4QFR - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   STRUCTURE OF AMPK IN COMPLEX WITH CL-A769662 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 :   3.34

Chains :   Asym. Unit : A,B,C
Biol. Unit 1: A,B,C  (1x)
Biol. Unit 2: A,B,C  (2x)
Biol. Unit 3: A (2x),B (2x),C (2x)

Keywords :   Cbm, Ampk, Kinase, 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
Biological Unit 3 (2x)	:	A (2x)	B (2x)	C (2x)

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (7, 12)

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

Biological Unit 1 (6, 7)

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

Biological Unit 2 (6, 14)

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

Biological Unit 3 (3, 6)

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

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	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
02	AC2	SOFTWARE	SER A:97 , ALA A:149	BINDING SITE FOR RESIDUE CL A 602
03	AC3	SOFTWARE	LYS A:34 , LYS A:41	BINDING SITE FOR RESIDUE CL A 603
04	AC4	SOFTWARE	VAL A:24	BINDING SITE FOR RESIDUE CL A 605
05	AC5	SOFTWARE	LEU A:18 , GLY A:19 , LYS A:29 , LYS A:31 , ILE A:46 , LYS A:51 , ASP A:88 , PHE A:90 , VAL B:81 , ARG B:83 , ARG B:107 , ASP B:108 , VAL B:113	BINDING SITE FOR RESIDUE 32J A 606
06	AC6	SOFTWARE	THR B:85 , ASP B:136	BINDING SITE FOR RESIDUE CL B 301
07	AC7	SOFTWARE	HIS C:150 , THR C:199 , ILE C:203 , ALA C:204 , VAL C:224 , SER C:225 , ALA C:226 , HIS C:297 , ARG C:298 , ILE C:311 , SER C:313 , SER C:315 , ASP C:316	BINDING SITE FOR RESIDUE AMP C 401
08	AC8	SOFTWARE	ARG C:69 , LYS C:169 , ILE C:239 , SER C:241 , PHE C:243 , ASP C:244 , ARG C:268 , LEU C:276 , VAL C:296 , HIS C:297 , ARG C:298	BINDING SITE FOR RESIDUE AMP C 402
09	AC9	SOFTWARE	ARG C:69 , MET C:84 , THR C:86 , THR C:88 , ASP C:89 , TYR C:120 , PRO C:127 , VAL C:129 , ILE C:149 , HIS C:150 , ARG C:151 , PRO C:153	BINDING SITE FOR RESIDUE ADP C 403
10	BC1	SOFTWARE	ARG C:151 , THR C:167 , LYS C:169	BINDING SITE FOR RESIDUE SO4 C 404

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

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

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

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

(no "Exon" information available for 4QFR)

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......eeeeee.....eeeeeeeehhhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhhh.ee........eee.....eee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhh.........ee......hhhhhhhhhhhhhhhhh.eeee....eeeeeee......eeeeeeeeee.....eeeeeeee...hhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfr 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:159
                                                                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee......eeee.hhh...ee.ee...eeeeee.....eeeeeeee..eee......eee.....eeeeee......hhhhhhhhhh.......hhhhhh...............hhhhh...eee.....eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfr B  79 PTVFRWTGGGKEVYLSGSFNNWSKLPLTRDQNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKAPPILPPHLLQVILNKSCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                                    88        98       108       118       128       138       148       158       168  ||   207       217|      231       241       251       261         
                                                                                                                      171|             217|                                                
                                                                                                                       201              222

Chain C from PDB  Type:PROTEIN  Length:279
                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh..eeeeeeee...hhhhhhhhhhhhh..eeeeee....eeeeeeehhhhhhhhhhhh......hhhhhh.hhhhhhhhhh..............hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhhhhhh..hhhhh.........ee...hhhhhhhhhhhh...eeeee.....eeeeee...hhhhhhh........hhhhhhhhh..ee....hhhhhhhhhhh....eeeee.....eeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qfr C  28 YTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHRVLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALV 322
                                    37        47        57        67        77        87        97       107       117       127       137       147       157       167       177  ||   197       207       217       227       237       247       257       267||     283       293       303       313         
                                                                                                                                                                                  180|                                                                          268|                                               
                                                                                                                                                                                   191                                                                           275

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 4QFR)

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

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

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	4qfr
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	2.7.11.1
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	2.7.11.26
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4qfg	SAME PROTEIN IN THE ABSENCE OF A SYNTHETIC ACTIVATOR
4qfs

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 12)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (85, 110)

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