3G25 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   1.9 ANGSTROM CRYSTAL STRUCTURE OF GLYCEROL KINASE (GLPK) FROM STAPHYLOCOCCUS AUREUS IN COMPLEX WITH GLYCEROL.

Authors :   G. Minasov, T. Skarina, O. Onopriyenko, A. Savchenko, W. F. Anderson, C Structural Genomics Of Infectious Diseases (Csgid)

Date :   30 Jan 09 (Deposition) - 17 Feb 09 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A,B  (1x)
Biol. Unit 2: A,B,C,D  (1x)
Biol. Unit 3: C,D  (1x)

Keywords :   Glycerol Kinase, Glycerol, Idp00743, Atp-Binding, Glycerol Metabolism, Kinase, Nucleotide-Binding, Transferase, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   G. Minasov, T. Skarina, O. Onopriyenko, A. Savchenko, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 9 Angstrom Crystal Structure Of Glycerol Kinase (Glpk) From Staphylococcus Aureus In Complex With Glycerol.
To Be Published
PubMed: search

Molecule 1 - GLYCEROL KINASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.1.30
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMCSG
	Expression System Strain	:	BL21-DE3
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	GLPK, SACOL1320
	Organism Scientific	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL
	Organism Taxid	:	93062
	Strain	:	STAPHYLOCOCCUS AUREUS SUBSP. AUREUS COL

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A	B
Biological Unit 2 (1x)	:	A	B	C	D
Biological Unit 3 (1x)	:			C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 68)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	44	Mod. Amino Acid	SELENOMETHIONINE
3	NA	7	Ligand/Ion	SODIUM ION
4	PO4	13	Ligand/Ion	PHOSPHATE ION

Biological Unit 1 (3, 33)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	9	Ligand/Ion	PHOSPHATE ION

Biological Unit 2 (3, 61)

No.	Name	Count	Type	Full Name
1	GOL	4	Ligand/Ion	GLYCEROL
2	MSE	44	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	13	Ligand/Ion	PHOSPHATE ION

Biological Unit 3 (3, 28)

No.	Name	Count	Type	Full Name
1	GOL	2	Ligand/Ion	GLYCEROL
2	MSE	22	Mod. Amino Acid	SELENOMETHIONINE
3	NA	-1	Ligand/Ion	SODIUM ION
4	PO4	4	Ligand/Ion	PHOSPHATE ION

Asymmetric Unit (24, 24)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:82 , GLU A:83 , TRP A:102 , TYR A:134 , ASP A:244 , GLN A:245 , PHE A:269 , NA A:500 , PO4 A:502	BINDING SITE FOR RESIDUE GOL A 499
02	AC2	SOFTWARE	THR A:266 , GLY A:267 , PHE A:269 , GOL A:499 , PO4 A:502	BINDING SITE FOR RESIDUE NA A 500
03	AC3	SOFTWARE	GLN A:22 , PHE A:452 , PO4 A:505	BINDING SITE FOR RESIDUE NA A 501
04	AC4	SOFTWARE	GLY A:11 , THR A:12 , ASP A:244 , GLY A:265 , THR A:266 , GOL A:499 , NA A:500 , HOH A:592 , HOH A:599 , HOH A:671	BINDING SITE FOR RESIDUE PO4 A 502
05	AC5	SOFTWARE	TYR A:331 , LYS A:372 , HOH A:669 , ARG B:320 , NA B:501	BINDING SITE FOR RESIDUE PO4 A 503
06	AC6	SOFTWARE	SER A:337 , THR A:338 , ARG A:377 , GLU A:381 , PHE A:420 , LEU A:481 , HOH A:579 , HOH A:595	BINDING SITE FOR RESIDUE PO4 A 504
07	AC7	SOFTWARE	GLN A:22 , TRP A:453 , GLU A:454 , SER A:455 , ASP A:458 , NA A:501 , LYS C:23	BINDING SITE FOR RESIDUE PO4 A 505
08	AC8	SOFTWARE	LYS A:171 , GLY A:174 , TYR A:229 , HIS A:230	BINDING SITE FOR RESIDUE PO4 A 506
09	AC9	SOFTWARE	ARG B:82 , GLU B:83 , TRP B:102 , TYR B:134 , ASP B:244 , GLN B:245 , PHE B:269 , PO4 B:503 , HOH B:663	BINDING SITE FOR RESIDUE GOL B 499
10	BC1	SOFTWARE	THR B:12 , THR B:13 , PO4 B:503	BINDING SITE FOR RESIDUE NA B 500
11	BC2	SOFTWARE	PO4 A:503	BINDING SITE FOR RESIDUE NA B 501
12	BC3	SOFTWARE	LYS B:171 , LYS B:175 , PO4 B:504	BINDING SITE FOR RESIDUE NA B 502
13	BC4	SOFTWARE	GLY B:11 , THR B:12 , GLY B:265 , THR B:266 , GOL B:499 , NA B:500 , HOH B:575 , HOH B:620 , HOH B:663	BINDING SITE FOR RESIDUE PO4 B 503
14	BC5	SOFTWARE	LYS B:171 , GLY B:174 , LYS B:175 , TYR B:229 , HIS B:230 , NA B:502	BINDING SITE FOR RESIDUE PO4 B 504
15	BC6	SOFTWARE	SER B:337 , THR B:338 , ARG B:377 , GLU B:381 , PHE B:420 , LEU B:481 , HOH B:671 , HOH B:957	BINDING SITE FOR RESIDUE PO4 B 505
16	BC7	SOFTWARE	ARG A:320 , TYR B:331 , LYS B:372 , HOH B:632 , HOH B:876 , HOH B:1115	BINDING SITE FOR RESIDUE PO4 B 506
17	BC8	SOFTWARE	GLN C:81 , ARG C:82 , GLU C:83 , TRP C:102 , TYR C:134 , ASP C:244 , GLN C:245 , PHE C:269 , PO4 C:500	BINDING SITE FOR RESIDUE GOL C 499
18	BC9	SOFTWARE	THR C:12 , THR C:13 , GLY C:265 , THR C:266 , GOL C:499 , HOH C:598 , HOH C:1083	BINDING SITE FOR RESIDUE PO4 C 500
19	CC1	SOFTWARE	GLN D:81 , ARG D:82 , GLU D:83 , TRP D:102 , TYR D:134 , ASP D:244 , GLN D:245 , PHE D:269 , PO4 D:502	BINDING SITE FOR RESIDUE GOL D 499
20	CC2	SOFTWARE	THR D:12 , THR D:13 , SER D:14 , ARG D:16 , PO4 D:502	BINDING SITE FOR RESIDUE NA D 500
21	CC3	SOFTWARE	LYS C:372 , ARG D:320 , PO4 D:504	BINDING SITE FOR RESIDUE NA D 501
22	CC4	SOFTWARE	THR D:12 , GLY D:265 , THR D:266 , GOL D:499 , NA D:500 , HOH D:842 , HOH D:1108	BINDING SITE FOR RESIDUE PO4 D 502
23	CC5	SOFTWARE	ARG C:320 , TYR D:331 , LYS D:372 , HOH D:965	BINDING SITE FOR RESIDUE PO4 D 503
24	CC6	SOFTWARE	TYR C:331 , LYS C:372 , ARG D:320 , NA D:501	BINDING SITE FOR RESIDUE PO4 D 504

(no "SS Bond" information available for 3G25)

Asymmetric Unit

No.	Residues
1	Thr A:352	-	Pro A:353
2	Thr B:352	-	Pro B:353
3	Thr C:352	-	Pro C:353
4	Thr D:352	-	Pro D:353

(no "SAP(SNP)/Variant" information available for 3G25)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_STAAC	361-381	4	A:361-381 B:361-381 C:361-381 D:361-381

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_STAAC	361-381	2	A:361-381 B:361-381 - -

Biological Unit 2 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_STAAC	361-381	4	A:361-381 B:361-381 C:361-381 D:361-381

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	FGGY_KINASES_2	PS00445	FGGY family of carbohydrate kinases signature 2.	GLPK_STAAC	361-381	2	- - C:361-381 D:361-381

(no "Exon" information available for 3G25)

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:499
 aligned with GLPK_STAAC | Q5HGD2 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:499
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489         
           GLPK_STAAC     - -MEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVMTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLMFNIHDLEWDDELLELLTVPKNMLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFMLMNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRMINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVMEAMSKDSGIDVQSLRVDGGAVKNNFIMQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKMDEGEREKLYRGWKKAVEATQVFKTE 498
               SCOP domains d3g25a1 A:0-252 automated matches                                                                                                                                                                                                                            d3g25a2 A:253-498 automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains 3g25A01 A:0-252  [code=3.30.420.40, no name defined]                                                                                                                                                                                                         3g25A02 A:253-498  [code=3.30.420.40, no name defined]                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeeehhhhhhhhhh.....eeehhhhh....ee....eehhhhhhhhh.hhhhh.eee..eeeeee.hhhhh.....eeeeeeehhhhhhhhh.......eeeee...eeeeee............eeeeeeee..eeeeeeeeee...hhhhhhhhhh.....hhhhhhhhhh........eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh.....hhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g25 A   0 AmEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVmTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLmFNIHDLEWDDELLELLTVPKNmLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFmLmNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRmINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVmEAmSKDSGIDVQSLRVDGGAVKNNFImQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKmDEGEREKLYRGWKKAVEATQVFKTE 498
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189|      199       209  |    219       229       239       249       259       269| |    279       289       299       309       319 |     329       339       349       359       369       379       389 |  |  399       409       419       429       439       449       459       469   |   479       489         
                             |                                                        59-MSE                                                                                                                            190-MSE               212-MSE                                                   270-MSE                                            321-MSE                                                               391-MSE                    418-MSE                                                473-MSE                     
                             1-MSE                                                                                                                                                                                                                                                                        272-MSE                                                                                                                   394-MSE

Chain B from PDB  Type:PROTEIN  Length:499
 aligned with GLPK_STAAC | Q5HGD2 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:499
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489         
           GLPK_STAAC     - -MEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVMTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLMFNIHDLEWDDELLELLTVPKNMLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFMLMNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRMINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVMEAMSKDSGIDVQSLRVDGGAVKNNFIMQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKMDEGEREKLYRGWKKAVEATQVFKTE 498
               SCOP domains d3g25b1 B:0-252 automated matches                                                                                                                                                                                                                            d3g25b2 B:253-498 automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeeehhhhhhhhhh.....eeehhhhh....ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhh.....eeeeeeehhhhhhhhh.......eeeee...eeeeee............eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.....hhhhhhhhhhh.......eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeehhhhhhhhhhhhhhhhhh..eeee...hhhhhhhhhhhhhhh.....hhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g25 B   0 AmEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVmTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLmFNIHDLEWDDELLELLTVPKNmLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFmLmNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRmINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVmEAmSKDSGIDVQSLRVDGGAVKNNFImQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKmDEGEREKLYRGWKKAVEATQVFKTE 498
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189|      199       209  |    219       229       239       249       259       269| |    279       289       299       309       319 |     329       339       349       359       369       379       389 |  |  399       409       419       429       439       449       459       469   |   479       489         
                             1-MSE                                                    59-MSE                                                                                                                            190-MSE               212-MSE                                                   270-MSE                                            321-MSE                                                               391-MSE                    418-MSE                                                473-MSE                     
                                                                                                                                                                                                                                                                                                          272-MSE                                                                                                                   394-MSE

Chain C from PDB  Type:PROTEIN  Length:498
 aligned with GLPK_STAAC | Q5HGD2 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:498
                                    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        
           GLPK_STAAC     1 MEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVMTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLMFNIHDLEWDDELLELLTVPKNMLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFMLMNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRMINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVMEAMSKDSGIDVQSLRVDGGAVKNNFIMQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKMDEGEREKLYRGWKKAVEATQVFKTE 498
               SCOP domains d3g25c1 C:1-252 automated matches                                                                                                                                                                                                                           d3g25c2 C:253-498 automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhh...hhh.eeeeeeee....eeeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhh...eeeeehhhhhhhhhh.....eeehhhhh....ee....eehhhhhhhh..hhhhh.eee..eeeeee.hhhhh.....eeeeeeehhhhhhhhh.......eeeee...eeeeee............eeeeeeee..eeeeeeeeee..hhhhhhhhhhh.....hhhhhhhhhh........eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh.....hhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3g25 C   1 mEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVmTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLmFNIHDLEWDDELLELLTVPKNmLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFmLmNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRmINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVmEAmSKDSGIDVQSLRVDGGAVKNNFImQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKmDEGEREKLYRGWKKAVEATQVFKTE 498
                            |       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        
                            1-MSE                                                    59-MSE                                                                                                                            190-MSE               212-MSE                                                   270-MSE                                            321-MSE                                                               391-MSE                    418-MSE                                                473-MSE                     
                                                                                                                                                                                                                                                                                                         272-MSE                                                                                                                   394-MSE

Chain D from PDB  Type:PROTEIN  Length:499
 aligned with GLPK_STAAC | Q5HGD2 from UniProtKB/Swiss-Prot  Length:498

    Alignment length:499
                             1                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489         
           GLPK_STAAC     - -MEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVMTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLMFNIHDLEWDDELLELLTVPKNMLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFMLMNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRMINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVMEAMSKDSGIDVQSLRVDGGAVKNNFIMQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKMDEGEREKLYRGWKKAVEATQVFKTE 498
               SCOP domains d3g25d1 D:0-252 automated matches                                                                                                                                                                                                                            d3g25d2 D:253-498 automated matches                                                                                                                                                                                                                    SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeee.....eeeeeeee...........eehhhhhhhhhhhhhhhhhhhh..hhh.eeeeeeee.....eeee.........ee......hhhhhhhhhhh.hhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhh..eeeehhhhhhhhhhh.....eeehhhhh....ee....eehhhhhhhhh.hhhhh.eee..eeeeee.hhhhh.....eeeeeeehhhhhhhhh.......eeeee...eeeeee............eeeeeeee..eeeeeeeeee..hhhhhhhhhhh........hhhhhhhhh......eee................eeeeee....hhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeeehhhhhhhhhhhhhhhhhh.eeeee...hhhhhhhhhhhhhhh.....hhhhhhhh.eeeee....hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------FGGY_KINASES_2       --------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3g25 D   0 AmEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVmTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLmFNIHDLEWDDELLELLTVPKNmLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFmLmNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRmINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVmEAmSKDSGIDVQSLRVDGGAVKNNFImQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKmDEGEREKLYRGWKKAVEATQVFKTE 498
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189|      199       209  |    219       229       239       249       259       269| |    279       289       299       309       319 |     329       339       349       359       369       379       389 |  |  399       409       419       429       439       449       459       469   |   479       489         
                             1-MSE                                                    59-MSE                                                                                                                            190-MSE               212-MSE                                                   270-MSE                                            321-MSE                                                               391-MSE                    418-MSE                                                473-MSE                     
                                                                                                                                                                                                                                                                                                          272-MSE                                                                                                                   394-MSE

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: Ribonuclease H-like motif (1424)

Superfamily: Actin-like ATPase domain (426)

Family: automated matches (111)

Protein domain: automated matches (111)

Staphylococcus aureus [TaxId: 93062] (2)

1a	d3g25a1	A:0-252
1b	d3g25a2	A:253-498
1c	d3g25b1	B:0-252
1d	d3g25b2	B:253-498
1e	d3g25c1	C:1-252
1f	d3g25c2	C:253-498
1g	d3g25d1	D:0-252
1h	d3g25d2	D:253-498

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: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.40, no name defined] (217)

Aureus col (Staphylococcus aureus subsp) (1)

1a	3g25A02	A:253-498
1b	3g25A01	A:0-252

(no "Pfam Domain" information available for 3G25)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (GLPK_STAAC | Q5HGD2)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004370	glycerol kinase activity	Catalysis of the reaction: ATP + glycerol = sn-glycerol 3-phosphate + ADP + 2 H(+).
	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:0016773	phosphotransferase activity, alcohol group as acceptor	Catalysis of the transfer of a phosphorus-containing group from one compound (donor) to an alcohol group (acceptor).
	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: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:0019563	glycerol catabolic process	The chemical reactions and pathways resulting in the breakdown of glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0006071	glycerol metabolic process	The chemical reactions and pathways involving glycerol, 1,2,3-propanetriol, a sweet, hygroscopic, viscous liquid, widely distributed in nature as a constituent of many lipids.
	GO:0006072	glycerol-3-phosphate metabolic process	The chemical reactions and pathways involving glycerol-3-phosphate, a phosphoric monoester of glycerol.
	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.

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		Thr D:352 - Pro D:353	[ RasMol ]

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	3g25
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	2.7.1.30
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	GLPK_STAAC \| Q5HGD2	:	3ge1

(no "Related Entries Specified in the PDB File" available for 3G25)

Description

Compounds

Structural Features

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Ligands, Modified Residues, Ions (4, 68)

Sites (24, 24)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

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