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(-) Description

Title :  CRYSTAL STRUCTURE OF ERK2 COMPLEXED WITH ALLOSTERIC AND ATP-COMPETITIVE INHIBITORS.
 
Authors :  T. Kinoshita, H. Sugiyama, Y. Mori, N. Takahashi, A. Tomonaga
Date :  14 Jul 15  (Deposition) - 10 Feb 16  (Release) - 10 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.98
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ternary Complex, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Kinoshita, H. Sugiyama, Y. Mori, N. Takahashi, A. Tomonaga
Identification Of Allosteric Erk2 Inhibitors Through In Silico Biased Screening And Competitive Binding Assay
Bioorg. Med. Chem. Lett. V. 26 955 2016
PubMed-ID: 26733474  |  Reference-DOI: 10.1016/J.BMCL.2015.12.056

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 1
    Chains: A
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21
    Expression System Plasmid: PGEX 6P-1
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Gene: MAPK1, ERK2, PRKM1, PRKM2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAPK 1,ERT1,EXTRACELLULAR SIGNAL-REGULATED KINASE 2,ERK-2, MAP KINASE ISOFORM P42,P42-MAPK,MITOGEN-ACTIVATED PROTEIN KINASE 2, MAPK 2
 
Molecule 2 - ALLOSTERIC AND ATP-COMPETITIVE INHIBITOR
    Chains: B
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
15ID1Ligand/Ion(2R,3R,4S,5R)-2-(4-AMINO-5-IODO-7H-PYRROLO[2,3-D]PYRIMIDIN-7-YL)-5-(HYDROXYMETHYL)TETRAHYDROFURAN-3,4-DIOL

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:22 , GLU A:24 , ALA A:43 , ASP A:97 , LEU A:98 , MET A:99 , ASP A:102 , LYS A:105 , SER A:144 , LEU A:147 , GLU B:360binding site for residue 5ID A 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5AX3)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5AX3)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5AX3)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5AX3)

(-) Exons   (0, 0)

(no "Exon" information available for 5AX3)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
  UniProt sequence: complete  aligned part    
   Show mapping: SCOP domains CATH domains Pfam domains Secondary structure (by author)
SAPs(SNPs) PROSITE motifs Exons
(details for a mapped element are shown in a popup box when the mouse pointer rests over it) 
Chain A from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............eeeeeeee...eeeeeee....eeeeeeee......hhhhhhhhhhhhhhhh.......eeeee..........eeeeee...eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.....................hhhhhhhhhhhhhhhhhh..........hhhhhhhhhh........hhhhhhhhh......hhhhhh...hhhhhhhhhhhh...............hhhhh........................hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5ax3 A   1 GPEMVRGQVFDVGPRYTNLSYIGEYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLRFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVAFLTEYVTRWYRAPEIMLGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLEQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGY 348
                                    10        20   ||   32        42        52        62        72        82        92       102       112       122       132       142       152       162  ||   181       191|      203       213       223       233       249       259       269       279       289       299       309       319       329       339         
                                                  24|                                                                                                                                       165|  179|       191|                                            241|                                                                                                    
                                                   27                                                                                                                                        174   181        194                                             248                                                                                                    


Chain B from PDB  Type:PROTEIN  Length:12
                                            
               SCOP domains ------------ SCOP domains
               CATH domains ------------ CATH domains
               Pfam domains ------------ Pfam domains
         Sec.struct. author ............ Sec.struct. author
                 SAPs(SNPs) ------------ SAPs(SNPs)
                    PROSITE ------------ PROSITE
                 Transcript ------------ Transcript
                 5ax3 B 349 LVKKYILALWNE 360
                                   358
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 5AX3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5AX3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5AX3)

(-) Gene Ontology  (183, 200)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        MK01_HUMAN | P28482: 1pme 1tvo 1wzy 2ojg 2oji 2ojj 2y9q 3d42 3d44 3i5z 3i60 3sa0 3tei 3w55 4fmq 4fux 4fuy 4fv0 4fv1 4fv2 4fv3 4fv4 4fv5 4fv6 4fv7 4fv8 4fv9 4g6n 4g6o 4h3p 4h3q 4iz5 4iz7 4iza 4n0s 4nif 4o6e 4qp1 4qp2 4qp3 4qp4 4qp6 4qp7 4qp8 4qp9 4qpa 4qta 4qte 4xj0 4zxt 4zzm 4zzn 4zzo 5bue 5bui 5buj 5bvd 5bve 5bvf 5k4i 5lcj 5lck 5ngu 5nhf 5nhh 5nhj 5nhl 5nho 5nhp 5nhv
        STAT3_HUMAN | P40763: 5u5s

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5AX3)