Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1K9S

PURINE NUCLEOSIDE PHOSPHORYLASE FROM E. COLI IN COMPLEX WITH FORMYCIN A DERIVATIVE AND PHOSPHATE

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004731	molecular_function	purine-nucleoside phosphorylase activity
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006152	biological_process	purine nucleoside catabolic process
A	0006974	biological_process	DNA damage response
A	0009116	biological_process	nucleoside metabolic process
A	0009164	biological_process	nucleoside catabolic process
A	0016020	cellular_component	membrane
A	0016763	molecular_function	pentosyltransferase activity
A	0019686	biological_process	purine nucleoside interconversion
A	0042278	biological_process	purine nucleoside metabolic process
A	0042802	molecular_function	identical protein binding
A	0047975	molecular_function	guanosine phosphorylase activity
B	0003824	molecular_function	catalytic activity
B	0004731	molecular_function	purine-nucleoside phosphorylase activity
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006152	biological_process	purine nucleoside catabolic process
B	0006974	biological_process	DNA damage response
B	0009116	biological_process	nucleoside metabolic process
B	0009164	biological_process	nucleoside catabolic process
B	0016020	cellular_component	membrane
B	0016763	molecular_function	pentosyltransferase activity
B	0019686	biological_process	purine nucleoside interconversion
B	0042278	biological_process	purine nucleoside metabolic process
B	0042802	molecular_function	identical protein binding
B	0047975	molecular_function	guanosine phosphorylase activity
C	0003824	molecular_function	catalytic activity
C	0004731	molecular_function	purine-nucleoside phosphorylase activity
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006152	biological_process	purine nucleoside catabolic process
C	0006974	biological_process	DNA damage response
C	0009116	biological_process	nucleoside metabolic process
C	0009164	biological_process	nucleoside catabolic process
C	0016020	cellular_component	membrane
C	0016763	molecular_function	pentosyltransferase activity
C	0019686	biological_process	purine nucleoside interconversion
C	0042278	biological_process	purine nucleoside metabolic process
C	0042802	molecular_function	identical protein binding
C	0047975	molecular_function	guanosine phosphorylase activity
D	0003824	molecular_function	catalytic activity
D	0004731	molecular_function	purine-nucleoside phosphorylase activity
D	0005737	cellular_component	cytoplasm
D	0005829	cellular_component	cytosol
D	0006139	biological_process	nucleobase-containing compound metabolic process
D	0006152	biological_process	purine nucleoside catabolic process
D	0006974	biological_process	DNA damage response
D	0009116	biological_process	nucleoside metabolic process
D	0009164	biological_process	nucleoside catabolic process
D	0016020	cellular_component	membrane
D	0016763	molecular_function	pentosyltransferase activity
D	0019686	biological_process	purine nucleoside interconversion
D	0042278	biological_process	purine nucleoside metabolic process
D	0042802	molecular_function	identical protein binding
D	0047975	molecular_function	guanosine phosphorylase activity
E	0003824	molecular_function	catalytic activity
E	0004731	molecular_function	purine-nucleoside phosphorylase activity
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0006139	biological_process	nucleobase-containing compound metabolic process
E	0006152	biological_process	purine nucleoside catabolic process
E	0006974	biological_process	DNA damage response
E	0009116	biological_process	nucleoside metabolic process
E	0009164	biological_process	nucleoside catabolic process
E	0016020	cellular_component	membrane
E	0016763	molecular_function	pentosyltransferase activity
E	0019686	biological_process	purine nucleoside interconversion
E	0042278	biological_process	purine nucleoside metabolic process
E	0042802	molecular_function	identical protein binding
E	0047975	molecular_function	guanosine phosphorylase activity
F	0003824	molecular_function	catalytic activity
F	0004731	molecular_function	purine-nucleoside phosphorylase activity
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0006139	biological_process	nucleobase-containing compound metabolic process
F	0006152	biological_process	purine nucleoside catabolic process
F	0006974	biological_process	DNA damage response
F	0009116	biological_process	nucleoside metabolic process
F	0009164	biological_process	nucleoside catabolic process
F	0016020	cellular_component	membrane
F	0016763	molecular_function	pentosyltransferase activity
F	0019686	biological_process	purine nucleoside interconversion
F	0042278	biological_process	purine nucleoside metabolic process
F	0042802	molecular_function	identical protein binding
F	0047975	molecular_function	guanosine phosphorylase activity

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 A 9902

Chain	Residue
A	GLY20
A	ARG24
A	ARG87
A	GLY89
A	SER90
A	FM29901
D	ARG43

site_id	AC2
Number of Residues	17
Details	BINDING SITE FOR RESIDUE FM2 A 9901

Chain	Residue
A	SER90
A	CYS91
A	GLY92
A	PHE159
A	VAL178
A	GLU179
A	MET180
A	GLU181
A	SER203
A	ASP204
A	HOH1022
A	HOH1082
A	PO49902
D	HIS4
D	ARG43
A	MET64
A	ARG87

site_id	AC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 B 9904

Chain	Residue
B	GLY20
B	ARG24
B	ARG87
B	GLY89
B	SER90
B	FM29903
E	ARG43

site_id	AC4
Number of Residues	17
Details	BINDING SITE FOR RESIDUE FM2 B 9903

Chain	Residue
B	MET64
B	ARG87
B	SER90
B	CYS91
B	GLY92
B	PHE159
B	VAL178
B	GLU179
B	MET180
B	GLU181
B	SER203
B	ASP204
B	HOH1022
B	HOH1109
B	PO49904
E	HIS4
E	ARG43

site_id	AC5
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 C 9906

Chain	Residue
C	GLY20
C	ARG24
C	ARG87
C	GLY89
C	SER90
C	FM29905
F	ARG43

site_id	AC6
Number of Residues	17
Details	BINDING SITE FOR RESIDUE FM2 C 9905

Chain	Residue
C	MET64
C	ARG87
C	SER90
C	CYS91
C	GLY92
C	PHE159
C	VAL178
C	GLU179
C	MET180
C	GLU181
C	SER203
C	ASP204
C	HOH1026
C	HOH1079
C	PO49906
F	HIS4
F	ARG43

site_id	AC7
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 D 9908

Chain	Residue
A	ARG43
D	PRO19
D	GLY20
D	ARG24
D	ARG87
D	GLY89
D	SER90
D	FM19907

site_id	AC8
Number of Residues	17
Details	BINDING SITE FOR RESIDUE FM1 D 9907

Chain	Residue
A	HIS4
A	ARG43
D	ARG87
D	SER90
D	CYS91
D	GLY92
D	PHE159
D	VAL178
D	GLU179
D	MET180
D	GLU181
D	ASP204
D	ILE206
D	HOH1070
D	HOH1098
D	PO49908
D	HOH9927

site_id	AC9
Number of Residues	7
Details	BINDING SITE FOR RESIDUE PO4 E 9910

Chain	Residue
E	ARG24
E	ARG87
E	GLY89
E	SER90
E	FM19909
B	ARG43
E	GLY20

site_id	BC1
Number of Residues	17
Details	BINDING SITE FOR RESIDUE FM1 E 9909

Chain	Residue
B	HIS4
B	ARG43
E	MET64
E	ARG87
E	SER90
E	CYS91
E	GLY92
E	PHE159
E	VAL178
E	GLU179
E	MET180
E	GLU181
E	ASP204
E	ILE206
E	HOH1059
E	PO49910
E	HOH9919

site_id	BC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE PO4 F 9912

Chain	Residue
C	ARG43
F	PRO19
F	GLY20
F	ARG24
F	ARG87
F	GLY89
F	SER90
F	FM19911

site_id	BC3
Number of Residues	18
Details	BINDING SITE FOR RESIDUE FM1 F 9911

Chain	Residue
C	HIS4
C	ARG43
F	MET64
F	ARG87
F	SER90
F	CYS91
F	GLY92
F	PHE159
F	VAL178
F	GLU179
F	MET180
F	GLU181
F	SER203
F	ASP204
F	HOH1036
F	HOH1063
F	HOH1064
F	PO49912

Functional Information from PROSITE/UniProt

site_id	PS01232
Number of Residues	16
Details	PNP_UDP_1 Purine and other phosphorylases family 1 signature. GhGMGiPScSIytkEL

Chain	Residue	Details
A	GLY61-LEU76

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	6
Details	Active site: {"description":"Proton donor","evidences":[{"source":"HAMAP-Rule","id":"MF_01627","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"30337572","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"30337572","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4TS3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TS9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	30
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"11786017","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21672603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30337572","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1K9S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ONV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3OOE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3OOH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3OPV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TS3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TS9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"11786017","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"21672603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30337572","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"1K9S","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3ONV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3OOE","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3OOH","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"3OPV","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TS3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TS9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	18
Details	Binding site: {"description":"in other chain","evidences":[{"source":"PubMed","id":"30337572","evidenceCode":"ECO:0000305"},{"source":"PDB","id":"4TS3","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TS9","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTA","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTI","evidenceCode":"ECO:0007744"},{"source":"PDB","id":"4TTJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	6
Details	Site: {"description":"Important for catalytic activity","evidences":[{"source":"HAMAP-Rule","id":"MF_01627","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"21672603","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"30337572","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Modified residue: {"description":"N6-acetyllysine","evidences":[{"source":"PubMed","id":"18723842","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

site_id	CSA1
Number of Residues	2
Details	Annotated By Reference To The Literature 1a69

Chain	Residue	Details
A	ASP204
A	ARG217

site_id	CSA2
Number of Residues	2
Details	Annotated By Reference To The Literature 1a69

Chain	Residue	Details
B	ASP204
B	ARG217

site_id	CSA3
Number of Residues	2
Details	Annotated By Reference To The Literature 1a69

Chain	Residue	Details
C	ASP204
C	ARG217

site_id	CSA4
Number of Residues	2
Details	Annotated By Reference To The Literature 1a69

Chain	Residue	Details
D	ASP204
D	ARG217

site_id	CSA5
Number of Residues	2
Details	Annotated By Reference To The Literature 1a69

Chain	Residue	Details
E	ASP204
E	ARG217

site_id	CSA6
Number of Residues	2
Details	Annotated By Reference To The Literature 1a69

Chain	Residue	Details
F	ASP204
F	ARG217

site_id	MCSA1
Number of Residues	7
Details	M-CSA 375

Chain	Residue	Details
A	GLY20	electrostatic stabiliser
A	ARG24	electrostatic stabiliser
A	ARG43	electrostatic stabiliser
A	ARG87	electrostatic stabiliser
A	SER90	electrostatic stabiliser
A	ASP204	proton shuttle (general acid/base)
A	ARG217	enhance reactivity

site_id	MCSA2
Number of Residues	7
Details	M-CSA 375

Chain	Residue	Details
B	GLY20	electrostatic stabiliser
B	ARG24	electrostatic stabiliser
B	ARG43	electrostatic stabiliser
B	ARG87	electrostatic stabiliser
B	SER90	electrostatic stabiliser
B	ASP204	proton shuttle (general acid/base)
B	ARG217	enhance reactivity

site_id	MCSA3
Number of Residues	7
Details	M-CSA 375

Chain	Residue	Details
C	GLY20	electrostatic stabiliser
C	ARG24	electrostatic stabiliser
C	ARG43	electrostatic stabiliser
C	ARG87	electrostatic stabiliser
C	SER90	electrostatic stabiliser
C	ASP204	proton shuttle (general acid/base)
C	ARG217	enhance reactivity

site_id	MCSA4
Number of Residues	7
Details	M-CSA 375

Chain	Residue	Details
D	GLY20	electrostatic stabiliser
D	ARG24	electrostatic stabiliser
D	ARG43	electrostatic stabiliser
D	ARG87	electrostatic stabiliser
D	SER90	electrostatic stabiliser
D	ASP204	proton shuttle (general acid/base)
D	ARG217	enhance reactivity

site_id	MCSA5
Number of Residues	7
Details	M-CSA 375

Chain	Residue	Details
E	GLY20	electrostatic stabiliser
E	ARG24	electrostatic stabiliser
E	ARG43	electrostatic stabiliser
E	ARG87	electrostatic stabiliser
E	SER90	electrostatic stabiliser
E	ASP204	proton shuttle (general acid/base)
E	ARG217	enhance reactivity

site_id	MCSA6
Number of Residues	7
Details	M-CSA 375

Chain	Residue	Details
F	GLY20	electrostatic stabiliser
F	ARG24	electrostatic stabiliser
F	ARG43	electrostatic stabiliser
F	ARG87	electrostatic stabiliser
F	SER90	electrostatic stabiliser
F	ASP204	proton shuttle (general acid/base)
F	ARG217	enhance reactivity

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)