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Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF THE PHOSPHORYLATED HUMAN ALPHA1 BETA2 GAMMA1 HOLO-AMPK COMPLEX BOUND TO AMP AND CYCLODEXTRIN

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 :   23 Sep 14 (Deposition) - 10 Dec 14 (Release) - 11 Mar 15 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   4.05

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

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

		1	2	3
Asymmetric/Biological Unit	:	A	B	G

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (6, 8)

No.	Name	Count	Type	Full Name
1	AMP	3	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	BCD	1	Ligand/Ion	BETA-CYCLODEXTRIN
3	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4	SEP	1	Mod. Amino Acid	PHOSPHOSERINE
5	STU	1	Ligand/Ion	STAUROSPORINE
6	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:24 , GLY A:25 , GLY A:27 , ALA A:45 , GLU A:96 , TYR A:97 , VAL A:98 , GLU A:102 , GLU A:145 , ASN A:146 , LEU A:148	BINDING SITE FOR RESIDUE STU A 601
2	AC2	SOFTWARE	LYS A:14 , GLY A:16 , THR A:87 , PRO B:78 , VAL B:80	BINDING SITE FOR RESIDUE EPE A 602
3	AC3	SOFTWARE	ILE A:232 , PHE A:233 , TYR A:234 , THR A:235 , PHE B:96 , TRP B:99 , PRO B:119 , LYS B:126 , GLN B:145 , LEU B:146 , THR B:148 , ASN B:150	BINDING SITE FOR RESIDUE BCD B 301
4	AC4	SOFTWARE	THR G:87 , THR G:89 , ASP G:90 , TYR G:121 , PRO G:128 , LEU G:129 , VAL G:130 , ILE G:150 , HIS G:151 , ARG G:152	BINDING SITE FOR RESIDUE AMP G 401
5	AC5	SOFTWARE	ARG G:70 , LYS G:170 , ILE G:240 , SER G:242 , PHE G:244 , ASP G:245 , ARG G:269 , GLY G:275 , LEU G:277 , VAL G:297 , HIS G:298 , ARG G:299	BINDING SITE FOR RESIDUE AMP G 402
6	AC6	SOFTWARE	HIS G:151 , THR G:200 , ASN G:203 , ALA G:205 , ARG G:224 , VAL G:225 , SER G:226 , ALA G:227 , HIS G:298 , ILE G:312 , SER G:314 , SER G:316 , ASP G:317	BINDING SITE FOR RESIDUE AMP G 403

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

Asymmetric/Biological Unit

No.	Residues
1	Val A:221	-	Pro A:222

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

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

(no "Exon" information available for 4RER)

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:459
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeeeee......eeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhh........eee......eeeeeee....eehhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh.ee........eee......ee......ee............................hhhhhhhhhhhhhhhh............hhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh...............hhhhhhhhhhh......hhhhhhh..........hhhhhhhhhhhhh...................hhhhhhhhhhhh.........eee..hhhhhhhhhhhhhhhh..eeeeee..eeeeeee......eeeeeeeeeeee..eeeeeee...........hhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rer A  11 GSVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRtSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRASIKDIREHEWFKQDLPKYLFPEDPSYSDDEALKEVCEKFECSEEEVLSCLYNRNHQDPLAVAYHLIIDNRRIMNEAKDFYLATSPPDDHHLTRPHPERVPFLVAETPRKAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTYSKMSLQLYQVDSRTYLLDFRSIDDGITPRPGSHTIEFFEMCANLIKILAQ 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     ||294       304       314       324       334       344    || 358       368     ||397       407       417       427       437       447       457       467    || 531       541         
                                                                                                                                                                                             174-TPO                                                                                                         286|                                                       349|                 374|                                                                           472|                       
                                                                                                                                                                                                                                                                                                              291                                                        354                  394                                                                            527

Chain B from PDB  Type:PROTEIN  Length:181
                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eee........eee..........ee.ee....eeeee.......ee.eee..eee......eee.....eeee..........................................hhhhhh...................hhhhh..eeee.....eeeeeeeee....eeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rer B  78 PTVIRWSEGGKEVFISGSFNNWSTKIPLIKsHNDFVAILDLPEGEHQYKFFVDGQWVHDPSEPVVTSQLGTINNLIHVKKSDFEVFDALKSSSPPGPYGQEMYAFRSEERFKSPPILPPHLLQVILNKDTNISCDPALLPEPNHVMLNHLYALSIKDSVMVLSATHRYKKKYVTTLLYKPI 272
                                    87        97       107|      117       127       137       147       157       167|      191       201       211       221       231       241       251       261       271 
                                                        108-SEP                                                    167|                                                                                          
                                                                                                                    182

Chain G from PDB  Type:PROTEIN  Length:300
                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh.hhhhhh..eeeeeeee...hhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhhhh.......hhhhhh.hhhhhhhhhh..............hhhhhhhhhhhh....eeee......eeeeehhhhhhhhhhhhh...........hhhhhh.........ee...hhhhhhhhhhhh...eeeee.....eeeeee...hhhhhhh........hhhhhhhhh........eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4rer G  25 NNSVYTSFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRSHYFEGVLKCYLHETLETIINRLVEAEVHRLVVVDENDVVKGIVSLSDILQALVL 324
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324

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 '\|'

(no "SCOP Domain" information available for 4RER)

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

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

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		AMP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		BCD	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		EPE	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SEP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		STU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		TPO	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
		Val A:221 - Pro A:222	[ RasMol ]

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	4rer
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		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
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	AAKB2_HUMAN \| O43741
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	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
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	2.7.11.1
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	2.7.11.26
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc
	2.7.11.27
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		Pathway	:	KEGG \| MetaCyc
	2.7.11.31
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		Disease Information	:	OMIM

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		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
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	AAKB2_HUMAN \| O43741
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	AAKG1_HUMAN \| P54619
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	AAPK1_HUMAN \| Q13131
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UniProtKB/Swiss-Prot
	AAKB2_HUMAN \| O43741	:	2f15 2v8q 2v92 2v9j 2y8l 2y8q 2ya3 4cfh 4eai 4eaj 4rew
	AAKG1_HUMAN \| P54619	:	2uv4 2uv5 2uv6 2uv7 4cfe 4cff 4rew 4zhx 5ezv 5iso
	AAPK1_HUMAN \| Q13131	:	4red 4rew 5ezv

4red	CRYSTAL STRUCTURE OF HUMAN AMPK ALPHA1 KD-AID WITH K43A MUTATION
4rew

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 8)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (0, 0)

CATH Domains (0, 0)

Pfam Domains (0, 0)

Gene Ontology (97, 130)

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File