1P29 - JenaLib

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Biol. Unit 1 - sites (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF GLYCOGEN PHOSPHORYLASE B IN COMPLEX WITH MALTOPENTAOSE

Authors :   N. Pinotsis, D. D. Leonidas, E. D. Chrysina, N. G. Oikonomakos, I. M. Mav

Date :   15 Apr 03 (Deposition) - 02 Sep 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Pinotsis, D. D. Leonidas, E. D. Chrysina, N. G. Oikonomakos, I. M. Mavridis
The Binding Of Beta- And Gamma-Cyclodextrins To Glycogen Phosphorylase B: Kinetic And Crystallographic Studies.
Protein Sci. V. 12 1914 2003
PubMed-ID: 12930991 | Reference-DOI: 10.1110/PS.03149503

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	:	GLYCOGEN PHOSPHORYLASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	GLC	5	Ligand/Ion	ALPHA-D-GLUCOSE
2	PLP	1	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Biological Unit 1 (2, 12)

No.	Name	Count	Type	Full Name
1	GLC	10	Ligand/Ion	ALPHA-D-GLUCOSE
2	PLP	2	Ligand/Ion	PYRIDOXAL-5'-PHOSPHATE

Asymmetric Unit (6, 6)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:426 , GLC A:844 , HOH A:1065	BINDING SITE FOR RESIDUE GLC A 843
2	AC2	SOFTWARE	LEU A:411 , ARG A:426 , SER A:429 , VAL A:431 , GLU A:433 , GLC A:843 , GLC A:845 , HOH A:1067	BINDING SITE FOR RESIDUE GLC A 844
3	AC3	SOFTWARE	TYR A:404 , ASN A:407 , GLU A:433 , LYS A:437 , GLC A:844 , GLC A:846	BINDING SITE FOR RESIDUE GLC A 845
4	AC4	SOFTWARE	TYR A:404 , GLU A:405 , GLC A:845 , GLC A:847 , HOH A:1294	BINDING SITE FOR RESIDUE GLC A 846
5	AC5	SOFTWARE	GLU A:405 , GLC A:846	BINDING SITE FOR RESIDUE GLC A 847
6	AC6	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:1047 , HOH A:1048 , HOH A:1050 , HOH A:1051 , HOH A:1088 , HOH A:1089 , HOH A:1091	BINDING SITE FOR RESIDUE PLP A 999

(no "SS Bond" information available for 1P29)

(no "Cis Peptide Bond" information available for 1P29)

(no "SAP(SNP)/Variant" information available for 1P29)

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 1P29)

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:809
 aligned with PYGM_RABIT | P00489 from UniProtKB/Swiss-Prot  Length:843

    Alignment length:825
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602       612       622       632       642       652       662       672       682       692       702       712       722       732       742       752       762       772       782       792       802       812       822       832     
           PYGM_RABIT    13 QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPNDFNLKDFNVGGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSSKFGCRDPVRTNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPA 837
               SCOP domains d1p29a_ A: Glycogen phosphorylase                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1p29A01 A:12-485,A:813-833 Glycogen Phosphorylase B;                                                                                                                                                                                                                                                                                                                                                                                                                                      1p29A02 A:486-812 Glycogen Phosphorylase B;                                                                                                                                                                                                                                                                                            1p29A01              --- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------Phosphorylase-1p29A01 A:111-829                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                ------- Pfam domains
         Sec.struct. author .hhhhh..hhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..eeeee...eeee.hhhhhhhhhhhhhhhhhhhhhh..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.hhhhhhhhhhhhhhhhhhhhhhhhhh.........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
                 1p29 A  12 QISVRGLAGVENVTELKKNFNRHLHFTLVKDRNVATPRDYYFALAHTVRDHLVGRWIRTQQHYYEKDPKRIYYLSLEFYMGRTLQNTMVNLALENACDEATYQLGLDMEELEEIEEDAGLGNGGLGRLAACFLDSMATLGLAAYGYGIRYEFGIFNQKICGGWQMEEADDWLRYGNPWEKARPEFTLPVHFYGRVEHTSQGAKWVDTQVVLAMPYDTPVPGYRNNVVNTMRLWSAKAPND--L-----GGYIQAVLDRNLAENISRVLYPNDNFFEGKELRLKQEYFVVAATLQDIIRRFKSS---------TNFDAFPDKVAIQLNDTHPSLAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVIPEALERWPVHLLETLLPRHLQIIYEINQRFLNRVAAAFPGDVDRLRRMSLVEEGAVKRINMAHLCIAGSHAVNGVARIHSEILKKTIFKDFYELEPHKFQNKTNGITPRRWLVLCNPGLAEIIAERIGEEYISDLDQLRKLLSYVDDEAFIRDVAKVKQENKLKFAAYLEREYKVHINPNSLFDVQVKRIHEYKRQLLNCLHVITLYNRIKKEPNKFVVPRTVMIGGKAAPGYHMAKMIIKLITAIGDVVNHDPVVGDRLRVIFLENYRVSLAEKVIPAADLSEQISTAGTEASGTGNMKFMLNGALTIGTMDGANVEMAEEAGEENFFIFGMRVEDVDRLDQRGYNAQEYYDRIPELRQIIEQLSSGFFSPKQPDLFKDIVNMLMHHDRFKVFADYEEYVKCQERVSALYKNPREWTRMVIRNIATSGKFSSDRTIAQYAREIWGVEPSRQRLPA 836
                                    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  |      -  |    331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531       541       551       561       571       581       591       601       611       621       631       641       651       661       671       681       691       701       711       721       731       741       751       761       771       781       791       801       811       821       831     
                                                                                                                                                                                                                                                                         251  |   260                                                   314       324                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                                                                                                                                                                                                                            254

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: Glycogen phosphorylase (86)

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

d1p29a_

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	1p29A02	A:486-812
1b	1p29A01	A:12-485,A:813-833

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-B (132)

Family: Phosphorylase (83)

Oryctolagus cuniculus (Rabbit) (71)

Phosphorylase-1p29A01

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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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1p29)

Biological Unit
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	1p29
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	PYGM_RABIT \| P00489
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	2.4.1.1
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1p2b	THE SAME PROTEIN COMPLEXED WITH MALTOHEPTAOSE
1p2d	THE SAME PROTEIN COMPLEXED WITH BETA CYCLODEXTRIN
1p2g	THE SAME PROTEIN COMPLEXED WITH GAMMA CYCLODEXTRIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 6)

Sites (6, 6)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 1)

Exons (0, 0)

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SCOP Domains (1, 1)

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Gene Ontology (10, 10)

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