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Title :   STRUCTURE OF AMPK IN COMPLEX WITH BR2-A769662CORE ACTIVATOR AND STAUROSPORINE INHIBITOR

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

Date :   21 May 14 (Deposition) - 06 Aug 14 (Release) - 20 Aug 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.55

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-Activator 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 ALPHA 1
	Gene	:	AMPK1, PRKAA1
	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 BETA 1
	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 GAMMA 1
	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 (6, 11)

No.	Name	Count	Type	Full Name
1	32H	1	Ligand/Ion	2-BROMO-3-(4-BROMOPHENYL)-4-HYDROXY-6-OXO-6,7-DIHYDROTHIENO[2,3-B]PYRIDINE-5-CARBONITRILE
2	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
3	CL	5	Ligand/Ion	CHLORIDE ION
4	SO4	2	Ligand/Ion	SULFATE ION
5	STU	1	Ligand/Ion	STAUROSPORINE
6	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 1 (5, 6)

No.	Name	Count	Type	Full Name
1	32H	1	Ligand/Ion	2-BROMO-3-(4-BROMOPHENYL)-4-HYDROXY-6-OXO-6,7-DIHYDROTHIENO[2,3-B]PYRIDINE-5-CARBONITRILE
2	AMP	1	Ligand/Ion	ADENOSINE MONOPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	SO4	2	Ligand/Ion	SULFATE ION
5	STU	1	Ligand/Ion	STAUROSPORINE
6	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 2 (5, 12)

No.	Name	Count	Type	Full Name
1	32H	2	Ligand/Ion	2-BROMO-3-(4-BROMOPHENYL)-4-HYDROXY-6-OXO-6,7-DIHYDROTHIENO[2,3-B]PYRIDINE-5-CARBONITRILE
2	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
3	CL	-1	Ligand/Ion	CHLORIDE ION
4	SO4	4	Ligand/Ion	SULFATE ION
5	STU	2	Ligand/Ion	STAUROSPORINE
6	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 , 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	LYS A:29 , ILE A:46 , LYS A:51 , ASP A:88 , ARG B:83 , ASP B:108 , VAL B:113	BINDING SITE FOR RESIDUE 32H A 602
3	AC3	SOFTWARE	VAL A:24	BINDING SITE FOR RESIDUE CL A 603
4	AC4	SOFTWARE	SER A:97 , ALA A:149	BINDING SITE FOR RESIDUE CL A 606
5	AC5	SOFTWARE	THR B:85 , ASP B:136	BINDING SITE FOR RESIDUE CL B 301
6	AC6	SOFTWARE	HIS C:150 , ILE C:203 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , HIS C:297 , SER C:313 , SER C:315 , ASP C:316	BINDING SITE FOR RESIDUE AMP C 401
7	AC7	SOFTWARE	ARG C:69 , THR C:86 , THR C:88 , ILE C:149 , HIS C:150 , ARG C:151	BINDING SITE FOR RESIDUE SO4 C 402
8	AC8	SOFTWARE	ARG C:69 , 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 4QFS)

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

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

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

(no "Exon" information available for 4QFS)

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:362
                                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeeeee.....eeeeeee.....eeeeeeee.hhhhhh.hhhhhhhhhhhhh...........eeee...eeeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..ee........eee.....eee.hhhhhee.................hhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh.........ee.eee..hhhhhhhhhhhhhhhhh.........eeeeee........eeeeeeeee.....eeeeeee....hhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfs A   9 GRVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRtSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDDSHTIEFFEMCANLIKILAQ 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       395       405       415       425       435       445       455       465  ||   536       546  
                                                                                                                                                                                             172-TPO                                                                                                  277|                                                                      468|                  
                                                                                                                                                                                                                                                                                                       395                                                                       530

Chain B from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.....eeeee.hhh...ee.ee...eeeeee.....eeeeeeee..eee......eee.....eeeeee......hhhhhhhhhh.......hhhhh...............hhhhh...eee.....eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfs B  79 PTVFRWTGGGKEVYLSGSFNNWSKLPLTRDQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKAPPILPPHLLQVILNKCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                                    88        98       108       118       128       138       148       158       168  ||   207       217|      232       242       252       262        
                                                                                                                      171|             217|                                               
                                                                                                                       201              223

Chain C from PDB  Type:PROTEIN  Length:267
                                                                                                                                                                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh...eeeeeeee...hhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhhhhh......hhhhhhhhhhhhhhhhh..............hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhh......hhhhh...ee...hhhhhhhhhhhhh..eeeee.....eeeeee...hhhhhhh........hhhhhhh.........hhhhhhhhhhhh...ee.......eehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfs C  28 YTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITSLEELQIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRLKCYLHETLEAIINRLVEAEVHRLVDVVKGIVSLSDILQALV 322
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  ||   203       213       223       233       243       253       263    || 280       290       300|      315       
                                                                                                                                                                                  180|  196|                                                              268|                     300|                
                                                                                                                                                                                   191   203                                                               276                      306

Legend:		→ Mismatch	(orange background)
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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 '\|'

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

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	4qfs
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	2.7.11.1
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4qfg	SAME PROTEIN IN THE ABSENCE OF A SYNTHETIC ACTIVATOR
4qfr	SAME PROTEIN BOUND TO A RELATED SYNTHETIC ACTIVATOR
4qfs

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (6, 11)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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Gene Ontology (85, 110)

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