2PYI - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE IN COMPLEX WITH GLUCOSYL TRIAZOLEACETAMIDE

Authors :   K. M. Alexacou, C. Tiraidis, S. E. Zographos, E. D. Chrysina, J. Hayes, N. G. Oikonomakos

Date :   16 May 07 (Deposition) - 01 Apr 08 (Release) - 25 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.88

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

Keywords :   Glycogenolysis, Inhibition, Type 2 Diabetes, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   K. M. Alexacou, J. M. Hayes, C. Tiraidis, S. E. Zographos, D. D. Leonidas, E. D. Chrysina, G. Archontis, N. G. Oikonomakos, J. V. Paul, B. Varghese, D. Loganathan
Crystallographic And Computational Studies On 4-Phenyl-N-(Beta-D-Glucopyranosyl)-1H-1, 2, 3-Triazole-1- Acetamide, An Inhibitor Of Glycogen Phosphorylase: Comparison With Alpha-D-Glucose, N-Acetyl-Beta-D-Glucopyranosylamine And N-Benzoyl-N'-Beta-D-Glucopyranosyl Urea Binding.
Proteins V. 71 1307 2007
PubMed-ID: 18041758 | Reference-DOI: 10.1002/PROT.21837

Molecule 1 - GLYCOGEN PHOSPHORYLASE, MUSCLE FORM
	Chains	:	A
	EC Number	:	2.4.1.1
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	MYOPHOSPHORYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 12)

No.	Name	Count	Type	Full Name
1	DL8	1	Ligand/Ion	N-[(4-PHENYL-1H-1,2,3-TRIAZOL-1-YL)ACETYL]-BETA-D-GLUCOPYRANOSYLAMINE
2	DMS	10	Ligand/Ion	DIMETHYL SULFOXIDE
3	LLP	1	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

Biological Unit 1 (3, 24)

No.	Name	Count	Type	Full Name
1	DL8	2	Ligand/Ion	N-[(4-PHENYL-1H-1,2,3-TRIAZOL-1-YL)ACETYL]-BETA-D-GLUCOPYRANOSYLAMINE
2	DMS	20	Ligand/Ion	DIMETHYL SULFOXIDE
3	LLP	2	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

Biological Unit 2 (3, 12)

No.	Name	Count	Type	Full Name
1	DL8	1	Ligand/Ion	N-[(4-PHENYL-1H-1,2,3-TRIAZOL-1-YL)ACETYL]-BETA-D-GLUCOPYRANOSYLAMINE
2	DMS	10	Ligand/Ion	DIMETHYL SULFOXIDE
3	LLP	1	Mod. Amino Acid	(2S)-2-AMINO-6-[[3-HYDROXY-2-METHYL-5-(PHOSPHONOOXYMETHYL)PYRIDIN-4-YL]METHYLIDENEAMINO]HEXANOIC ACID

Asymmetric Unit (11, 11)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:136 , ASN A:282 , ASP A:283 , ASN A:284 , PHE A:286 , ASP A:339 , HIS A:341 , HIS A:377 , ALA A:383 , ASN A:484 , TYR A:573 , GLU A:672 , ALA A:673 , SER A:674 , GLY A:675 , HOH A:1042 , HOH A:1166 , HOH A:1266 , HOH A:1413 , HOH A:1685	BINDING SITE FOR RESIDUE DL8 A 998
02	AC2	SOFTWARE	TRP A:67 , ILE A:68 , ARG A:193	BINDING SITE FOR RESIDUE DMS A 931
03	AC3	SOFTWARE	GLN A:219 , LYS A:294	BINDING SITE FOR RESIDUE DMS A 936
04	AC4	SOFTWARE	HIS A:201 , TRP A:215 , ARG A:351 , LEU A:356 , HOH A:1067	BINDING SITE FOR RESIDUE DMS A 937
05	AC5	SOFTWARE	ARG A:519 , GLU A:701 , GLU A:702 , ALA A:703 , GLY A:704 , HOH A:1153	BINDING SITE FOR RESIDUE DMS A 938
06	AC6	SOFTWARE	GLU A:706 , PHE A:708 , PHE A:709 , ARG A:786 , HOH A:1743	BINDING SITE FOR RESIDUE DMS A 939
07	AC7	SOFTWARE	ARG A:66 , LEU A:102 , ARG A:234 , ASN A:236 , ARG A:833 , HOH A:1104	BINDING SITE FOR RESIDUE DMS A 940
08	AC8	SOFTWARE	TYR A:548 , GLU A:552 , TYR A:553 , ARG A:649 , HOH A:1321 , HOH A:1700	BINDING SITE FOR RESIDUE DMS A 942
09	AC9	SOFTWARE	GLN A:264 , LEU A:267 , ASP A:268 , ASN A:270 , LEU A:271 , ASN A:274	BINDING SITE FOR RESIDUE DMS A 945
10	BC1	SOFTWARE	TYR A:553 , PHE A:644 , LEU A:645 , GLU A:646 , HOH A:1120	BINDING SITE FOR RESIDUE DMS A 946
11	BC2	SOFTWARE	LEU A:271 , ASN A:274 , HOH A:1605	BINDING SITE FOR RESIDUE DMS A 972

(no "SS Bond" information available for 2PYI)

(no "Cis Peptide Bond" information available for 2PYI)

(no "SAP(SNP)/Variant" information available for 2PYI)

Asymmetric Unit (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHORYLASE	PS00102	Phosphorylase pyridoxal-phosphate attachment site.	PYGM_RABIT	673-685	1	A:672-684

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHORYLASE	PS00102	Phosphorylase pyridoxal-phosphate attachment site.	PYGM_RABIT	673-685	2	A:672-684

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PHOSPHORYLASE	PS00102	Phosphorylase pyridoxal-phosphate attachment site.	PYGM_RABIT	673-685	1	A:672-684

(no "Exon" information available for 2PYI)

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:807
 aligned with PYGM_RABIT | P00489 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:826
                                    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       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760       770       780       790       800       810       820       830      
           PYGM_RABIT    11 RKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLP 836
               SCOP domains d2pyia_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pyiA01 A:10-485,A:813-835 Glycogen Phosphorylase B;                                                                                                                                                                                                                                                                                                                                                                                                                                        2pyiA02 A:486-812 Glycogen Phosphorylase B;                                                                                                                                                                                                                                                                                            2pyiA01                 CATH domains
               Pfam domains -----------------------------------------------------------------------------------------------------Phosphorylase-2pyiA01 A:111-829                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ------ Pfam domains
         Sec.struct. author ...hhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeee.hhhhhhhhh.hhhhhhhhhhhh..hhhhhhh....eee..hhhhhhhhhhhhhhhhh...eeeeee.......eeeee..eeeee............ee.hhhheeeee..eeee....eeee..eeeeeeeeeeeee......eeeeeeeeee...----------hhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhhhhhhhhh..---------hhhhhhhheeeeee.....hhhhhhhhhhhhh...hhhhhhhhhhhheeee....hhhhh.eeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.ee.....eeehhhhhhhh..eeee.hhhhhhhhhhh.hhhhhhhh...eee..............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeeee.......hhhhhhhhhhhhhhhhhhh.......eeeeee......hhhhhhhhhhhhhhhhhhh....hhh.eeeeee...hhhhhhhhhhhh.eeee..........hhhhhhhhh..eeee....hhhhhhhhhhhhhhee...hhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHORYLASE------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pyi A  10 RKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPN----------GYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSK---------NFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMkFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLP 835
                                    19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249|        - |     269       279       289       299       309     |   -     | 329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609       619       629       639       649       659       669       679|      689       699       709       719       729       739       749       759       769       779       789       799       809       819       829      
                                                                                                                                                                                                                                                                          250        261                                                   315       325                                                                                                                                                                                                                                                                                                                                                                680-LLP

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

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

Fold: UDP-Glycosyltransferase/glycogen phosphorylase (296)

Superfamily: UDP-Glycosyltransferase/glycogen phosphorylase (296)

Family: Oligosaccharide phosphorylase (199)

Protein domain: automated matches (106)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (99)

d2pyia_

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: Glycogen Phosphorylase B; (202)

Rabbit (Oryctolagus cuniculus) (113)

1a	2pyiA02	A:486-812
1b	2pyiA01	A:10-485,A:813-835

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-B (132)

Family: Phosphorylase (83)

Oryctolagus cuniculus (Rabbit) (71)

Phosphorylase-2pyiA01

A:111-829

Asymmetric Unit(hide GO term definitions)

Chain A (PYGM_RABIT | P00489)

molecular function
	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:0008184	glycogen phosphorylase activity	Catalysis of the reaction: glycogen + phosphate = maltodextrin + alpha-D-glucose 1-phosphate.
	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:0004645	phosphorylase activity	Catalysis of the reaction: 1,4-alpha-D-glucosyl(n) + phosphate = 1,4-alpha-D-glucosyl(n-1) + alpha-D-glucose 1-phosphate. The name should be qualified in each instance by adding the name of the natural substrate, e.g. maltodextrin phosphorylase, starch phosphorylase, glycogen phosphorylase.
	GO:0030170	pyridoxal phosphate binding	Interacting selectively and non-covalently with pyridoxal 5' phosphate, 3-hydroxy-5-(hydroxymethyl)-2-methyl4-pyridine carboxaldehyde 5' phosphate, the biologically active form of vitamin B6.
	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.
	GO:0016757	transferase activity, transferring glycosyl groups	Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
biological process
	GO:0005975	carbohydrate metabolic process	The chemical reactions and pathways involving carbohydrates, any of a group of organic compounds based of the general formula Cx(H2O)y. Includes the formation of carbohydrate derivatives by the addition of a carbohydrate residue to another molecule.
	GO:0005977	glycogen metabolic process	The chemical reactions and pathways involving glycogen, a polydisperse, highly branched glucan composed of chains of D-glucose residues in alpha-(1->4) glycosidic linkage, joined together by alpha-(1->6) glycosidic linkages.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.

Asymmetric Unit
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	2pyi
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2pyd	SAME PROTEIN WITH GLUCOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (11, 11)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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