16PK - JenaLib

Asym./Biol. Unit - manually (Jmol Viewer)

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   PHOSPHOGLYCERATE KINASE FROM TRYPANOSOMA BRUCEI BISUBSTRATE ANALOG

Authors :   B. E. Bernstein, J. Bressi, M. Blackburn, M. Gelb, W. G. J. Hol

Date :   18 May 98 (Deposition) - 25 Nov 98 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.60

Chains :   Asym./Biol. Unit : A

Keywords :   Kinase, Phosphoglycerate, Ternary Complex, Glycolysis, Transferase, Bisubstrate, Analog (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   B. E. Bernstein, D. M. Williams, J. C. Bressi, P. Kuhn, M. H. Gelb, G. M. Blackburn, W. G. Hol
A Bisubstrate Analog Induces Unexpected Conformational Changes In Phosphoglycerate Kinase From Trypanosoma Brucei.
J. Mol. Biol. V. 279 1137 1998
PubMed-ID: 9642090 | Reference-DOI: 10.1006/JMBI.1998.1835
(for further references see the PDB file header)

Molecule 1 - 3-PHOSPHOGLYCERATE KINASE
	Chains	:	A
	EC Number	:	2.7.2.3
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21
	Expression System Plasmid	:	PET21A
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Mutation	:	YES
	Organelle	:	GLYCOSOME
	Organism Scientific	:	TRYPANOSOMA BRUCEI
	Organism Taxid	:	5691
	Synonym	:	PGK
	Variant	:	GLYCOSOMAL VERSION

		1
Asymmetric/Biological Unit	:	A

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 2)

No.	Name	Count	Type	Full Name
1	BIS	1	Ligand/Ion	1,1,5,5-TETRAFLUOROPHOSPHOPENTYLPHOSPHONIC ACIDADENYLATE ESTER
2	EPE	1	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:217 , ALA A:218 , LYS A:223 , GLY A:241 , ALA A:242 , TYR A:245 , ALA A:314 , LEU A:315 , GLY A:339 , PRO A:340 , GLY A:342 , VAL A:343 , GLU A:345 , GLY A:397 , GLY A:398 , GLY A:399 , HOH A:505 , HOH A:514 , HOH A:523 , HOH A:571 , HOH A:673 , HOH A:766 , HOH A:768 , HOH A:779 , HOH A:781 , HOH A:799 , HOH A:872 , HOH A:874 , HOH A:902 , HOH A:981 , HOH A:1020 , HOH A:1032 , HOH A:1034 , HOH A:1037	BINDING SITE FOR RESIDUE BIS A 499
2	AC2	SOFTWARE	LYS A:49 , THR A:52 , GLU A:53 , GLN A:251 , GLY A:252 , TYR A:253 , ALA A:296 , GLU A:345 , MET A:346 , VAL A:347 , PRO A:348 , HOH A:567 , HOH A:676 , HOH A:809 , HOH A:871	BINDING SITE FOR RESIDUE EPE A 430

(no "SS Bond" information available for 16PK)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:209	-	Pro A:210

Asymmetric/Biological Unit (1, 1)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PGKC_TRYBB_001 *	G	75	D	PGKC_TRYBB	---	---	A	G	75	D
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric/Biological Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGLYCERATE_KINASE	PS00111	Phosphoglycerate kinase signature.	PGKC_TRYBB	18-28	1	A:18-28

(no "Exon" information available for 16PK)

Asymmetric/Biological 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:415
 aligned with PGKC_TRYBB | P07378 from UniProtKB/Swiss-Prot  Length:440

    Alignment length:415
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414     
           PGKC_TRYBB     5 EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEGGSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKALSELLLRPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYSIGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITEDQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTFAIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLELLEGKTLPGVTVLDEK 419
               SCOP domains d16pka_ A: Phosphoglycerate kinase                                                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 16pkA01 A:5-192  [code=3.40.50.1260, no name defined]                                                                                                                                       ------16pkA02 A:199-406  [code=3.40.50.1270, no name defined]                                                                                                                                                         ------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhh......eeeeee..............hhhhhhhhhhhhhhh...eeeee..........hhhhhhhhh........hhh..hhhhhhhhhhh....eee......hhhhh......eeee..hhh.hhhh...hhhhhhhhhhhhhh..eeeee.hhh.........hhhhhh......hhhhhhhhhhhhhh......eeeee.....hhhhhhhhhhhhh..eeee..hhhhhhhhhh..........hhhhhhhhhhhhhhhh...eee....eeee.....................eeeee.hhhhhhhhhhhhh..eeeee........hhh.hhhhhhhhhhhhhhhhh..eeee..hhhhhhhhh.............hhhhhhhh.....hhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------D-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------PGLYCERATE_------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 16pk A   5 EKKSINECDLKGKKVLIRVDFNVPVKNGKITNDYRIRSALPTLKKVLTEGGSCVLMSHLGRPKGIPMAQAGKIRSTGGVPGFQQKATLKPVAKRLSELLLRPVTFAPDCLNAADVVSKMSPGDVVLLENVRFYKEEGSKKAKDREAMAKILASYGDVYISDAFGTAHRDSATMTGIPKILGNGAAGYLMEKEISYFAKVLGNPPRPLVAIVGGAKVSDKIQLLDNMLQRIDYLLIGGAMAYTFLKAQGYSIGKSKCEESKLEFARSLLKKAEDRKVQVILPIDHVCHTEFKAVDSPLITEDQNIPEGHMALDIGPKTIEKYVQTIGKCKSAIWNGPMGVFEMVPYSKGTFAIAKAMGRGTHEHGLMSIIGGGDSASAAELSGEAKRMSHVSTGGGASLELLEGKTLPGVTVLDDK 419
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414

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 '\|'

Asymmetric/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

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Class: Alpha and beta proteins (a/b) (23833)

Fold: Phosphoglycerate kinase (42)

Superfamily: Phosphoglycerate kinase (42)

Family: Phosphoglycerate kinase (39)

Protein domain: Phosphoglycerate kinase (16)

Trypanosome (Trypanosoma brucei) [TaxId: 5691] (2)

d16pka_

(no "Pfam Domain" information available for 16PK)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A (PGKC_TRYBB | P07378)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0016301	kinase activity	Catalysis of the transfer of a phosphate group, usually from ATP, to a substrate molecule.
	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:0004618	phosphoglycerate kinase activity	Catalysis of the reaction: 3-phospho-D-glycerate + ATP = 3-phospho-D-glyceroyl phosphate + ADP + H(+).
	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.
cellular component
	GO:0020015	glycosome	A membrane-bounded organelle found in organisms from the order Kinetoplastida that houses the enzymes of glycolysis.
	GO:0005777	peroxisome	A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Arg A:209 - Pro A:210	[ RasMol ]

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	16pk
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(no "Related Entries Specified in the PDB File" available for 16PK)

Description

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Ligands, Modified Residues, Ions (2, 2)

Sites (2, 2)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

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