Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE NON-PHOSPHORYLATED HUMAN ALPHA1 BETA2 GAMMA1 HOLO-AMPK COMPLEX
 
Authors :  X. E. Zhou, J. Ke, X. Li, L. Wang, X. Gu, P. W. De Waal, M. H. E. Tan, D. Wang, H. E. Xu, K. Melcher
Date :  24 Sep 14  (Deposition) - 10 Dec 14  (Release) - 11 Mar 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  4.58
Chains :  Asym./Biol. Unit :  A,B,G
Keywords :  Human Alpha1 Beta2 Gamma1 Holo-Ampk Complex, Serine/Threonine Protein Kinase, Axin, Camkkbeta, Lkb1, Glycogen, Phosphorylation, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  X. Li, L. Wang, X. E. Zhou, J. Ke, P. W. De Waal, X. Gu, M. H. Tan, D. Wang, D. Wu, H. E. Xu, K. Melcher
Structural Basis Of Ampk Regulation By Adenine Nucleotides And Glycogen.
Cell Res. V. 25 50 2015
PubMed-ID: 25412657  |  Reference-DOI: 10.1038/CR.2014.150

(-) 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 Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HUMAN AMPK ALPHA1 SUBUNIT [G11-Q550]
    Gene: AMPK1, HUMAN HOLO-AMPK ALPHA1 SUBUNIT, PRKAA1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    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 Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HUMAN AMPK BETA2 SUBUNIT [A76-I272]
    Gene: HUMAN HOLO-AMPK BETA2 SUBUNIT, 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: G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: HUMAN AMPK GAMMA1 SUBUNIT [S24-G327]
    Gene: HUMAN HOLO-AMPK GAMMA1 SUBUNIT, PRKAG1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: AMPK GAMMA1, AMPK SUBUNIT GAMMA-1, AMPKG

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit : ABG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1AMP3Ligand/IonADENOSINE MONOPHOSPHATE
2STU1Ligand/IonSTAUROSPORINE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:24 , GLY A:25 , GLY A:27 , ALA A:45 , MET A:95 , GLU A:96 , TYR A:97 , VAL A:98 , GLU A:102 , GLU A:145 , ASN A:146 , LEU A:148 , ASP A:159BINDING SITE FOR RESIDUE STU A 601
2AC2SOFTWAREMET G:84 , THR G:86 , THR G:88 , ASP G:89 , TYR G:120 , LEU G:128 , VAL G:129 , ILE G:149 , HIS G:150 , ARG G:151BINDING SITE FOR RESIDUE AMP G 401
3AC3SOFTWAREPRO A:363 , ARG G:69 , LYS G:169 , ILE G:239 , SER G:241 , PHE G:243 , ASP G:244 , ARG G:268 , LEU G:276 , VAL G:296 , HIS G:297 , ARG G:298BINDING SITE FOR RESIDUE AMP G 402
4AC4SOFTWAREHIS G:150 , THR G:199 , ASN G:202 , ALA G:204 , VAL G:224 , SER G:225 , ALA G:226 , HIS G:297 , ILE G:311 , SER G:313 , SER G:315 , ASP G:316BINDING SITE FOR RESIDUE AMP G 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Val A:221 -Pro A:222
2Ala B:195 -Phe B:196
3Ser B:204 -Pro B:205

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4REW)

(-) 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:411
                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..ee...eee......eeeeee.....eeeeeeeehhhhhhh...hhhhhhhhhhhhh.......eee......eeeeeee.....hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........ee.......ee......ee............................hhhhhhhhhhhhhhhhhhh.........hhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh..........hhhhhhhhhh...................hhhhhhh..........ee..hhhhhhhhhhhhhh....eee......eeeeeee......eee.eeeeee.....eeeeee.........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rew A  11 GSVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRTSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWFKQDLPKYLFPEIDNRRIMNEAKDFYLATSPPDHHLTRPHPERVPFLVAETRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDGPRPGSHTIEFFEMCANLIKILAQ 550
                                    20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280||     338       348||     363       373|      403       413       423       433       443       453       463       529       539       549 
                                                                                                                                                                                                                                                                                                        281|                349|               373|                                                                          471|                      
                                                                                                                                                                                                                                                                                                         330                 355                394                                                                           528                      


Chain B from PDB  Type:PROTEIN  Length:79
                                                                                                               
               SCOP domains ------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............hhhhhh..........................eeee.....eeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------- Transcript
                 4rew B 194 YAFRSEERFKSPPILPPHLLQVILNKDTNISCDPALLPEPNHVMLNHLYALSIKDSVMVLSATHRYKKKYVTTLLYKPI 272
                                   203       213       223       233       243       253       263         


Chain G from PDB  Type:PROTEIN  Length:301
                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhh.hhhhh...eeeeeeee...hhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhhhh........hhhhhhhhhhhhhhhh..............hhhhhhhhhhhh....eeee......eeeeehhhhhhhhhhhhh...........hhhhhh.........ee...hhhhhhhhhhhh...eeeee.....eeeeee.hhhhhhhhh........hhhhhhhhh........eee...hhhhhhhhhhhhh..eeeee.......eeeehhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rew G  24 NNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHRLVVVDENDVVKGIVSLSDILQALVLT 324
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323
   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 4REW)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (97, 130)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    AMP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    STU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ala B:195 - Phe B:196   [ RasMol ]  
    Ser B:204 - Pro B:205   [ RasMol ]  
    Val A:221 - Pro A:222   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4rew
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  AAKB2_HUMAN | O43741
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  AAKG1_HUMAN | P54619
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  AAPK1_HUMAN | Q13131
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.7.11.1
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.11.26
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.11.27
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.11.31
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  AAKB2_HUMAN | O43741
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  AAKG1_HUMAN | P54619
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  AAPK1_HUMAN | Q13131
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 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 4eaj 4rer
        AAKG1_HUMAN | P54619: 2uv4 2uv5 2uv6 2uv7 4cfe 4cff 4rer 4zhx 5ezv 5iso
        AAPK1_HUMAN | Q13131: 4red 4rer 5ezv

(-) Related Entries Specified in the PDB File

4red CRYSTAL STRUCTURE OF HUMAN AMPK ALPHA1 KD-AID WITH K43A MUTATION
4rer CRYSTAL STRUCTURE OF THE PHOSPHORYLATED HUMAN ALPHA1 BETA2 GAMMA1 HOLO-AMPK COMPLEX BOUND TO AMP AND CYCLODEXTRIN