3QV6 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF LEISHMANIA MEXICANA PYRUVATE KINASE(LMPYK)IN COMPLEX WITH ACID BLUE 80.

Authors :   H. P. Morgan, D. S. Auld, I. W. Mcnae, M. W. Nowicki, P. A. M. Michels, L. A. Fothergill-Gilmore, M. D. Walkinshaw

Date :   25 Feb 11 (Deposition) - 29 Jun 11 (Release) - 21 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.85

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

Keywords :   Pyruvate Kinase, Glycolysis, Tim Barrel, Sugar Kinase, Adp/Atp Binding, Cytosol, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   H. P. Morgan, I. W. Mcnae, M. W. Nowicki, W. Zhong, P. A. Michels, D. S. Auld, L. A. Fothergill-Gilmore, M. D. Walkinshaw
The Trypanocidal Drug Suramin And Other Trypan Blue Mimetic Are Inhibitors Of Pyruvate Kinases And Bind To The Adenosin Site.
J. Biol. Chem. V. 286 31232 2011
PubMed-ID: 21733839 | Reference-DOI: 10.1074/JBC.M110.212613

Molecule 1 - PYRUVATE KINASE
	Chains	:	A, D
	EC Number	:	2.7.1.40
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET3A
	Expression System Strain	:	ROSETTA 2 PLYSS
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	PYK
	Organism Scientific	:	LEISHMANIA MEXICANA
	Organism Taxid	:	5665
	Strain	:	BEL46
	Synonym	:	PK

		1	2
Asymmetric Unit	:	A	D
Biological Unit 1 (2x)	:	A	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	K	4	Ligand/Ion	POTASSIUM ION
2	PO4	2	Ligand/Ion	PHOSPHATE ION
3	QV6	2	Ligand/Ion	3-({4-[(2,4-DIMETHYL-5-SULFOPHENYL)AMINO]-9,10-DIOXO-9,10-DIHYDROANTHRACEN-1-YL}AMINO)-2,4,6-TRIMETHYLBENZENESULFONIC ACID

Biological Unit 1 (2, 8)

No.	Name	Count	Type	Full Name
1	K	-1	Ligand/Ion	POTASSIUM ION
2	PO4	4	Ligand/Ion	PHOSPHATE ION
3	QV6	4	Ligand/Ion	3-({4-[(2,4-DIMETHYL-5-SULFOPHENYL)AMINO]-9,10-DIOXO-9,10-DIHYDROANTHRACEN-1-YL}AMINO)-2,4,6-TRIMETHYLBENZENESULFONIC ACID

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	QV6 A:500	BINDING SITE FOR RESIDUE QV6 A 499
2	AC2	SOFTWARE	THR A:26 , PRO A:29 , ARG A:49 , ASN A:51 , HIS A:54 , TYR A:59 , TYR A:304 , SER A:330 , GLY A:331 , ALA A:334 , LYS A:335 , QV6 A:499	BINDING SITE FOR RESIDUE QV6 A 500
3	AC3	SOFTWARE	ASN A:51 , SER A:53 , ASP A:83 , THR A:84 , SER A:211 , LYS A:238 , HOH A:553	BINDING SITE FOR RESIDUE K A 501
4	AC4	SOFTWARE	GLN A:354 , LEU A:357 , GLU A:359 , HOH A:537	BINDING SITE FOR RESIDUE K A 502
5	AC5	SOFTWARE	SER A:400 , ASN A:401 , THR A:402 , ARG A:404 , SER A:405 , ALA A:481	BINDING SITE FOR RESIDUE PO4 A 503
6	AC6	SOFTWARE	ASN D:51 , SER D:53 , ASP D:83 , THR D:84 , SER D:211 , LYS D:238 , HOH D:526	BINDING SITE FOR RESIDUE K D 499
7	AC7	SOFTWARE	GLN D:354 , LEU D:357 , GLU D:359 , HOH D:550	BINDING SITE FOR RESIDUE K D 500
8	AC8	SOFTWARE	SER D:400 , ASN D:401 , THR D:402 , GLY D:403 , ARG D:404 , SER D:405 , ASP D:482 , HOH D:548	BINDING SITE FOR RESIDUE PO4 D 501

(no "SS Bond" information available for 3QV6)

Asymmetric Unit

No.	Residues
1	Val A:95	-	Gly A:96
2	Ile A:372	-	Pro A:373
3	Ile D:372	-	Pro D:373

(no "SAP(SNP)/Variant" information available for 3QV6)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRUVATE_KINASE	PS00110	Pyruvate kinase active site signature.	KPYK_LEIME	234-246	2	A:233-245 D:233-245

Biological Unit 1 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PYRUVATE_KINASE	PS00110	Pyruvate kinase active site signature.	KPYK_LEIME	234-246	4	A:233-245 D:233-245

(no "Exon" information available for 3QV6)

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:493
 aligned with KPYK_LEIME | Q27686 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:498
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491        
           KPYK_LEIME     2 SQLAHNLTLSIFDPVANYRAARIICTIGPSTQSVEALKGLIQSGMSVARMNFSHGSHEYHQTTINNVRQAAAELGVNIAIALDTKGPEIRTGQFVGGDAVMERGATCYVTTDPAFADKGTKDKFYIDYQNLSKVVRPGNYIYIDDGILILQVQSHEDEQTLECTVTNSHTISDRRGVNLPGCDVDLPAVSAKDRVDLQFGVEQGVDMIFASFIRSAEQVGDVRKALGPKGRDIMIICKIENHQGVQNIDSIIEESDGIMVARGDLGVEIPAEKVVVAQKILISKCNVAGKPVICATQMLESMTYNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSALNEYVFFNSIKKLQHIPMSADEAVCSSAVNSVYETKAKAMVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQGVESVFFDADKLGHDEGKEHRVAAGVEFAKSKGYVQTGDYCVVIHADHKVKGYANQTRILLVE 499
               SCOP domains d3qv6a1 A:1-87,A:187-357 Pyruvate kinase, N-terminal domain                            d3qv6a2 A:88-186 Pyruvate kinase (PK)                                                              d3qv6a1 A:1-87,A:187-357 Pyruvate kinase, N-terminal domain                                                                                                                d3qv6a3 A:358-498 Pyruvate kinase, C-terminal domain                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhh............eeeee......hhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhhhhhhh....eeeee..............eeee....eeeee.hhhhh......eee....hhhhhh....eeee....eeeeeeee....eeeeee...eeee....ee...........hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh.....eeeee.hhhhhhhhhhh..eeeee...........hhhhhhhhhhhhhhh.......eeeeee..-----...eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRUVATE_KINA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qv6 A   1 SQLAHNLTLSIFDPVANYRAARIICTIGPSTQSVEALKGLIQSGMSVARMNFSHGSHEYHQTTINNVRQAAAELGVNIAIALDTKGPEIRTGQFVGGDAVMERGATCYVTTDPAFADKGTKDKFYIDYQNLSKVVRPGNYIYIDDGILILQVQSHEDEQTLECTVTNSHTISDRRGVNLPGCDVDLPAVSAKDRVDLQFGVEQGVDMIFASFIRSAEQVGDVRKALGPKGRDIMIICKIENHQGVQNIDSIIEESDGIMVARGDLGVEIPAEKVVVAQKILISKCNVAGKPVICATQMLESMTYNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSALNEYVFFNSIKKLQHIPMSADEAVCSSAVNSVYETKAKAMVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQGVESVFFDADKLGHDEGKEHRVAAGVEFAKSKGYVQTGDYCVVIHAD-----YANQTRILLVE 498
                                    10        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       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480 |     490        
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                           482   488

Chain D from PDB  Type:PROTEIN  Length:394
 aligned with KPYK_LEIME | Q27686 from UniProtKB/Swiss-Prot  Length:499

    Alignment length:498
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491        
           KPYK_LEIME     2 SQLAHNLTLSIFDPVANYRAARIICTIGPSTQSVEALKGLIQSGMSVARMNFSHGSHEYHQTTINNVRQAAAELGVNIAIALDTKGPEIRTGQFVGGDAVMERGATCYVTTDPAFADKGTKDKFYIDYQNLSKVVRPGNYIYIDDGILILQVQSHEDEQTLECTVTNSHTISDRRGVNLPGCDVDLPAVSAKDRVDLQFGVEQGVDMIFASFIRSAEQVGDVRKALGPKGRDIMIICKIENHQGVQNIDSIIEESDGIMVARGDLGVEIPAEKVVVAQKILISKCNVAGKPVICATQMLESMTYNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSALNEYVFFNSIKKLQHIPMSADEAVCSSAVNSVYETKAKAMVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQGVESVFFDADKLGHDEGKEHRVAAGVEFAKSKGYVQTGDYCVVIHADHKVKGYANQTRILLVE 499
               SCOP domains d3qv6d1 D:1-87,D:187-357 Pyruvate kinase, N-terminal domain                                                                                                                              -d3qv6d1 D:1-87,D:187-357 Pyruvate kinase, N-terminal domain                                                                                                                d3qv6d2 D:358-498 Pyruvate kinase, C-terminal domain                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----------------PK-3qv6D01 D:18-363                                                                                                                                                                                                                                                                                                                                       -------------PK_C-3qv6D03 D:377-496                                                                                                  -- Pfam domains (1)
           Pfam domains (2) -----------------PK-3qv6D02 D:18-363                                                                                                                                                                                                                                                                                                                                       -------------PK_C-3qv6D04 D:377-496                                                                                                  -- Pfam domains (2)
         Sec.struct. author hhhhhhhhh............eeeee......hhhhhhhhhhhheeeeeee....hhhhhhhhhhhhhhhhhhh....eeeee....--------------------------------------------------------------------------------------------------....hhhhhhhhhhhhhh...eeee....hhhhhhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhh.eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhh..eeee...hhhhhh....hhhhhhhhhhhhhhh..eeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..eeeee...hhhhhhhhhh.....eeeee.hhhhhhhhhhh..eeeee.hhhhhh....hhhhhhhhhhhhhhh.......eeeeee..------..eeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PYRUVATE_KINA------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3qv6 D   1 SQLAHNLTLSIFDPVANYRAARIICTIGPSTQSVEALKGLIQSGMSVARMNFSHGSHEYHQTTINNVRQAAAELGVNIAIALDTKGP--------------------------------------------------------------------------------------------------LPAVSAKDRVDLQFGVEQGVDMIFASFIRSAEQVGDVRKALGPKGRDIMIICKIENHQGVQNIDSIIEESDGIMVARGDLGVEIPAEKVVVAQKILISKCNVAGKPVICATQMLESMTYNPRPTRAEVSDVANAVFNGADCVMLSGETAKGKYPNEVVQYMARICLEAQSALNEYVFFNSIKKLQHIPMSADEAVCSSAVNSVYETKAKAMVVLSNTGRSARLVAKYRPNCPIVCVTTRLQTCRQLNITQGVESVFFDADKLGHDEGKEHRVAAGVEFAKSKGYVQTGDYCVVIHAD------ANQTRILLVE 498
                                    10        20        30        40        50        60        70        80      |  -         -         -         -         -         -         -         -         -         -     | 190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480 |     490        
                                                                                                                 87                                                                                                186                                                                                                                                                                                                                                                                                                     482    489

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 "CATH Domain" information available for 3QV6)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: PK_TIM (63)

Family: PK (17)

Leishmania mexicana (6)

1a	PK-3qv6D01	D:18-363
1b	PK-3qv6D02	D:18-363

Clan: no clan defined [family: PK_C] (19)

Family: PK_C (19)

Leishmania mexicana (6)

2a	PK_C-3qv6D03	D:377-496
2b	PK_C-3qv6D04	D:377-496

Asymmetric Unit(hide GO term definitions)

Chain A,D (KPYK_LEIME | Q27686)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	GO:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0030955	potassium ion binding	Interacting selectively and non-covalently with potassium (K+) ions.
	GO:0004743	pyruvate kinase activity	Catalysis of the reaction: ATP + pyruvate = ADP + phosphoenolpyruvate.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0006096	glycolytic process	The chemical reactions and pathways resulting in the breakdown of a carbohydrate into pyruvate, with the concomitant production of a small amount of ATP and the reduction of NAD(P) to NAD(P)H. Glycolysis begins with the metabolism of a carbohydrate to generate products that can enter the pathway and ends with the production of pyruvate. Pyruvate may be converted to acetyl-coenzyme A, ethanol, lactate, or other small molecules.
	GO:0016310	phosphorylation	The process of introducing a phosphate group into a molecule, usually with the formation of a phosphoric ester, a phosphoric anhydride or a phosphoric amide.

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Ile A:372 - Pro A:373	[ RasMol ]
		Ile D:372 - Pro D:373	[ RasMol ]
		Val A:95 - Gly A:96	[ RasMol ]

Biological Unit
	Complete Structure
		Biological Unit 1	[ Jena3D ]

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Access by PDB/NDB ID
	3qv6
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	KPYK_LEIME \| Q27686
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	2.7.1.40
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		Interatomic Contacts of Structural Units	:	CSU
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	KPYK_LEIME \| Q27686
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UniProtKB/Swiss-Prot
	KPYK_LEIME \| Q27686	:	1pkl 3e0v 3e0w 3hqn 3hqo 3hqp 3hqq 3is4 3ktx 3pp7 3qv7 3qv8 3srk

1pkl	APO STRUCTURE
3qv7
3qv8
3qv9

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

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SCOP Domains (3, 5)

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Pfam Domains (2, 4)

Gene Ontology (11, 11)

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