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(-) Description

Title :  CO-CRYSTAL OF AMPK CORE WITH AMP SOAKED 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 :  2.61
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-2
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 189-272
    Gene: PRKAB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AMPK SUBUNIT BETA-2
 
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
1AMP1Ligand/IonADENOSINE MONOPHOSPHATE
2ATP2Ligand/IonADENOSINE-5'-TRIPHOSPHATE

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG C:69 , ARG C:151 , LYS C:169 , ILE C:239 , SER C:241 , PHE C:243 , ASP C:244 , ARG C:268 , PHE C:272 , GLY C:274 , VAL C:275 , LEU C:276 , VAL C:296 , HIS C:297 , ARG C:298BINDING SITE FOR RESIDUE ATP C 401
2AC2SOFTWAREARG C:69 , MET C:84 , THR C:86 , ILE C:87 , THR C:88 , ASP C:89 , PRO C:127 , VAL C:129 , HIS C:150 , ARG C:151 , PRO C:153 , SER C:225 , HOH C:507BINDING SITE FOR RESIDUE ATP C 402
3AC3SOFTWAREHIS C:150 , THR C:199 , ASN C:202 , ILE C:203 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , PRO C:228 , HIS C:297 , SER C:313 , SER C:315 , ASP C:316 , HOH C:502 , HOH C:507BINDING SITE FOR RESIDUE AMP C 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1Gly A:470 -Gly A:471
2Gly A:472 -Gly A:473
3Gly A:473 -Gly A:474
4Pro B:210 -His B:211
5Phe C:182 -Pro C:183

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4EAJ)

(-) 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:100
                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.eee..hhhhhhhhhhhhhhhhh.eeeeee..eeeeeee......eeeeeeeeee.....eeeeeee..........hhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                 4eaj A 394 AKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDDGGGGGGGSHTIEFFEMCANLIKILA 493
                                   403       413       423       433       443       453       463       473       483       493


Chain B from PDB  Type:PROTEIN  Length:51
                                                                                   
               SCOP domains --------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------- Pfam domains
         Sec.struct. author ...........eee.......eee......eeeeeeeee..eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------- Transcript
                 4eaj B 204 SPPILPPHLLQVILNVMLNHLYALSIKDSVMVLSATHRYKKKYVTTLLYKP 271
                                   213    || 240       250       260       270 
                                        218|                                   
                                         236                                   


Chain C from PDB  Type:PROTEIN  Length:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhh.hhhhhh..eeeeeeee...hhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhhhhhhhhh.........hhhhhhhhh..........hhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhh.....hhhhhhhhhhhh.........ee...hhhhhhhhhhhhh..eeeee.....eeeeee...hhhhh.....hhhhhh...........ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4eaj C  26 SVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAANLDVSVTKALQHRSHYFEGVLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALVLT 324
                                    35        45        55        65        75        85        95       105       115    || 130       140       150       160       170       180       190       200       210       220       230       240       250|      265       275       285       295       305       315         
                                                                                                                        120|                                                                                                                         250|                                                                    
                                                                                                                         126                                                                                                                          256
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 4EAJ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (92, 113)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Gly A:470 - Gly A:471   [ RasMol ]  
    Gly A:472 - Gly A:473   [ RasMol ]  
    Gly A:473 - Gly A:474   [ RasMol ]  
    Phe C:182 - Pro C:183   [ RasMol ]  
    Pro B:210 - His B:211   [ RasMol ]  
 

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  4eaj
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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
        AAKB2_HUMAN | O43741: 2f15 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eai 4rer 4rew
        AAKG1_RAT | P80385: 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eag 4eai 4eak 4eal 4qfg 4qfr 4qfs 5kq5 5t5t 5ufu
        AAPK1_RAT | P54645: 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eai 4eak 4eal 4f2l 4qfg 4qfr 4qfs 5kq5 5t5t 5ufu

(-) Related Entries Specified in the PDB File

4eag 4eai 4eak 4eal