Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

3G25

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0004370	molecular_function	glycerol kinase activity
A	0005524	molecular_function	ATP binding
A	0005829	cellular_component	cytosol
A	0005975	biological_process	carbohydrate metabolic process
A	0006071	biological_process	glycerol metabolic process
A	0006072	biological_process	glycerol-3-phosphate metabolic process
A	0016301	molecular_function	kinase activity
A	0016740	molecular_function	transferase activity
A	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
A	0019563	biological_process	glycerol catabolic process
B	0000166	molecular_function	nucleotide binding
B	0004370	molecular_function	glycerol kinase activity
B	0005524	molecular_function	ATP binding
B	0005829	cellular_component	cytosol
B	0005975	biological_process	carbohydrate metabolic process
B	0006071	biological_process	glycerol metabolic process
B	0006072	biological_process	glycerol-3-phosphate metabolic process
B	0016301	molecular_function	kinase activity
B	0016740	molecular_function	transferase activity
B	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
B	0019563	biological_process	glycerol catabolic process
C	0000166	molecular_function	nucleotide binding
C	0004370	molecular_function	glycerol kinase activity
C	0005524	molecular_function	ATP binding
C	0005829	cellular_component	cytosol
C	0005975	biological_process	carbohydrate metabolic process
C	0006071	biological_process	glycerol metabolic process
C	0006072	biological_process	glycerol-3-phosphate metabolic process
C	0016301	molecular_function	kinase activity
C	0016740	molecular_function	transferase activity
C	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
C	0019563	biological_process	glycerol catabolic process
D	0000166	molecular_function	nucleotide binding
D	0004370	molecular_function	glycerol kinase activity
D	0005524	molecular_function	ATP binding
D	0005829	cellular_component	cytosol
D	0005975	biological_process	carbohydrate metabolic process
D	0006071	biological_process	glycerol metabolic process
D	0006072	biological_process	glycerol-3-phosphate metabolic process
D	0016301	molecular_function	kinase activity
D	0016740	molecular_function	transferase activity
D	0016773	molecular_function	phosphotransferase activity, alcohol group as acceptor
D	0019563	biological_process	glycerol catabolic process

Functional Information from PDB Data

site_id	AC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL A 499

Chain	Residue
A	ARG82
A	GLU83
A	TRP102
A	TYR134
A	ASP244
A	GLN245
A	PHE269
A	NA500
A	PO4502

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA A 500

Chain	Residue
A	THR266
A	GLY267
A	PHE269
A	GOL499
A	PO4502

site_id	AC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA A 501

Chain	Residue
A	GLN22
A	PHE452
A	PO4505

site_id	AC4
Number of Residues	10
Details	BINDING SITE FOR RESIDUE PO4 A 502

Chain	Residue
A	GLY11
A	THR12
A	ASP244
A	GLY265
A	THR266
A	GOL499
A	NA500
A	HOH592
A	HOH599
A	HOH671

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE PO4 A 503

Chain	Residue
A	TYR331
A	LYS372
A	HOH669
B	ARG320
B	NA501

site_id	AC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 A 504

Chain	Residue
A	SER337
A	THR338
A	ARG377
A	GLU381
A	PHE420
A	LEU481
A	HOH579
A	HOH595

site_id	AC7
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 A 505

Chain	Residue
A	GLN22
A	TRP453
A	GLU454
A	SER455
A	ASP458
A	NA501
C	LYS23

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 A 506

Chain	Residue
A	LYS171
A	GLY174
A	TYR229
A	HIS230

site_id	AC9
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL B 499

Chain	Residue
B	ARG82
B	GLU83
B	TRP102
B	TYR134
B	ASP244
B	GLN245
B	PHE269
B	PO4503
B	HOH663

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 500

Chain	Residue
B	THR12
B	THR13
B	PO4503

site_id	BC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE NA B 501

Chain	Residue
A	PO4503

site_id	BC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA B 502

Chain	Residue
B	LYS171
B	LYS175
B	PO4504

site_id	BC4
Number of Residues	9
Details	BINDING SITE FOR RESIDUE PO4 B 503

Chain	Residue
B	GLY11
B	THR12
B	GLY265
B	THR266
B	GOL499
B	NA500
B	HOH575
B	HOH620
B	HOH663

site_id	BC5
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 B 504

Chain	Residue
B	LYS171
B	GLY174
B	LYS175
B	TYR229
B	HIS230
B	NA502

site_id	BC6
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 B 505

Chain	Residue
B	SER337
B	THR338
B	ARG377
B	GLU381
B	PHE420
B	LEU481
B	HOH671
B	HOH957

site_id	BC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE PO4 B 506

Chain	Residue
A	ARG320
B	TYR331
B	LYS372
B	HOH632
B	HOH876
B	HOH1115

site_id	BC8
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL C 499

Chain	Residue
C	TRP102
C	TYR134
C	ASP244
C	GLN245
C	PHE269
C	PO4500
C	GLN81
C	ARG82
C	GLU83

site_id	BC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 C 500

Chain	Residue
C	THR12
C	THR13
C	GLY265
C	THR266
C	GOL499
C	HOH598
C	HOH1083

site_id	CC1
Number of Residues	9
Details	BINDING SITE FOR RESIDUE GOL D 499

Chain	Residue
D	GLN81
D	ARG82
D	GLU83
D	TRP102
D	TYR134
D	ASP244
D	GLN245
D	PHE269
D	PO4502

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE NA D 500

Chain	Residue
D	THR12
D	THR13
D	SER14
D	ARG16
D	PO4502

site_id	CC3
Number of Residues	3
Details	BINDING SITE FOR RESIDUE NA D 501

Chain	Residue
C	LYS372
D	ARG320
D	PO4504

site_id	CC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 D 502

Chain	Residue
D	THR12
D	GLY265
D	THR266
D	GOL499
D	NA500
D	HOH842
D	HOH1108

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 D 503

Chain	Residue
C	ARG320
D	TYR331
D	LYS372
D	HOH965

site_id	CC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PO4 D 504

Chain	Residue
C	TYR331
C	LYS372
D	ARG320
D	NA501

Functional Information from PROSITE/UniProt

site_id	PS00445
Number of Residues	21
Details	FGGY_KINASES_2 FGGY family of carbohydrate kinases signature 2. GaIFGLtrgteke.HFIRATLE

Chain	Residue	Details
A	GLY361-GLU381

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	44
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00186","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00186","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"2.7 Angstrom crystal structure of glycerol kinase (glpk) from Staphylococcus aureus in complex with ADP and glycerol.","authoringGroup":["Center for structural genomics of infectious diseases (CSGID)"]}},{"source":"PDB","id":"3GE1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_00186","evidenceCode":"ECO:0000255"},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"JAN-2009","submissionDatabase":"PDB data bank","title":"1.9 Angstrom crystal structure of glycerol kinase (glpk) from Staphylococcus aureus in complex with glycerol.","authoringGroup":["Center for structural genomics of infectious diseases (CSGID)"]}},{"source":"Reference","evidenceCode":"ECO:0000269","citation":{"citationType":"submission","publicationDate":"FEB-2009","submissionDatabase":"PDB data bank","title":"2.7 Angstrom crystal structure of glycerol kinase (glpk) from Staphylococcus aureus in complex with ADP and glycerol.","authoringGroup":["Center for structural genomics of infectious diseases (CSGID)"]}},{"source":"PDB","id":"3G25","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3GE1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	4
Details	Modified residue: {"description":"Phosphohistidine; by HPr","evidences":[{"source":"HAMAP-Rule","id":"MF_00186","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)