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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN ERK2 COMPLEXED WITH A MAPK DOCKING PEPTIDE
 
Authors :  G. Gogl, I. Toeroe, A. Remenyi
Date :  14 Sep 12  (Deposition) - 27 Feb 13  (Release) - 26 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Kinase Domain, Signaling, Linear Motif, Surface Mutation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Gogl, I. Toeroe, A. Remenyi
Protein-Peptide Complex Crystallization: A Case Study On Th Erk2 Mitogen-Activated Protein Kinase
Acta Crystallogr. , Sect. D V. 69 486 2013
PubMed-ID: 23519423  |  Reference-DOI: 10.1107/S0907444912051062

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 1
    Chains: A, D
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: MG950
    Fragment: KINASE DOMAIN
    Gene: MAPK1, ERK2, PRKM1, PRKM2
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAP KINASE 1, MAPK 1, ERT1, EXTRACELLULAR SIGNAL-REGULATED KINASE 2, ERK-2, MAP KINASE ISOFORM P42, P42-MAPK, MITOGEN-ACTIVATED PROTEIN KINASE 2, MAP KINASE 2, MAPK 2
 
Molecule 2 - RIBOSOMAL PROTEIN S6 KINASE ALPHA-1
    Chains: B, E
    EC Number: 2.7.11.1
    Engineered: YES
    Fragment: C-TERMINAL DOCKING PEPTIDE, UNP RESIDUES 712-735
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Other Details: SYNTHETIC CONSTRUCT
    Synonym: S6K-ALPHA-1, 90 KDA RIBOSOMAL PROTEIN S6 KINASE 1, P90-RSK 1, P90RSK1, P90S6K, MAP KINASE-ACTIVATED PROTEIN KINASE 1A, MAPK- ACTIVATED PROTEIN KINASE 1A, MAPKAP KINASE 1A, MAPKAPK-1A, RIBOSOMAL S6 KINASE 1, RSK-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABDE
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1ANP2Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1ANP1Ligand/IonPHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:34 , VAL A:39 , ALA A:52 , GLN A:105 , ASP A:106 , MET A:108 , ASP A:111 , LYS A:114 , SER A:153 , ASN A:154 , ASP A:167 , HOH A:548 , HOH A:572BINDING SITE FOR RESIDUE ANP A 401
2AC2SOFTWAREGLY D:34 , GLY D:37 , VAL D:39 , ALA D:52 , GLN D:105 , ASP D:106 , MET D:108 , ASP D:111 , LYS D:114 , SER D:153 , ASN D:154 , LEU D:156 , ASP D:167 , HOH D:520 , HOH D:561BINDING SITE FOR RESIDUE ANP D 401

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4H3P)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Gly A:22 -Pro A:23
2Pro A:176 -Asp A:177
3Gly D:22 -Pro D:23
4Pro D:176 -Asp D:177

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4H3P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4H3P)

(-) Exons   (0, 0)

(no "Exon" information available for 4H3P)

(-) Sequences/Alignments

Asymmetric 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eee..eee.....eeeeeeeee...eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeeee...eehhhhhh....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee..............hhhhh.......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..............hhhhhhh................hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhh................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4h3p A  11 PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLAFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHEYVATRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLAQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYR 359
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357  
                                                                                                                                                                                                 178|                                                                                                                                                                             
                                                                                                                                                                                                  186                                                                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:16
                                                
               SCOP domains ---------------- SCOP domains
               CATH domains ---------------- CATH domains
               Pfam domains ---------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------- SAPs(SNPs)
                    PROSITE ---------------- PROSITE
                 Transcript ---------------- Transcript
                 4h3p B 712 PQLKPIEASILAARRV 727
                                   721      


Chain D from PDB  Type:PROTEIN  Length:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee..eee.....eeeeeeeee...eeeeeeee....eeeeeeee....hhhhhhhhhhhhhhhhhh.........eee..........eeeeee...eehhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee.....hhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh...............hhhhhhh...............hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhh................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4h3p D  11 PEMVRGQVFDVGPRYTNLSYIGEGAYGMVCSAYDNVNKVRVAIKKISPFEHQTYCQRTLREIKILLAFRHENIIGINDIIRAPTIEQMKDVYIVQDLMETDLYKLLKTQHLSNDHICYFLYQILRGLKYIHSANVLHRDLKPSNLLLNTTCDLKICDFGLARVADPDHTRWYRAPEIMLNSKGYTKSIDIWSVGCILAEMLSNRPIFPGKHYLDQLNHILGILGSPSQEDLNCIINLKARNYLLSLPHKNKVPWNRLFPNADSKALDLLDKMLTFNPHKRIEVEQALAHPYLAQYYDPSDEPIAEAPFKFDMELDDLPKEKLKELIFEETARFQPGYR 359
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351        
                                                                                                                                                                                                 178|                                                                                                                                                                         
                                                                                                                                                                                                  190                                                                                                                                                                         


Chain E from PDB  Type:PROTEIN  Length:17
                                                 
               SCOP domains ----------------- SCOP domains
               CATH domains ----------------- CATH domains
               Pfam domains ----------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ----------------- SAPs(SNPs)
                    PROSITE ----------------- PROSITE
                 Transcript ----------------- Transcript
                 4h3p E 712 PQLKPIEASILAARRVR 728
                                   721
   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 4H3P)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4H3P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4H3P)

(-) Gene Ontology  (120, 136)

Asymmetric Unit(hide GO term definitions)

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  4h3p
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  KS6A1_HUMAN | Q15418
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  MK01_HUMAN | P28482
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  2.7.11.1
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 Related Entries

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

UniProtKB/Swiss-Prot
        KS6A1_HUMAN | Q15418: 2wnt 2z7q 2z7r 2z7s 3rny 3tei 4nif 5csf 5csi 5csj 5csn
        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 4h3q 4iz5 4iz7 4iza 4n0s 4nif 4o6e 4qp1 4qp2 4qp3 4qp4 4qp6 4qp7 4qp8 4qp9 4qpa 4qta 4qte 4xj0 4zxt 4zzm 4zzn 4zzo 5ax3 5bue 5bui 5buj 5bvd 5bve 5bvf 5k4i 5lcj 5lck 5ngu 5nhf 5nhh 5nhj 5nhl 5nho 5nhp 5nhv

(-) Related Entries Specified in the PDB File

3tei 4h3q