1LWO - JenaLib

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Title :   CRYSTAL STRUCTURE OF RABBIT MUSCLE GLYCOGEN PHOSPHORYLASE A IN COMPLEX WITH A POTENTIAL HYPOGLYCAEMIC DRUG AT 2.0 A RESOLUTION

Authors :   N. G. Oikonomakos, E. D. Chrysina, M. N. Kosmopoulou, D. D. Leonidas

Date :   01 Jun 02 (Deposition) - 19 Jun 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Type 2 Diabetes, Glycogen Phosphorylase, Inhibitor, New Allosteric Site, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. G. Oikonomakos, E. D. Chrysina, M. N. Kosmopoulou, D. D. Leonidas
Crystal Structure Of Rabbit Muscle Glycogen Phosphorylase A In Complex With A Potential Hypoglycaemic Drug At 2. 0 A Resolution
Biochem. Biophys. Acta V. 1647 325 2003 Proteins & Proteomics
PubMed-ID: 12686153 | Reference-DOI: 10.1016/S1570-9639(03)00085-2
(for further references see the PDB file header)

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

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 4)

No.	Name	Count	Type	Full Name
1	CHI	1	Ligand/Ion	5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID [1-(4-FLUOROBENZYL)-2-(4-HYDROXYPIPERIDIN-1YL)-2-OXOETHYL]AMIDE
2	GLC	1	Ligand/Ion	ALPHA-D-GLUCOSE
3	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 1 (4, 8)

No.	Name	Count	Type	Full Name
1	CHI	2	Ligand/Ion	5-CHLORO-1H-INDOLE-2-CARBOXYLIC ACID [1-(4-FLUOROBENZYL)-2-(4-HYDROXYPIPERIDIN-1YL)-2-OXOETHYL]AMIDE
2	GLC	2	Ligand/Ion	ALPHA-D-GLUCOSE
3	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE
4	SEP	2	Mod. Amino Acid	PHOSPHOSERINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:135 , LEU A:136 , ASN A:284 , HIS A:377 , ASN A:484 , TYR A:573 , GLU A:672 , ALA A:673 , SER A:674 , GLY A:675 , HOH A:1039 , HOH A:1093 , HOH A:1163 , HOH A:1262	BINDING SITE FOR RESIDUE GLC A 998
2	AC2	SOFTWARE	TRP A:491 , LYS A:568 , LYS A:574 , TYR A:648 , ARG A:649 , VAL A:650 , GLY A:675 , THR A:676 , GLY A:677 , LYS A:680 , HOH A:1036 , HOH A:1134 , HOH A:1135 , HOH A:1137 , HOH A:1163	BINDING SITE FOR RESIDUE PLP A 999
3	AC3	SOFTWARE	THR A:38 , VAL A:40 , PHE A:53 , HIS A:57 , ARG A:60 , VAL A:64 , TRP A:67 , GLY A:186 , ASN A:187 , PRO A:188 , TRP A:189 , GLU A:190 , LYS A:191 , PRO A:229 , HOH A:1062 , HOH A:1251	BINDING SITE FOR RESIDUE CHI A 920

(no "SS Bond" information available for 1LWO)

(no "Cis Peptide Bond" information available for 1LWO)

(no "SAP(SNP)/Variant" information available for 1LWO)

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

(no "Exon" information available for 1LWO)

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:815
 aligned with PYGM_RABIT | P00489 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:834
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625       635       645       655       665       675       685       695       705       715       725       735       745       755       765       775       785       795       805       815       825       835    
           PYGM_RABIT     6 SDQEKRKQISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPD 839
               SCOP domains d1lwoa_ A: Glycogen phosphorylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains -----1lwoA01 A:10-485,A:813-835 Glycogen Phosphorylase B;                                                                                                                                                                                                                                                                                                                                                                                                                                        1lwoA02 A:486-812 Glycogen Phosphorylase B;                                                                                                                                                                                                                                                                                            1lwoA01                --- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------Phosphorylase-1lwoA01 A:111-829                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                --------- Pfam domains
         Sec.struct. author ...hhhhh..........hhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee........hhhhhhhhh.hhhhhhhhhhh...hhhhhhh.........hhhhhhhhhhhhhhhhh...eeeeee.......eeeee..eeeee............ee.hhhheeeee..eeeee..eeeee..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...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------PHOSPHORYLASE---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1lwo A   5 SDQEKRKQIsVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPND---------GYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSS----------NFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPAPD 838
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244      |  -      |264       274       284       294       304       314         -|      334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624       634       644       654       664       674       684       694       704       714       724       734       744       754       764       774       784       794       804       814       824       834    
                                    14-SEP                                                                                                                                                                                                                                      251       261                                                  314        325

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(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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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: Glycogen phosphorylase (86)

Rabbit (Oryctolagus cuniculus) [TaxId: 9986] (69)

d1lwoa_

Asymmetric Unit

Classes(

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Architectures( (-)

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Topologies( (-)

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Homologous Superfamilies( (-)

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Organisms( (-)

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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	1lwoA02	A:486-812
1b	1lwoA01	A:10-485,A:813-835

Asymmetric Unit

Clans(

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Families(

)

Organisms( (-)

)

Clan: GT-B (132)

Family: Phosphorylase (83)

Oryctolagus cuniculus (Rabbit) (71)

Phosphorylase-1lwoA01

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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Biological Unit
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	1lwo
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1h5u	1H5U CONTAINS GLYCOGEN PHOSPHORYLAS B COMPLEXED WITH GLUCOSE, AND CP320626, A POTENTIAL ANTIDIABETIC DRUG AT 1.76 A RESOLUTION.
1lwn	1LWN CONTATINS THE SAME PROTEIN COMPLEXED WITH GLUCOSE.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 4)

Sites (3, 3)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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