POP-OUT | CLOSE
 
Crystal of human arginase in complex with L-ornithine. Resolution 1.43 A.
Biology and Chemistry Report
3GMZ
  •   Structure Details   Hide

    Structure Keywords

    Keywords Hydrolase/Hydrolase Inhibitor
    Text ornithine binding, Arginine metabolism, Metal-binding, Phosphoprotein, Urea cycle, Hydrolase-Hydrolase Inhibitor complex

    Polymeric Molecules

    Chain A,B
    Description Arginase-1 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 34780.2 
    Source Method genetically manipulated  
    Entity Name Type I arginase, Liver-type arginase 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    MN  MANGANESE (II) ION  Mn   54.94  View 
    ORN  L-ornithine  C5 H12 N2 O2   132.16  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,B ARGI1_HUMAN A6NEA0     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    A B  3.5.3.1      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,B
    GO ID   Ontology GO Term Definition
    50   Urea Cycle  The Sequence of Reactions by Which Arginine Is Synthesized From Ornithine Then Cleaved to Yield Urea and Regenerate Ornithine. the Overall Reaction Equation Is Nh3 + Co2 + Aspartate + 3 ATP + 2 H2o = Urea + Fumarate + 2 Adp + 2 Phosphate + AMP + Diphosphate. 
    6525   Arginine Metabolic Process  The Chemical Reactions and Pathways Involving Arginine 2 Amino 5 (carbamimidamido)pentanoic Acid. 
    5737   Cytoplasm  All of the Contents of a Cell Excluding the Plasma Membrane and Nucleus But Including Other Subcellular Structures. 
    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. 
    46872   Metal Ion Binding  Interacting Selectively and Non Covalently with Any Metal Ion. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain A,B
    Common Name Human
    Scientific Name Homo sapiens  
    Gene arg1
    Host Scientific Name Escherichia coli  
    Host Plasmid Name pet11d


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    6 6q23 383     arginase 1 ARG1    

    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
    rs149310631 LS-SNP   dbSNP   A 8 I - > K Beta Ladder 0% (Buried) 6 131894445
    rs28941474 LS-SNP   dbSNP   A 11 I - > T Beta Ladder 0% (Buried) 6 131894454
    rs147419581 LS-SNP   dbSNP   A 12 G - > A Beta Ladder 0% (Buried) 6 131894457
    rs144994895 LS-SNP   dbSNP   A 21 R - > Q Coil 25% (Intermediate) 6 131897807
    rs11544411 LS-SNP   dbSNP   A 26 E - > G 3/10 Helix 41% (Exposed) 6 131897822
    rs147146526 LS-SNP   dbSNP   A 57 D - > G Coil 75% (Exposed) 6 131900290
    rs111640755 LS-SNP   dbSNP   A 62 S - > N Coil 20% (Intermediate) 6 131900305
    rs148619575 LS-SNP   dbSNP   A 79 Q - > H Helix 23% (Intermediate) 6 131900357
    rs142107090 LS-SNP   dbSNP   A 81 A - > S Helix 0% (Buried) 6 131900361
    rs1063493 LS-SNP   dbSNP   A 86 E - > Q Helix 42% (Exposed) 6 131900376
    rs34724840 LS-SNP   dbSNP   A 94 S - > T Beta Ladder 0% (Buried) 6 131900401
    rs140549609 LS-SNP   dbSNP   A 128 D - > G Coil 0% (Buried) 6 131902436 MN,ORN
    rs104893943 LS-SNP   dbSNP   A 138 G - > V Coil 0% (Buried) 6 131902466
    rs200319835 LS-SNP   dbSNP   A 156 I - > T Bend 24% (Intermediate) 6 131903762
    rs201484132 LS-SNP   dbSNP   A 161 G - > A Turn 36% (Intermediate) 6 131903777
    rs201926198 LS-SNP   dbSNP   A 179 L - > F Coil 2% (Buried) 6 131903832
    rs141449121 LS-SNP   dbSNP   A 185 G - > R Helix 31% (Intermediate) 6 131903848
    rs200496725 LS-SNP   dbSNP   A 214 E - > K Helix 26% (Intermediate) 6 131904279
    rs145177175 LS-SNP   dbSNP   A 222 R - > K Bend 87% (Exposed) 6 131904304
    rs104893948 LS-SNP   dbSNP   A 235 G - > R 3/10 Helix 0% (Buried) 6 131904532
    rs182650447 LS-SNP   dbSNP   A 249 V - > L Bend 85% (Exposed) 6 131904574
    rs111253965 LS-SNP   dbSNP   A 266 K - > N Helix 72% (Exposed) 6 131904627
    rs104893942 LS-SNP   dbSNP   A 290 T - > S Helix 50% (Exposed) 6 131904948
    rs148113697 LS-SNP   dbSNP   A 303 C - > G Helix 0% (Buried) 6 131904986
    rs202219126 LS-SNP   dbSNP   A 315 I - > T Bend 64% (Exposed) 6 131905023
    rs73544627 LS-SNP   dbSNP   A 318 L - > P Coil 101% (Exposed) 6 131905032
    rs147409787 LS-SNP   dbSNP   A 319 N - > S Coil 101% (Exposed) 6 131905035