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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF AN AMPK CORE WITH ATP
 
Authors :  L. Chen, J. Wang, Y. -Y. Zhang, S. F. Yan, D. Neumann, U. Schlattner, Z. -X W. Wu
Date :  22 Mar 12  (Deposition) - 06 Jun 12  (Release) - 21 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Ampk, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Chen, J. Wang, Y. -Y. Zhang, S. F. Yan, D. Neumann, U. Schlattner, Z. -X. Wang, J. -W. Wu
Amp-Activated Protein Kinase Undergoes Nucleotide-Dependent Conformational Changes
Nat. Struct. Mol. Biol. V. 19 716 2012
PubMed-ID: 22659875  |  Reference-DOI: 10.1038/NSMB.2319

(-) Compounds

Molecule 1 - 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1
    Chains: A
    EC Number: 2.7.11.1, 2.7.11.27, 2.7.11.31, 2.7.11.26
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRKAA1, AMPK1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Other Details: CHIMERA PROTEIN OF RESIDUES 405-479 AND RESIDUES 540- 559 FROM 5'-AMP-ACTIVATED PROTEIN KINASE CATALYTIC SUBUNIT ALPHA-1 (UNIPROT P54645), LINKED BY LINKER GGGGGG
    Synonym: AMPK SUBUNIT ALPHA-1,ACETYL-COA CARBOXYLASE KINASE,ACACA KINASE,HYDROXYMETHYLGLUTARYL-COA REDUCTASE KINASE,HMGCR KINASE,TAU- PROTEIN KINASE PRKAA1
 
Molecule 2 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT BETA-1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 200-270
    Gene: PRKAB1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPKB,5'-AMP-ACTIVATED PROTEIN KINASE 40 KDA SUBUNIT
 
Molecule 3 - 5'-AMP-ACTIVATED PROTEIN KINASE SUBUNIT GAMMA-1
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: PRKAG1
    Organism Common: RAT
    Organism Scientific: RATTUS NORVEGICUS
    Organism Taxid: 10116
    Synonym: AMPKG

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
1ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE
2TAM1Ligand/IonTRIS(HYDROXYETHYL)AMINOMETHANE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:69 , MET C:84 , THR C:86 , ILE C:87 , THR C:88 , ASP C:89 , GLN C:122 , PRO C:127 , VAL C:129 , ILE C:149 , HIS C:150 , ARG C:151 , PRO C:153 , PHE C:243 , HOH C:501 , HOH C:506 , HOH C:520BINDING SITE FOR RESIDUE ATP C 401
2AC2SOFTWAREHIS C:150 , THR C:199 , ILE C:203 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , HIS C:297 , ARG C:298 , ILE C:311 , SER C:313 , LEU C:314 , SER C:315 , ASP C:316 , HOH C:502BINDING SITE FOR RESIDUE ATP C 402
3AC3SOFTWAREARG C:69 , LYS C:169 , ARG C:170 , HIS C:297BINDING SITE FOR RESIDUE TAM C 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EAK)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EAK)

(-) 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:92
                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.eee..hhhhhhhhhhhhhhhhh.eeeeee..eeeeeee......eeeeeeeeee.....eeeeeee...hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------- Transcript
                 4eak A 396 WHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDGSHTIEFFEMCANLIKILAQ 548
                                   405       415       425       435       445       455       465 ||    536       546  
                                                                                                 467|                   
                                                                                                  529                   


Chain B from PDB  Type:PROTEIN  Length:42
                                                                          
               SCOP domains ------------------------------------------ SCOP domains
               CATH domains ------------------------------------------ CATH domains
               Pfam domains ------------------------------------------ Pfam domains
         Sec.struct. author ...........ee......eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------ PROSITE
                 Transcript ------------------------------------------ Transcript
                 4eak B 202 APPIHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                               ||  238       248       258       268  
                             205|                                     
                              233                                     


Chain C from PDB  Type:PROTEIN  Length:285
                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh...eeeee....eeeeeehhhhhhhhhh......hhhhhhhhhhhhhhh.........hhhhhhhhhhhh....eeee......eeeeehhhhhhhhhhhhhhhh..hhhhh.hhhhhh.........ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh......hhhhhhh.....ee....hhhhhhhhhhhh...eeeee.....eeeeeehhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eak C  23 SNSSVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTNLDVSVTKALQHRSVLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALVLT 324
                                    32        42        52        62        72        82        92   ||  112       122       132       142       152       162       172       182       192       202       212       222       232       242       252||     264    || 279       289       299       309       319     
                                                                                                    96|                                                                                                                                               253|          269|                                                 
                                                                                                    107                                                                                                                                                256           275
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  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 4EAK)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (85, 110)

Asymmetric/Biological Unit(hide GO term definitions)

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  4eak
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  AAKB1_RAT | P80386
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  AAKG1_RAT | P80385
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  AAPK1_RAT | P54645
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  2.7.11.1
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  2.7.11.26
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  2.7.11.27
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 Related Entries

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

UniProtKB/Swiss-Prot
        AAKB1_RAT | P80386: 1z0m 1z0n 4eag 4eal 4qfg 4qfr 4qfs 4yef 5kq5 5t5t 5ufu
        AAKG1_RAT | P80385: 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eag 4eai 4eaj 4eal 4qfg 4qfr 4qfs 5kq5 5t5t 5ufu
        AAPK1_RAT | P54645: 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eai 4eaj 4eal 4f2l 4qfg 4qfr 4qfs 5kq5 5t5t 5ufu

(-) Related Entries Specified in the PDB File

4eag 4eai 4eaj 4eal