement Activation Alternative Pathway  Any Process Involved in the Activation of Any of the Steps of the Alternative Pathway of the Complement Cascade Which Allows For the Direct Killing of Microbes and the Regulation of Other Immune Processes. 
    30449   Regulation of Complement Activation  Any Process That Modulates the Frequency Rate or Extent of Complement Activation. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    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. 
    5886   Plasma Membrane  The Membrane Surrounding a Cell That Separates the Cell From Its External Environment. It Consists of a Phospholipid Bilayer and Associated Proteins. 
    70062   Extracellular 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. Extracellular Exosomes Also Simply Called Exosomes Have a Diameter of About 40 100 Nm. 
    72562   Blood Microparticle  A Phospholipid Microvesicle That Is Derived From Any of Several Cell Types Such As Platelets Blood Cells Endothelial Cells or Others and Contains Membrane Receptors As Well As Other Proteins Characteristic of the Parental Cell. Microparticles Are Heterogeneous in Size and Are Characterized As Microvesicles Free of Nucleic Acids. 
    1848   Complement Binding  Interacting Selectively and Non Covalently with Any Component or Product of the Complement Cascade. 
    4252   Serine Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    8233   Peptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond. a Peptide Bond Is a Covalent Bond Formed When the Carbon Atom From the Carboxyl Group of One Amino Acid Shares Electrons with the Nitrogen Atom From the Amino Group of a Second Amino Acid. 
    8236   Serine Type Peptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    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. 
    Chain I,J
    GO ID   Ontology GO Term Definition
    2376   Immune System Process  Any Process Involved in the Development or Functioning of the Immune System an Organismal System For Calibrated Responses to Potential Internal or Invasive Threats. 
    2576   Platelet Degranulation  The Regulated Exocytosis of Secretory Granules Containing Preformed Mediators Such As Histamine and Serotonin by a Platelet. 
    6508   Proteolysis  The Hydrolysis of Proteins Into Smaller Polypeptides And/or Amino Acids by Cleavage of Their Peptide Bonds. 
    6956   Complement Activation  Any Process Involved in the Activation of Any of the Steps of the Complement Cascade Which Allows For the Direct Killing of Microbes the Disposal of Immune Complexes and the Regulation of Other Immune Processes; the Initial Steps of Complement Activation Involve One of Three Pathways the Classical Pathway the Alternative Pathway and the Lectin Pathway All of Which Lead to the Terminal Complement Pathway. 
    6957   Complement Activation Alternative Pathway  Any Process Involved in the Activation of Any of the Steps of the Alternative Pathway of the Complement Cascade Which Allows For the Direct Killing of Microbes and the Regulation of Other Immune Processes. 
    7596   Blood Coagulation  The Sequential Process in Which the Multiple Coagulation Factors of the Blood Interact Ultimately Resulting in the Formation of an Insoluble Fibrin Clot; It May Be Divided Into Three Stages: Stage 1 the Formation of Intrinsic and Extrinsic Prothrombin Converting Principle; Stage 2 the Formation of Thrombin; Stage 3 the Formation of Stable Fibrin Polymers. 
    30168   Platelet Activation  A Series of Progressive Overlapping Events Triggered by Exposure of the Platelets to Subendothelial Tissue. These Events Include Shape Change Adhesiveness Aggregation and Release Reactions. When Carried Through to Completion These Events Lead to the Formation of a Stable Hemostatic Plug. 
    45087   Innate Immune Response  Innate Immune Responses Are Defense Responses Mediated by Germline Encoded Components That Directly Recognize Components of Potential Pathogens. 
    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. 
    31093   Platelet Alpha Granule Lumen  The Volume Enclosed by the Membrane of the Platelet Alpha Granule. 
    70062   Extracellular 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. Extracellular Exosomes Also Simply Called Exosomes Have a Diameter of About 40 100 Nm. 
    4252   Serine Type Endopeptidase Activity  Catalysis of the Hydrolysis of Internal Alpha Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    8233   Peptidase Activity  Catalysis of the Hydrolysis of a Peptide Bond. a Peptide Bond Is a Covalent Bond Formed When the Carbon Atom From the Carboxyl Group of One Amino Acid Shares Electrons with the Nitrogen Atom From the Amino Group of a Second Amino Acid. 
    8236   Serine Type Peptidase Activity  Catalysis of the Hydrolysis of Peptide Bonds in a Polypeptide Chain by a Catalytic Mechanism That Involves a Catalytic Triad Consisting of a Serine Nucleophile That Is Activated by a Proton Relay Involving an Acidic Residue (e.g. Aspartate or Glutamate) and a Basic Residue (usually Histidine). 
    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. 


     
  •   Gene Details   Hide

    Natural Source

    Chain B,D
    Common Name Human
    Scientific Name Homo sapiens  
    Organ Blood
    Tissue Plasma
    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Organ Blood
    Tissue Plasma

    Genetic Source

    Chain I,J
    Common Name Human
    Scientific Name Homo sapiens  
    Organ Blood
    Tissue Plasma
    Host Common Name Human
    Host Scientific Name Homo sapiens  
    Host Cell Line Hek293 Es
    Host Vector Pupe06.08
    Host Plasmid Name PUPE.05.05


    Chain F,H
    Common Name Human
    Scientific Name Homo sapiens  
    Organ Blood
    Tissue Plasma
    Host Common Name Human
    Host Scientific Name Homo sapiens  
    Host Cell Line Hek293 Es
    Host Vector Pupe06.08
    Host Plasmid Name PUPE.06.08


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6p21.3 629     complement factor B CFB    
    19 19p13.3-p13.2 718     complement component 3 C3    
    19 19p13.3 1675     complement factor D (adipsin) CFD    

    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
    rs201572119 LS-SNP   dbSNP   A 2 P - > L Coil 46% (Exposed) 19 6720530
    rs141447426 LS-SNP   dbSNP   A 26 D - > N Bend 60% (Exposed) 19 6719347
    rs2230199 LS-SNP   dbSNP   A 80 R - > G Bend 58% (Exposed) 19 6718387
    rs201985442 LS-SNP   dbSNP   A 102 S - > N Beta Ladder 7% (Buried) 19 6718320
    rs199970572 LS-SNP   dbSNP   A 123 V - > I Beta Ladder 0% (Buried) 19 6718258
    rs147859257 LS-SNP   dbSNP   A 133 K - > Q Turn 46% (Exposed) 19 6718146
    rs199831618 LS-SNP   dbSNP   A 152 P - > L Beta Ladder 13% (Intermediate) 19 6714441
    rs146130553 LS-SNP   dbSNP   A 153 V - > I Beta Ladder 29% (Intermediate) 19 6714439
    rs147549358 LS-SNP   dbSNP   A 177 V - > I Coil 13% (Intermediate) 19 6714367
    rs201681678 LS-SNP   dbSNP   A 185 R - > Q Beta Ladder 33% (Intermediate) 19 6714239
    rs149906766 LS-SNP   dbSNP   A 189 E - > K Turn 43% (Exposed) 19 6714228
    rs200918899 LS-SNP   dbSNP   A 235 A - > T Beta Ladder 0% (Buried) 19 6714007
    rs140126161 LS-SNP   dbSNP   A 255 D - > E Coil 54% (Exposed) 19 6713463
    rs146167974 LS-SNP   dbSNP   A 257 E - > K Bend 103% (Exposed) 19 6713459
    rs200538609 LS-SNP   dbSNP   A 279 V - > M Beta Ladder 42% (Exposed) 19 6713302
    rs139527231 LS-SNP   dbSNP   A 288 G - > R Helix 32% (Intermediate) 19 6713275
    rs1047286 LS-SNP   dbSNP   A 292 P - > L Bend 93% (Exposed) 19 6713262
    rs138945756 LS-SNP   dbSNP   A 302 L - > F Beta Ladder 0% (Buried) 19 6713231
    rs192989551 LS-SNP   dbSNP   A 315 D - > E Coil 10% (Intermediate) 19 6712627
    rs141737564 LS-SNP   dbSNP   A 326 I - > V Coil 1% (Buried) 19 6712596
    rs201714568 LS-SNP   dbSNP   A 403 R - > L Beta Ladder 19% (Intermediate) 19 6711203
    rs200967589 LS-SNP   dbSNP   A 403 R - > C Beta Ladder 19% (Intermediate) 19 6711204
    rs146158711 LS-SNP   dbSNP   A 410 S - > P Coil 43% (Exposed) 19 6711183
    rs143430438 LS-SNP   dbSNP   A 430 S - > T Coil 25% (Intermediate) 19 6711123
    rs148820222 LS-SNP   dbSNP   A 446 G - > R Turn 85% (Exposed) 19 6711075
    rs11569422 LS-SNP   dbSNP   A 447 E - > D Coil 45% (Exposed) 19 6711070
    rs149692538 LS-SNP   dbSNP   A 460 A - > T Turn 57% (Exposed) 19 6711033
    rs200165327 LS-SNP   dbSNP   A 483 R - > H Beta Ladder 12% (Intermediate) 19 6710822
    rs139744070 LS-SNP   dbSNP   A 491 D - > N Bend 63% (Exposed) 19 6710799
    rs142290953 LS-SNP   dbSNP   A 501 T - > A Bend 35% (Intermediate) 19 6710769
    rs201237210 LS-SNP   dbSNP   A 518 A - > S Turn 42% (Exposed) 19 6710718
    rs143887460 LS-SNP   dbSNP   A 520 G - > D Turn 56% (Exposed) 19 6710711
    rs200541526 LS-SNP   dbSNP   A 540 S - > L Coil 30% (Intermediate) 19 6710651
    rs121909583 LS-SNP   dbSNP   A 570 R - > Q Beta Ladder 23% (Intermediate) 19 6709765
    rs140637006 LS-SNP   dbSNP   A 585 K - > E Coil 67% (Exposed) 19 6709721
    rs201572752 LS-SNP   dbSNP   A 590 T - > M Coil 44% (Exposed) 19 6709705
    rs113676835 LS-SNP   dbSNP   A 597 V - > A Helix 40% (Exposed) 19 6707930
    rs146613648 LS-SNP   dbSNP   A 597 V - > M Helix 40% (Exposed) 19 6707931
    rs144432231 LS-SNP   dbSNP   A 603 I - > F Bend 7% (Buried) 19 6707913
    rs140655115 LS-SNP   dbSNP   A 611 K - > R Bend 56% (Exposed) 19 6707888
    rs145886287 LS-SNP   dbSNP   A 614 A - > ST Helix 10% (Intermediate) 19 6707880
    rs149850773 LS-SNP   dbSNP   A 615 G - > R Helix 4% (Buried) 19 6707877
    rs145461148 LS-SNP   dbSNP   A 627 S - > T Bend 25% (Intermediate) 19 6707840
    rs139893485 LS-SNP   dbSNP   A 631 Q - > R Beta 43% (Exposed) 19 6707828
    rs112187261 LS-SNP   dbSNP   A 641 P - > L Coil 68% (Exposed) 19 6707536
    rs117314762 LS-SNP   dbSNP   F 49 R - > H Beta Ladder 10% (Intermediate) 6_ssto_hap7 3247016
    rs11754061 LS-SNP   dbSNP   F 93 S - > A Coil 30% (Intermediate) 6_ssto_hap7 3247547
    rs185367862 LS-SNP   dbSNP   F 113 R - > Q Beta Ladder 24% (Intermediate) 6 31914898
    rs111969243 LS-SNP   dbSNP   F 167 S - > G Coil 27% (Intermediate) 6_ssto_hap7 3247924
    rs141965248 LS-SNP   dbSNP   F 207 E - > K Helix 28% (Intermediate) 6 31915554
    rs144812066 LS-SNP   dbSNP   F 217 I - > L Helix 1% (Buried) 6_ssto_hap7 3248294
    rs147564718 LS-SNP   dbSNP   F 254 D - > E Turn 27% (Intermediate) 6_ssto_hap7 3248508 MG
    rs117905900 LS-SNP   dbSNP   F 261 F - > L Helix 1% (Buried) 6_ssto_hap7 3248529
    rs140338493 LS-SNP   dbSNP   F 264 A - > V Helix 0% (Buried) 6 31915827
    rs121909748 LS-SNP   dbSNP   F 298 K - > E Coil 27% (Intermediate) 6_ssto_hap7 3248930
    rs140166479 LS-SNP   dbSNP   F 301 E - > D Bend 37% (Exposed) 6_ssto_hap7 3248941
    rs200986170 LS-SNP   dbSNP   F 309 W - > C Helix 39% (Exposed) 6_ssto_hap7 3248965
    rs199725026 LS-SNP   dbSNP   F 321 D - > E 3/10 Helix 41% (Exposed) 6_ssto_hap7 3249318
    rs148898364 LS-SNP   dbSNP   F 323 K - > M Bend 69% (Exposed) 6_ssto_hap7 3249323
    rs143558190 LS-SNP   dbSNP   F 332 K - > E Helix 39% (Exposed) 6 31916639
    rs146477718 LS-SNP   dbSNP   F 332 K - > T Helix 39% (Exposed) 6 31916640
    rs1803306 LS-SNP   dbSNP   F 340 M - > I Helix 7% (Buried) 6_ssto_hap7 3249375
    rs200890358 LS-SNP   dbSNP   F 344 P - > L Coil 97% (Exposed) 6_ssto_hap7 3249386
    rs141298291 LS-SNP   dbSNP   F 344 P - > A Coil 97% (Exposed) 6_ssto_hap7 3249385
    rs199930185 LS-SNP   dbSNP   F 355 T - > P Coil 17% (Intermediate) 6_ssto_hap7 3249418
    rs141984066 LS-SNP   dbSNP   F 371 G - > R Bend 10% (Intermediate) 6 31917037
    rs150398964 LS-SNP   dbSNP   F 390 R - > H Bend 51% (Exposed) 6 31917095
    rs200837114 LS-SNP   dbSNP   F 433 M - > I Coil 3% (Buried) 6_ssto_hap7 3250010
    rs201798809 LS-SNP   dbSNP   F 444 I - > M Coil 8% (Buried) 6_ssto_hap7 3250043
    rs144339757 LS-SNP   dbSNP   F 484 E - > K Beta Ladder 15% (Intermediate) 6 31918081
    rs149101394 LS-SNP   dbSNP   F 508 K - > R Coil 50% (Exposed) 6_ssto_hap7 3250864
    rs202094896 LS-SNP   dbSNP   F 510 H - > Y 3/10 Helix 78% (Exposed) 6_ssto_hap7 3250869
    rs4151659 LS-SNP   dbSNP   F 540 K - > E Turn 67% (Exposed) 6_ssto_hap7 3251174
    rs45484591 LS-SNP   dbSNP   F 541 E - > A Turn 102% (Exposed) 6_ssto_hap7 3251178
    rs199518433 LS-SNP   dbSNP   F 552 V - > I Coil 0% (Buried) 6_ssto_hap7 3251210
    rs201754399 LS-SNP   dbSNP   F 588 T - > IN Coil 5% (Buried) 6_ssto_hap7 3251414
    rs4151660 LS-SNP   dbSNP   F 626 D - > E Turn 42% (Exposed) 6_ssto_hap7 3251728
    rs200095748 LS-SNP   dbSNP   F 644 V - > L Coil 22% (Intermediate) 6_ssto_hap7 3251876
    rs11541541 LS-SNP   dbSNP   F 704 K - > R Coil 62% (Exposed) 6_ssto_hap7 3252408
    rs35186399 LS-SNP   dbSNP   I 44 E - > K Bend 47% (Exposed) 19 860766
    rs112469647 LS-SNP   dbSNP   I 61 S - > L Bend 62% (Exposed) 19 860905
    rs185649590 LS-SNP   dbSNP   I 99 A - > T Coil 5% (Buried) 19 861711
    rs150646348 LS-SNP   dbSNP   I 104 A - > T Turn 7% (Buried) 19 861726
    rs139666945 LS-SNP   dbSNP   I 112 R - > C Coil 27% (Intermediate) 19 861750
    rs146314090 LS-SNP   dbSNP   I 136 R - > C Coil 51% (Exposed) 19 861822
    rs199541702 LS-SNP   dbSNP   I 140 S - > R Beta 15% (Intermediate) 19 861836
    rs201757567 LS-SNP   dbSNP   I 167 R - > H Turn 38% (Exposed) 19 861916
    rs201046554 LS-SNP   dbSNP   I 176 R - > Q Coil 28% (Intermediate) 19 861943
    rs139756616 LS-SNP   dbSNP   I 222 W - > C Helix 15% (Intermediate) 19 863217
    rs2230216 LS-SNP   dbSNP   I 223 I - > M Helix 1% (Buried) 19 863220