5T5T - JenaLib

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Title :   AMPK BOUND TO ALLOSTERIC ACTIVATOR

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

Date :   31 Aug 16 (Deposition) - 29 Mar 17 (Release) - 26 Apr 17 (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 :   Ampk, Kinase, Allostery, Activator, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. T. Salatto, R. A. Miller, K. O. Cameron, E. Cokorinos, A. Reyes, J. Ward, M. F. Calabrese, R. G. Kurumbail, F. Rajamohan, A. S. Kalgutkar, D. A. Tess, A. Shavnya, N. E. Genung, D. J. Edmonds, A. Jatkar, B. S. Maciejewski, M. Amaro, H. Gandhok, M. Monetti, K. Cialdea, E. Bollinger, J. M. Kreeger, T. M. Coskran, A. C. Opsahl, G. G. Boucher, M. J. Birnbaum, P. Dasilva-Jardine, T. Rolph
Selective Activation Of Ampk Beta 1-Containing Isoforms Improves Kidney Function In A Rat Model Of Diabetic Nephropathy.
J. Pharmacol. Exp. Ther. V. 361 303 2017
PubMed-ID: 28289077 | Reference-DOI: 10.1124/JPET.116.237925

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
	Gene	:	PRKAA1, AMPK1
	Organism Common	:	RAT
	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
	Gene	:	PRKAB1
	Mutation	:	YES
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	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
	Gene	:	PRKAG1
	Organism Common	:	RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	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 (7, 11)

No.	Name	Count	Type	Full Name
1	75O	1	Ligand/Ion	6-CHLORO-5-[6-(DIMETHYLAMINO)-2-METHOXYPYRIDIN-3-YL]-1H-INDOLE-3-CARBOXYLIC ACID
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
4	CL	3	Ligand/Ion	CHLORIDE ION
5	SO4	2	Ligand/Ion	SULFATE ION
6	STU	1	Ligand/Ion	STAUROSPORINE
7	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 1 (6, 8)

No.	Name	Count	Type	Full Name
1	75O	1	Ligand/Ion	6-CHLORO-5-[6-(DIMETHYLAMINO)-2-METHOXYPYRIDIN-3-YL]-1H-INDOLE-3-CARBOXYLIC ACID
2	ADP	1	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	AMP	2	Ligand/Ion	ADENOSINE MONOPHOSPHATE
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	SO4	2	Ligand/Ion	SULFATE ION
6	STU	1	Ligand/Ion	STAUROSPORINE
7	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE

Biological Unit 2 (6, 16)

No.	Name	Count	Type	Full Name
1	75O	2	Ligand/Ion	6-CHLORO-5-[6-(DIMETHYLAMINO)-2-METHOXYPYRIDIN-3-YL]-1H-INDOLE-3-CARBOXYLIC ACID
2	ADP	2	Ligand/Ion	ADENOSINE-5'-DIPHOSPHATE
3	AMP	4	Ligand/Ion	ADENOSINE MONOPHOSPHATE
4	CL	-1	Ligand/Ion	CHLORIDE ION
5	SO4	4	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 , VAL A:24 , GLY A:25 , VAL A:30 , ALA A:43 , MET A:93 , GLU A:94 , TYR A:95 , VAL A:96 , GLY A:99 , GLU A:100 , GLU A:143 , ASN A:144 , LEU A:146 , 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	GLY A:210	binding site for residue CL A 603
04	AC4	SOFTWARE	GLY A:23 , VAL A:24	binding site for residue CL A 604
05	AC5	SOFTWARE	LYS A:34 , LYS A:41	binding site for residue SO4 A 605
06	AC6	SOFTWARE	LEU A:18 , GLY A:19 , LYS A:29 , LYS A:31 , ILE A:46 , ASP A:88 , VAL B:81 , ARG B:83 , ASP B:108 , ASN B:111 , VAL B:113 , ILE B:115	binding site for residue 75O B 4000
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 , 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 , 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 , VAL C:300	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 , LEU C:128 , VAL C:129 , ILE C:149 , HIS C:150 , ARG C:151	binding site for residue ADP C 403
10	AD1	SOFTWARE	ARG C:151 , THR C:167	binding site for residue SO4 C 404

(no "SS Bond" information available for 5T5T)

(no "Cis Peptide Bond" information available for 5T5T)

(no "SAP(SNP)/Variant" information available for 5T5T)

(no "PROSITE Motif" information available for 5T5T)

(no "Exon" information available for 5T5T)

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:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee..eeeeeeeee....eeeeeee.....eeeeeeee.hhhhhh.hhhhhhhhhhhhhhh.......eeeeee...eeeeeee....eehhhhhhhh...hhhhhhhhhhhhhhhhhhhhh..ee........eee.....eee......ee.................hhhhhh.....hhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhh.........hhhhhhhhhhhh........hhhhhhhhhhhhh..hhhhh....eee......hhhhhhhhhhhhhh....eeee....eeeeeee......eeeeeeeeee.....eeeeeeee......hhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t5t A   9 GRVKIGHYILGDTLGVGTFGKVKVGKHELTGHKVAVKILNRQKIRSLDVVGKIRREIQNLKLFRHPHIIKLYQVISTPSDIFMVMEYVSGGELFDYICKNGRLDEKESRRLFQQILSGVDYCHRHMVVHRDLKPENVLLDAHMNAKIADFGLSNMMSDGEFLRtSCGSPNYAAPEVISGRLYAGPEVDIWSSGVILYALLCGTLPFDDDHVPTLFKKICDGIFYTPQYLNPSVISLLKHMLQVDPMKRATIKDIREHEWFKQDLPKYLFPEAKWHLGIRSQSRPNDIMAEVCRAIKQLDYEWKVVNPYYLRVRRKNPVTSTFSKMSLQLYQVDSRTYLLDFRSIDDERPGSHTIEFFEMCANLIKILAQ 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||     402       412       422       432       442       452       462      |529       539         
                                                                                                                                                                                             172-TPO                                                                                                    279|                                                                        469|                     
                                                                                                                                                                                                                                                                                                         394                                                                         527

Chain B from PDB  Type:PROTEIN  Length:163
                                                                                                                                                                                                   
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee......eeeee.hhh...ee.ee....eeeeeee..eeeeeeeee..eee......eee.....eeeeeeehhhhhhhhhhhhhhhhhh.......hhhhhh..............hhhhh...eeeeee..eeeeeeeeee..eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t5t B  77 ARPTVFRWTGGGKEVYLSGSFNNWSKLPLTRDHNNFVAILDLPEGEHQYKFFVDGQWTHDPSEPIVTSQLGTVNNIIQVKKTDFEVFDALMVDSQKCSKAPPILPPHLLQVILNKCDPALLPEPNHVMLNHLYALSIKDGVMVLSATHRYKKKYVTTLLYKPI 270
                                    86        96       106       116       126       136       146       156       166       202       212    || 227       237       247       257       267   
                                                                                                                           174|             217|                                               
                                                                                                                            201              223

Chain C from PDB  Type:PROTEIN  Length:293
                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhh..hhhhhh..eeeeeeee...hhhhhhhhhhhhh...eeee......eeeeehhhhhhhhhhhhh......hhhhhh.hhhhhhhhhh..............hhhhhhhhhhhh...eeeee......eeeeeehhhhhhhhhhhhh..........hhhhhh.........ee...hhhhhhhhhhhhh..eeeee.....eeeeee...hhhhhhh........hhhhhhhhh....ee....hhhhhhhhhhhhh..eeeee.....eeeeeehhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t5t C  26 SVYTTFMKSHRCYDLIPTSSKLVVFDTSLQVKKAFFALVTNGVRAAPLWDSKKQSFVGMLTITDFINILHRYYKSALVQIYELEEHKIETWREVYLQDSFKPLVCISPNASLFDAVSSLIRNKIHRLPVIDPESGNTLYILTHKRILKFLKLFITEFPKPEFMSKSLEELQIGTYANIAMVRTTTPVYVALGIFVQHRVSALPVVDEKGRVVDIYSKFDVINLAAEKTYNNLDVSVTKALQHREGVLKCYLHETLEAIINRLVEAEVHRLVVVDEHDVVKGIVSLSDILQALV 322
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265  ||   279       289       299       309       319   
                                                                                                                                                                                                                                                                            268|                                                 
                                                                                                                                                                                                                                                                             273

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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 5T5T)

(no "CATH Domain" information available for 5T5T)

(no "Pfam Domain" information available for 5T5T)

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (7, 11)

Sites (10, 10)

SS Bonds (0, 0)

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