3PMG - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   STRUCTURE OF RABBIT MUSCLE PHOSPHOGLUCOMUTASE AT 2.4 ANGSTROMS RESOLUTION. USE OF FREEZING POINT DEPRESSANT AND REDUCED TEMPERATURE TO ENHANCE DIFFRACTIVITY

Authors :   W. J. Ray Junior, Y. Liu, S. Baranidharan

Date :   02 Mar 95 (Deposition) - 07 Dec 95 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.40

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

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

Reference :   Y. Liu, W. J. Ray, S. Baranidharan
Structure Of Rabbit Muscle Phosphoglucomutase Refined At 2. 4 A Resolution.
Acta Crystallogr. , Sect. D V. 53 392 1997
PubMed-ID: 15299905 | Reference-DOI: 10.1107/S0907444997000875
(for further references see the PDB file header)

Molecule 1 - ALPHA-D-GLUCOSE-1,6-BISPHOSPHATE
	Chains	:	A, B
	EC Number	:	5.4.2.2
	Organism Common	:	RABBIT
	Organism Scientific	:	ORYCTOLAGUS CUNICULUS
	Organism Taxid	:	9986
	Synonym	:	PHOSPHOGLUCOMUTASE
	Tissue	:	MUSCLE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	MG	2	Ligand/Ion	MAGNESIUM ION
2	SEP	2	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	MG	-1	Ligand/Ion	MAGNESIUM ION
2	SEP	1	Mod. Amino Acid	PHOSPHOSERINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	SEP A:116 , ASP A:287 , ASP A:289 , ASP A:291 , HOH A:733	BINDING SITE FOR RESIDUE MG A 562
2	AC2	SOFTWARE	SEP B:116 , ASP B:287 , ASP B:289 , ASP B:291 , HOH B:758	BINDING SITE FOR RESIDUE MG B 562
3	MBA	AUTHOR	ASP A:287 , ASP A:289 , ASP A:291 , SEP A:116	METAL BINDING SITE IN MONOMER A
4	MBB	AUTHOR	ASP B:287 , ASP B:289 , ASP B:291 , SEP B:116	METAL BINDING SITE IN MONOMER B

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

(no "Cis Peptide Bond" information available for 3PMG)

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	PGM1_RABIT	111-120	2	A:110-119 B:110-119

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	PGM1_RABIT	111-120	1	- B:110-119

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PGM_PMM	PS00710	Phosphoglucomutase and phosphomannomutase phosphoserine signature.	PGM1_RABIT	111-120	1	A:110-119 -

(no "Exon" information available for 3PMG)

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:561
 aligned with PGM1_RABIT | P00949 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:561
                                    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       501       511       521       531       541       551       561 
           PGM1_RABIT     2 VKIVTVKTKAYPDQKPGTSGLRKRVKVFQSSTNYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWHKFGRNFFTRYDYEEVEAEGATKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYHDPVDGSVSKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDNAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT 562
               SCOP domains d3pmga1 A:1-190 Phosphoglucomutase                                                                                                                                                            d3pmga2 A:191-303 Phosphoglucomutase                                                                             d3pmga3 A:304-420 Phosphoglucomutase                                                                                 d3pmga4 A:421-561 Phosphoglucomutase                                                                                                          SCOP domains
               CATH domains 3pmgA01 A:1-197 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                                                                                                3pmgA02 A:198-300 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                3pmgA03 A:301-400 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                             3pmgA04 A:401-561 Major birch pollen allergen Bet v 1                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.............eeeehhhhhh...hhhhhhhhhhhh..hhh....eeeeee.....hhhhhhhhhhhhhh....eeeeehhh...hhhhhhhhhhh...eeeee...........eeeeeeee.......hhhhhhhhhhhhh..eeee...........eeeee........eeeeee...hhhhhhhh....hhhhhhhhh......eeee......hhhhhhhh.......hhh.........hhh..........hhhhhhhhh....eeeee......eeeeehhh....hhhhhhhhhh.hhh.hhhhhh....eeee.....hhhhhhhh....eeee...hhhhhhhhh.....eeee...eeee.......hhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhhhhhhh.......eeee..eeeeeeeeee................eeeee....eeeeeeee.....eeeeeeeeeee.........hhhhhhhhhhhhhhhh.hhhhh......eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------PGM_PMM   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pmg A   1 VKIVTVKTKAYPDQKPGTSGLRKRVKVFQSSTNYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTAsHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWHKFGRNFFTRYDYEEVEAEGATKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYHDPVDGSVSKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDNAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT 561
                                    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       500       510       520       530       540       550       560 
                                                                                                                                             116-SEP

Chain B from PDB  Type:PROTEIN  Length:561
 aligned with PGM1_RABIT | P00949 from UniProtKB/Swiss-Prot  Length:562

    Alignment length:561
                                    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       501       511       521       531       541       551       561 
           PGM1_RABIT     2 VKIVTVKTKAYPDQKPGTSGLRKRVKVFQSSTNYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTASHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWHKFGRNFFTRYDYEEVEAEGATKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYHDPVDGSVSKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDNAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT 562
               SCOP domains d3pmgb1 B:1-190 Phosphoglucomutase                                                                                                                                                            d3pmgb2 B:191-303 Phosphoglucomutase                                                                             d3pmgb3 B:304-420 Phosphoglucomutase                                                                                 d3pmgb4 B:421-561 Phosphoglucomutase                                                                                                          SCOP domains
               CATH domains 3pmgB01 B:1-197 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                                                                                                                3pmgB02 B:198-300 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                                3pmgB03 B:301-400 Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3                             3pmgB04 B:401-561 Major birch pollen allergen Bet v 1                                                                                                             CATH domains
           Pfam domains (1) ------------PGM_PMM_I-3pmgB07 B:13-157                                                                                                                       ----------------------------------PGM_PMM_II-3pmgB03 B:192-300                                                                                 ----PGM_PMM_III-3pmgB01 B:305-419                                                                                      ---------------------PGM_PMM_IV-3pmgB05 B:441-544                                                                            ----------------- Pfam domains (1)
           Pfam domains (2) ------------PGM_PMM_I-3pmgB08 B:13-157                                                                                                                       ----------------------------------PGM_PMM_II-3pmgB04 B:192-300                                                                                 ----PGM_PMM_III-3pmgB02 B:305-419                                                                                      ---------------------PGM_PMM_IV-3pmgB06 B:441-544                                                                            ----------------- Pfam domains (2)
         Sec.struct. author ...eeee.............eeeehhhhhh...hhhhhhhhhhhh..hhh....eeeeee.....hhhhhhhhhhhhhh....eeeeehhh...hhhhhhhhhhh...eeeee...........eeeeeeee.......hhhhhhhhhhhhh..eeee...........eeeee........eeeeee...hhhhhhhhhh..hhhhhhhhh......eeee....hhhhhhhhhh.......hhh.........hhh..........hhhhhhhh.....eeeee......eeeeehhh....hhhhhhhhhhhhhh.hhhhhh....eeee....hhhhhhhhhh...eeee....hhhhhhhh.....eeee...eeee.......hhhhhhhhhhhhhhh...hhhhhhhhhhhh.eeeeeeeee....hhhhhhhhhhhhhhh........eee....eeeeeeeee................eeeee....eeeeee.........eeeeeeeee.........hhhhhhhhhhhhhhhh.hhhhh......eee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------PGM_PMM   ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3pmg B   1 VKIVTVKTKAYPDQKPGTSGLRKRVKVFQSSTNYAENFIQSIISTVEPAQRQEATLVVGGDGRFYMKEAIQLIVRIAAANGIGRLVIGQNGILSTPAVSCIIRKIKAIGGIILTAsHNPGGPNGDFGIKFNISNGGPAPEAITDKIFQISKTIEEYAICPDLKVDLGVLGKQQFDLENKFKPFTVEIVDSVEAYATMLRNIFDFNALKELLSGPNRLKIRIDAMHGVVGPYVKKILCEELGAPANSAVNCVPLEDFGGHHPDPNLTYAADLVETMKSGEHDFGAAFDGDGDRNMILGKHGFFVNPSDSVAVIAANIFSIPYFQQTGVRGFARSMPTSGALDRVANATKIALYETPTGWKFFGNLMDASKLSLCGEESFGTGSDHIREKDGLWAVLAWLSILATRKQSVEDILKDHWHKFGRNFFTRYDYEEVEAEGATKMMKDLEALMFDRSFVGKQFSANDKVYTVEKADNFEYHDPVDGSVSKNQGLRLIFADGSRIIFRLSGTGSAGATIRLYIDSYEKDNAKINQDPQVMLAPLISIALKVSQLQERTGRTAPTVIT 561
                                    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       500       510       520       530       540       550       560 
                                                                                                                                             116-SEP

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: TATA-Binding Protein (118)

Homologous Superfamily: Major birch pollen allergen Bet v 1 (22)

Rabbit (Oryctolagus cuniculus) (6)

1a	3pmgA04	A:401-561
1b	3pmgB04	B:401-561

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

Topology: Alpha-D-Glucose-1,6-Bisphosphate; Chain A, domain 3 (24)

Homologous Superfamily: Alpha-D-Glucose-1,6-Bisphosphate, subunit A, domain 3 (24)

Rabbit (Oryctolagus cuniculus) (6)

2a	3pmgA02	A:198-300
2b	3pmgB02	B:198-300
2c	3pmgA03	A:301-400
2d	3pmgB03	B:301-400
2e	3pmgA01	A:1-197
2f	3pmgB01	B:1-197

Asymmetric Unit(hide GO term definitions)

Chain A,B (PGM1_RABIT | P00949)

molecular function
	GO:0016868	intramolecular transferase activity, phosphotransferases	Catalysis of the transfer of a phosphate group from one position to another within a single molecule.
	GO:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0004614	phosphoglucomutase activity	Catalysis of the reaction: alpha-D-glucose 1-phosphate = alpha-D-glucose 6-phosphate.
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:0006006	glucose metabolic process	The chemical reactions and pathways involving glucose, the aldohexose gluco-hexose. D-glucose is dextrorotatory and is sometimes known as dextrose; it is an important source of energy for living organisms and is found free as well as combined in homo- and hetero-oligosaccharides and polysaccharides.
	GO:0071704	organic substance metabolic process	The chemical reactions and pathways involving an organic substance, any molecular entity containing carbon.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0016529	sarcoplasmic reticulum	A fine reticular network of membrane-limited elements that pervades the sarcoplasm of a muscle cell; continuous over large portions of the cell and with the nuclear envelope; that part of the endoplasmic reticulum specialized for calcium release, uptake and storage.

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