4QFG - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF AMPK IN COMPLEX WITH STAUROSPORINE INHIBITOR AND IN THE ABSENCE OF A SYNTHETIC ACTIVATOR

Authors :   M. F. Calabrese, R. G. Kurumbail

Date :   20 May 14 (Deposition) - 06 Aug 14 (Release) - 20 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.46

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,B,C  (2x)

Keywords :   Cbm, Kinase, Ampk, Signaling Protein-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. F. Calabrese, F. Rajamohan, M. S. Harris, N. L. Caspers, R. Magyar, J. M. Withka, H. Wang, K. A. Borzilleri, P. V. Sahasrabudhe, L. R. Hoth, K. F. Geoghegan, S. Han, J. Brown, T. A. Subashi, A. R. Reyes, R. K. Frisbie, J. Ward, R. A. Miller, J. A. Landro, A. T. Londregan, P. A. Carpino, S. Cabral, A. C. Smith, E. L. Conn, K. O. Cameron, X. Qiu, R. G. Kurumbail
Structural Basis For Ampk Activation: Natural And Synthetic Ligands Regulate Kinase Activity From Opposite Poles By Different Molecular Mechanisms.
Structure V. 22 1161 2014
PubMed-ID: 25066137 | Reference-DOI: 10.1016/J.STR.2014.06.009

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
	Fragment	:	AMPK ALPHA1
	Gene	:	AMPK1, PRKAA1, PRKAA1 AMPK1
	Mutation	:	YES
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	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
	Fragment	:	AMPK BETA1
	Gene	:	PRKAB1
	Mutation	:	YES
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	AMPK SUBUNIT BETA-1, 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
	Fragment	:	AMPK GAMMA1
	Gene	:	PRKAG1
	Organism Common	:	BROWN RAT,RAT,RATS
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	AMPK GAMMA1, AMPK SUBUNIT GAMMA-1, AMPKG

		1	2	3
Asymmetric Unit	:	A	B	C
Biological Unit 1 (1x)	:	A	B	C
Biological Unit 2 (2x)	:	A	B	C

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (5, 9)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	3	Ligand/Ion	CHLORIDE ION
3	SO4	3	Ligand/Ion	SULFATE ION
4	STU	1	Ligand/Ion	STAUROSPORINE
5	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 1 (4, 6)

No.	Name	Count	Type	Full Name
1	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SO4	3	Ligand/Ion	SULFATE ION
4	STU	1	Ligand/Ion	STAUROSPORINE
5	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 2 (4, 12)

No.	Name	Count	Type	Full Name
1	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
2	CL	-1	Ligand/Ion	CHLORIDE ION
3	SO4	6	Ligand/Ion	SULFATE ION
4	STU	2	Ligand/Ion	STAUROSPORINE
5	TPO	2	Mod. Amino Acid	PHOSPHOTHREONINE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LEU A:22 , GLY A:23 , GLY A:25 , VAL A:30 , ALA A:43 , ILE A:77 , GLU A:94 , TYR A:95 , VAL A:96 , GLY A:99 , GLU A:100 , GLU A:143 , ASN A:144 , LEU A:146 , ALA A:156 , ASP A:157	BINDING SITE FOR RESIDUE STU A 601
2	AC2	SOFTWARE	VAL A:24	BINDING SITE FOR RESIDUE CL A 602
3	AC3	SOFTWARE	LYS A:34 , LYS A:41	BINDING SITE FOR RESIDUE CL A 603
4	AC4	SOFTWARE	SER A:97 , ALA A:149	BINDING SITE FOR RESIDUE CL A 604
5	AC5	SOFTWARE	LYS A:29 , ASN A:48 , LYS A:51 , ARG B:83 , ASN B:110	BINDING SITE FOR RESIDUE SO4 A 605
6	AC6	SOFTWARE	HIS C:150 , THR C:199 , ILE C:203 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , ARG C:298 , ILE C:311 , SER C:313 , SER C:315 , ASP C:316	BINDING SITE FOR RESIDUE AMP C 401
7	AC7	SOFTWARE	THR C:86 , ILE C:87 , THR C:88 , HIS C:150 , ARG C:151	BINDING SITE FOR RESIDUE SO4 C 402
8	AC8	SOFTWARE	SER C:241 , PHE C:243 , HIS C:297 , ARG C:298	BINDING SITE FOR RESIDUE SO4 C 403

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

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

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

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

(no "Exon" information available for 4QFG)

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:366
                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...ee..eeeeeeee.....eeeeeee.....eeeeeeeehhhhh...hhhhhhhhhhhhhhh.......eeeeee...eeeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..eee.......eee.....eee.....eee.................hhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhh........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.........ee.eee..hhhhhhhhhhhhhhhh..eeee....eeeeeee......eeeeeeeee......eeeeeeee......hhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qfg A   9 GRVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRtSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDDERPGSHTIEFFEMCANLIKILAQ 548
                                    18        28        38        48        58        68        78        88        98       108       118       128       138       148       158       168   |   178       188       198       208       218       228       238       248       258       268       278|      405       415       425       435       445       455       465   ||  532       542      
                                                                                                                                                                                             172-TPO                                                                                                   278|                                                                      469|                     
                                                                                                                                                                                                                                                                                                        396                                                                       527

Chain B from PDB  Type:PROTEIN  Length:161
                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee......eeeee.hhh...ee.ee....eeeeee...eeeeeeeee...ee......eee.....eeeeeee.......hhhhhhhhh......hhhhh................hhhhh...eee.....eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfg B  77 ARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRDQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKAPPILPPHLLQVILNKSCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                                    86        96       106       116       126       136       146       156       166    || 205       215 ||    229       239       249       259       269 
                                                                                                                        171|             217|                                                
                                                                                                                         201              222

Chain C from PDB  Type:PROTEIN  Length:287
                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhhhh.......hhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhhhhhhhhh..hhhhhhhhhhhh.........ee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhhhh........hhhhhhhhh.eee...hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfg C  25 SSVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALV 322
                                    34        44        54        64        74        84        94       104       114       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268|      285       295       305       315       
                                                                                                                           122|                                                                                                                                          268|                                              
                                                                                                                            127                                                                                                                                           276

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 4QFG)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric 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 ]
		CL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		SO4	[ 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 ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4qfg)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 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)

Access by PDB/NDB ID
	4qfg
		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
	AAKB1_RAT \| P80386
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	AAKG1_RAT \| P80385
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt
	AAPK1_RAT \| P54645
		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

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
	AAKB1_RAT \| P80386
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	AAKG1_RAT \| P80385
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)
	AAPK1_RAT \| P54645
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 9)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

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 (85, 110)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File