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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ERK5 KINASE DOMAIN IN COMPLEX WITH AN MKK5 BINDING FRAGMENT
 
Authors :  G. Gogl, A. Remenyi
Date :  10 Dec 12  (Deposition) - 13 Feb 13  (Release) - 07 Aug 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  D,E  (1x)
Keywords :  Kinase Domain, Signaling Protein Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Glatz, G. Gogl, A. Alexa, A. Remenyi
Structural Mechanism For The Specific Assembly And Activation Of The Extracellular Signal Regulated Kinase 5 (Erk5) Module.
J. Biol. Chem. V. 288 8596 2013
PubMed-ID: 23382384  |  Reference-DOI: 10.1074/JBC.M113.452235

(-) Compounds

Molecule 1 - MITOGEN-ACTIVATED PROTEIN KINASE 7
    Chains: A, D
    EC Number: 2.7.11.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MAPK7, BMK1, ERK5, PRKM7
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAP KINASE 7, MAPK 7, BIG MAP KINASE 1, BMK-1, EXTRACELLULAR SIGNAL-REGULATED KINASE 5, ERK-5
 
Molecule 2 - DUAL SPECIFICITY MITOGEN-ACTIVATED PROTEIN KINASE KINASE 5
    Chains: E, B
    EC Number: 2.7.12.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: MAP2K5, MEK5, MKK5, PRKMK5
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: MAP KINASE KINASE 5, MAPKK 5, MAPK/ERK KINASE 5, MEK 5

 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:62 , ALA A:65 , TYR A:66 , VAL A:69 , ALA A:82 , LYS A:84 , ARG A:98 , ILE A:115 , ASP A:138 , MET A:140 , LEU A:189 , ASP A:200 , HOH A:629BINDING SITE FOR RESIDUE ANP A 501
2AC2SOFTWAREGLY D:62 , GLY D:64 , ALA D:65 , TYR D:66 , GLY D:67 , VAL D:69 , ALA D:82 , LYS D:84 , ARG D:98 , LEU D:137 , ASP D:138 , MET D:140 , LEU D:189 , ASP D:200BINDING SITE FOR RESIDUE ANP D 501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4IC7)

(-) Cis Peptide Bonds  (22, 22)

Asymmetric Unit
No.Residues
1Val A:125 -Pro A:126
2Leu A:207 -Cys A:208
3Ala A:212 -Glu A:213
4Thr A:219 -Glu A:220
5Arg A:392 -Glu A:393
6Glu D:56 -Ile D:57
7Pro D:123 -Thr D:124
8Gly D:128 -Glu D:129
9Glu D:129 -Phe D:130
10Leu D:207 -Cys D:208
11Thr D:219 -Glu D:220
12His E:34 -Ser E:35
13Ser E:35 -Gly E:36
14Gly E:36 -Pro E:37
15Pro E:37 -Gln E:38
16Pro E:112 -Gly E:113
17His B:34 -Ser B:35
18Ser B:35 -Gly B:36
19Gly B:36 -Pro B:37
20Pro B:37 -Gln B:38
21Pro B:112 -Gly B:113
22Gly B:132 -Arg B:133

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4IC7)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4IC7)

(-) Exons   (0, 0)

(no "Exon" information available for 4IC7)

(-) 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:355
                                                                                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4ic7a_ A: automated matches                                                                                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........eeee.........eeeeeee.....eeeeeee.....hhhhhhhhhhhhhhhhhh.......eeee............eeeeee...eehhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.ee....hhh.eee.....eee......ee........hhhhh.........hhhhhhh.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh..hhhhhh......hhhhhh........hhhhhh...hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhh...hhhhh................hhhhhhhhhhhhhhhhhhh....eee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ic7 A  46 DVTFDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGIRQQIR 400
                                    55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395     


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee...eeeeee.......hhhhhhhhhhhhh.......eeee.....eeee...hhhhhhhhhhhhhhhhhhhh......eeeee................................ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ic7 B  16 VLVIRIKIPNSGAVDWTVHSGPQLLFRDVLDVIGQVLPEATTTAFEYEDEDGDRITVRSDEEMKAMLSYYYSTVMEQQVNGQLIEPLQIFPRACKPPGERNIHGLKVNTRAGPSQSGRHHHHH 138
                                    25        35        45        55        65        75        85        95       105       115       125       135   


Chain D from PDB  Type:PROTEIN  Length:353
                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains d4ic7d_ D: automated matches                                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........eeee.........eeeeeee.....eeeeeeee....hhhhhhhhhhhhhhhhhh.......eeee...........eeeeee....eehhhhhh.....hhhhhhhhhhhhhhhhhhhhhh.......hhh.eee.....eee...........hhhhh..............hhhhhh......hhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhh...hhhhhhh.....hhhhhh........hhhhhh...hhhhhhhhhhhh..hhhhh.hhhhhh.hhhhh...hhhhh........hhhhhhhh...hhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ic7 D  47 VTFDVGDEYEIIETIGNGAYGVVSSARRRLTGQQVAIKKIPNAFDVVTNAKRTLRELKILKHFKHDNIIAIKDILRPTVPYGEFKSVYVVLDLMESDLHQIIHSSQPLTLEHVRYFLYQLLRGLKYMHSAQVIHRDLKPSNLLVNENCELKIGDFGMARGLCTSPAEHQYFMTEYVATRWYRAPELMLSLHEYTQAIDLWSVGCIFGEMLARRQLFPGKNYVHQLQLIMMVLGTPSPAVIQAVGAERVRAYIQSLPPRQPVPWETVYPGADRQALSLLGRMLRFEPSARISAAAALRHPFLAKYHDPDDEPDCAPPFDFAFDREALTRERIKEAIVAEIEDFHARREGIRQQI 399
                                    56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396   


Chain E from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee......hhhhhhhhhhhhh.......eeee.....eeee...hhhhhhhhhhhhhhhhhhhh......eeeee.................. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 4ic7 E  14 GSVLVIRIKIPNSGAVDWTVHSGPQLLFRDVLDVIGQVLPEATTTAFEYEDEDGDRITVRSDEEMKAMLSYYYSTVMEQQVNGQLIEPLQIFPRACKPPGERNIHGLKVNT 124
                                    23        33        43        53        63        73        83        93       103       113       123
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4IC7)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4IC7)

(-) Gene Ontology  (58, 79)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:212 - Glu A:213   [ RasMol ]  
    Arg A:392 - Glu A:393   [ RasMol ]  
    Glu D:129 - Phe D:130   [ RasMol ]  
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 Related Entries

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

UniProtKB/Swiss-Prot
        MK07_HUMAN | Q13164: 2q8y 4b99 4ic8 4zsg 4zsj 4zsl 5byy 5byz
        MP2K5_HUMAN | Q13163: 2npt 2o2v

(-) Related Entries Specified in the PDB File

4ic8