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Structure of NEDD8-activating enzyme in complex with NEDD8 and MLN4924
Biology and Chemistry Report
3GZN
  •   Structure Details   Hide

    Structure Keywords

    Keywords PROTEIN BINDING/Ligase
    Text NEDD8, E1-activating enzyme, MLN4924, PROTEIN BINDING-Ligase complex

    Polymeric Molecules

    Chain A,C
    Description NEDD8-activating enzyme E1 regulatory subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 60315.7 
    Source Method genetically manipulated  
    Entity Name Amyloid protein-binding protein 1, Amyloid beta precursor protein-binding protein 1, 59 kDa, APP-BP1, Proto-oncogene protein 1 
    Chain B,D
    Description NEDD8-activating enzyme E1 catalytic subunit 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 51906.7 
    Source Method genetically manipulated  
    Entity Name Ubiquitin-like modifier-activating enzyme 3, Ubiquitin-activating enzyme 3, NEDD8-activating enzyme E1C, Ubiquitin-activating enzyme E1C 
    Chain I,J
    Description NEDD8 
    Nonstandard Linkage no 
    Nonstandard Monomers no 
    Polymer Type polypeptide(L) 
    Formula Weight 9403.0 
    Source Method genetically manipulated  
    Entity Name Ubiquitin-like protein Nedd8, Neddylin, Neural precursor cell expressed developmentally down-regulated protein 8, NEDD-8 

    Ligands and Prosthetic Groups

    ID Name Chemical Formula Weight Ligand Structure
    B39  [(1S,2S,4R)-4-{4-[(1S)-2,3-dihydro-1H-inden-1-ylamino]-7H-pyrrolo[2,3-d]pyrimidin-7-yl}-2-hydroxycyclopentyl]methyl sulfamate  C21 H25 N5 O4 S   443.52  View 
    ZN  ZINC ION  Zn   65.41  View 
     
  •   Protein Details   Hide

    UniProtKB Information

    Chain SWS/UNP ID SWS/UNP Accession(s)
    A,C ULA1_HUMAN A6NCK0     
    B,D UBA3_HUMAN A6NLB5     
    I,J NEDD8_HUMAN Q15843     

    Keywords and Names

    Chain(s) RCSB Name UniProtKB Name UniProtKB Keywords

    EC, Associated Pathways and Catalytic Sites

    Chain(s) IUBMB KEGG BioCyc
    B D  6.3.2      
    C: Cellular Location | F: Molecular Function | P: Biological Process
    Chain A,C
    GO ID   Ontology GO Term Definition
    6915   Apoptotic Process  A Programmed Cell Death Process Which Begins When a Cell Receives an Internal (e.g. DNA Damage) or External Signal (e.g. an Extracellular Death Ligand) and Proceeds Through a Series of Biochemical Events (signaling Pathway Phase) Which Trigger an Execution Phase. the Execution Phase Is the Last Step of an Apoptotic Process and Is Typically Characterized by Rounding Up of the Cell Retraction of Pseudopodes Reduction of Cellular Volume (pyknosis) Chromatin Condensation Nuclear Fragmentation (karyorrhexis) Plasma Membrane Blebbing and Fragmentation of the Cell Into Apoptotic Bodies. When the Execution Phase Is Completed the Cell Has Died. 
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    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. 
    16020   Membrane  Double Layer of Lipid Molecules That Encloses All Cells and in Eukaryotes Many Organelles; May Be a Single or Double Lipid Bilayer; Also Includes Associated Proteins. 
    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). 
    31625   Ubiquitin Protein Ligase Binding  Interacting Selectively and Non Covalently with a Ubiquitin Protein Ligase Enzyme Any of the E3 Proteins. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain B,D
    GO ID   Ontology GO Term Definition
    7049   Cell Cycle  The Progression of Biochemical and Morphological Phases and Events That Occur in a Cell During Successive Cell Replication or Nuclear Replication Events. Canonically the Cell Cycle Comprises the Replication and Segregation of Genetic Material Followed by the Division of the Cell But in Endocycles or Syncytial Cells Nuclear Replication or Nuclear Division May Not Be Followed by Cell Division. 
    166   Nucleotide Binding  Interacting Selectively and Non Covalently with a Nucleotide Any Compound Consisting of a Nucleoside That Is Esterified with (ortho)phosphate or an Oligophosphate At Any Hydroxyl Group On the Ribose or Deoxyribose. 
    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). 
    5524   ATP Binding  Interacting Selectively and Non Covalently with ATP Adenosine 5' Triphosphate a Universally Important Coenzyme and Enzyme Regulator. 
    16874   Ligase Activity  Catalysis of the Joining of Two Substances or Two Groups Within a Single Molecule with the Concomitant Hydrolysis of the Diphosphate Bond in ATP or a Similar Triphosphate. 
    46982   Protein Heterodimerization Activity  Interacting Selectively and Non Covalently with a Nonidentical Protein to Form a Heterodimer. 
    Chain I,J
    GO ID   Ontology GO Term Definition
    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. 
    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). 
    31625   Ubiquitin Protein Ligase Binding  Interacting Selectively and Non Covalently with a Ubiquitin Protein Ligase Enzyme Any of the E3 Proteins. 


     
  •   Gene Details   Hide

    Genetic Source

    Chain I,J
    Common Name Human
    Scientific Name Homo sapiens  
    Gene nedd8
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf9
    Host Vector Type Baculovirus


    Chain B,D
    Common Name Human
    Scientific Name Homo sapiens  
    Gene uba3, ube1c
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf9
    Host Vector Type Baculovirus


    Chain A,C
    Common Name Human
    Scientific Name Homo sapiens  
    Gene appbp1, hpp1, nae1
    Host Scientific Name Spodoptera frugiperda  
    Host Strain Sf9
    Host Vector Type Baculovirus


    Genome Information

    Chromosome Locus Gene ID Gene Name Symbol
    3 3p14.1 9039     ubiquitin-like modifier activating enzyme 3 UBA3    
    14 14q12 4738     neural precursor cell expressed, developmentally down-regulated 8 NEDD8    
    16 16q22 8883     NEDD8 activating enzyme E1 subunit 1 NAE1    

    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
    rs11556607 LS-SNP   dbSNP   A 39 H - > Y Beta Ladder 5% (Buried) 16 66860643
    rs199964855 LS-SNP   dbSNP   A 50 T - > N Helix 0% (Buried) 16 66860609
    rs137985751 LS-SNP   dbSNP   A 63 S - > L Beta Ladder 2% (Buried) 16 66860477
    rs77699528 LS-SNP   dbSNP   A 80 N - > I Coil 2% (Buried) 16 66860426
    rs200163314 LS-SNP   dbSNP   A 97 M - > V Helix 14% (Intermediate) 16 66857485
    rs363212 LS-SNP   dbSNP   A 108 S - > F Beta Ladder 38% (Exposed) 16 66857451
    rs140382369 LS-SNP   dbSNP   A 122 N - > S Helix 72% (Exposed) 16 66857187
    rs111458825 LS-SNP   dbSNP   A 162 T - > A Beta Ladder 0% (Buried) 16 66855401
    rs143652293 LS-SNP   dbSNP   A 172 I - > V Beta Ladder 5% (Buried) 16 66855371
    rs200923446 LS-SNP   dbSNP   A 211 M - > I Coil 28% (Intermediate) 16 66852440
    rs201659718 LS-SNP   dbSNP   A 244 Y - > D Helix 48% (Exposed) 16 66850907
    rs149417383 LS-SNP   dbSNP   A 244 Y - > C Helix 48% (Exposed) 16 66850906
    rs201813040 LS-SNP   dbSNP   A 269 E - > K Coil 7% (Buried) 16 66850540
    rs200655956 LS-SNP   dbSNP   A 276 I - > M Helix 8% (Buried) 16 66850517
    rs35391524 LS-SNP   dbSNP   A 316 R - > H Helix 22% (Intermediate) 16 66847575
    rs186580935 LS-SNP   dbSNP   A 363 A - > T Helix 10% (Intermediate) 16 66844644
    rs187763841 LS-SNP   dbSNP   A 457 V - > I Helix 24% (Intermediate) 16 66839912
    rs141920415 LS-SNP   dbSNP   A 475 Y - > C Turn 5% (Buried) 16 66839857
    rs11556608 LS-SNP   dbSNP   A 487 H - > N Helix 45% (Exposed) 16 66839822
    rs150893619 LS-SNP   dbSNP   A 516 I - > V Helix 8% (Buried) 16 66836992
    rs141151787 LS-SNP   dbSNP   A 517 T - > S Helix 8% (Buried) 16 66836988
    rs139734072 LS-SNP   dbSNP   B 65 F - > L Helix 73% (Exposed) 3 69124650
    rs186063144 LS-SNP   dbSNP   B 68 D - > G Helix 51% (Exposed) 3 69124642
    rs142785164 LS-SNP   dbSNP   B 69 T - > I Helix 49% (Exposed) 3 69124639
    rs71302167 LS-SNP   dbSNP   B 81 G - > R Helix 0% (Buried) 3 69124604
    rs188636684 LS-SNP   dbSNP   B 137 P - > L Turn 21% (Intermediate) 3 69117097
    rs11544139 LS-SNP   dbSNP   B 143 P - > Q Beta Ladder 43% (Exposed) 3 69117079
    rs199541209 LS-SNP   dbSNP   B 180 I - > V Helix 7% (Buried) 3 69112288
    rs149049620 LS-SNP   dbSNP   B 203 T - > A Beta Ladder 4% (Buried) 3 69112219
    rs144568523 LS-SNP   dbSNP   B 217 M - > K Turn 58% (Exposed) 3 69112176
    rs150571999 LS-SNP   dbSNP   B 224 T - > M Turn 10% (Intermediate) 3 69112155
    rs150359494 LS-SNP   dbSNP   B 242 M - > K Coil 19% (Intermediate) 3 69111299
    rs11544137 LS-SNP   dbSNP   B 255 M - > V Helix 43% (Exposed) 3 69111261
    rs141743890 LS-SNP   dbSNP   B 260 K - > Q Helix 40% (Exposed) 3 69111246
    rs116820810 LS-SNP   dbSNP   B 266 E - > G Turn 92% (Exposed) 3 69111078
    rs201471678 LS-SNP   dbSNP   B 298 T - > M Coil 51% (Exposed) 3 69110982
    rs140550798 LS-SNP   dbSNP   B 381 K - > I Coil 19% (Intermediate) 3 69105376
    rs182961972 LS-SNP   dbSNP   B 420 S - > T Turn 74% (Exposed) 3 69105047
    rs137972832 LS-SNP   dbSNP   B 426 R - > K 3/10 Helix 54% (Exposed) 3 69105028
    rs147779512 LS-SNP   dbSNP   B 445 A - > V Beta Ladder 23% (Intermediate) 3 69104646
    rs199555987 LS-SNP   dbSNP   B 446 V - > G Beta Ladder 1% (Buried) 3 69104643
    rs201227095 LS-SNP   dbSNP   B 455 V - > A Beta Ladder 8% (Buried) 3 69104616
    rs145114621 LS-SNP   dbSNP   B 456 L - > P Beta Ladder 38% (Exposed) 3 69104613
    rs74744808 LS-SNP   dbSNP   I 38 P - > Q 3/10 Helix 29% (Intermediate) 14 24687375
    rs113779918 LS-SNP   dbSNP   I 48 K - > E Beta Ladder 8% (Buried) 14 24687346