Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6DZ2

Crystal structure of human 5'-deoxy-5'-methylthioadenosine phosphorylase in complex with (3R,4S)-1-((4-amino-5H-pyrrolo[3,2-d]pyrimidin-7-yl)methyl)-4-(((3-(1-benzyl-1H-1,2,3-triazol-4-yl)propyl)thio)methyl)pyrrolidin-3-ol

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003824	molecular_function	catalytic activity
A	0004645	molecular_function	1,4-alpha-oligoglucan phosphorylase activity
A	0005515	molecular_function	protein binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005829	cellular_component	cytosol
A	0006139	biological_process	nucleobase-containing compound metabolic process
A	0006166	biological_process	purine ribonucleoside salvage
A	0006738	biological_process	nicotinamide riboside catabolic process
A	0009116	biological_process	nucleoside metabolic process
A	0016757	molecular_function	glycosyltransferase activity
A	0016763	molecular_function	pentosyltransferase activity
A	0017061	molecular_function	S-methyl-5-thioadenosine phosphorylase activity
A	0019509	biological_process	L-methionine salvage from methylthioadenosine
A	0032259	biological_process	methylation
A	0033574	biological_process	response to testosterone
A	0070062	cellular_component	extracellular exosome
B	0003824	molecular_function	catalytic activity
B	0004645	molecular_function	1,4-alpha-oligoglucan phosphorylase activity
B	0005515	molecular_function	protein binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005829	cellular_component	cytosol
B	0006139	biological_process	nucleobase-containing compound metabolic process
B	0006166	biological_process	purine ribonucleoside salvage
B	0006738	biological_process	nicotinamide riboside catabolic process
B	0009116	biological_process	nucleoside metabolic process
B	0016757	molecular_function	glycosyltransferase activity
B	0016763	molecular_function	pentosyltransferase activity
B	0017061	molecular_function	S-methyl-5-thioadenosine phosphorylase activity
B	0019509	biological_process	L-methionine salvage from methylthioadenosine
B	0032259	biological_process	methylation
B	0033574	biological_process	response to testosterone
B	0070062	cellular_component	extracellular exosome
C	0003824	molecular_function	catalytic activity
C	0004645	molecular_function	1,4-alpha-oligoglucan phosphorylase activity
C	0005515	molecular_function	protein binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005829	cellular_component	cytosol
C	0006139	biological_process	nucleobase-containing compound metabolic process
C	0006166	biological_process	purine ribonucleoside salvage
C	0006738	biological_process	nicotinamide riboside catabolic process
C	0009116	biological_process	nucleoside metabolic process
C	0016757	molecular_function	glycosyltransferase activity
C	0016763	molecular_function	pentosyltransferase activity
C	0017061	molecular_function	S-methyl-5-thioadenosine phosphorylase activity
C	0019509	biological_process	L-methionine salvage from methylthioadenosine
C	0032259	biological_process	methylation
C	0033574	biological_process	response to testosterone
C	0070062	cellular_component	extracellular exosome

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue EDO A 301

Chain	Residue
A	LEU280
A	HOH493
B	EDO301
C	EDO302

site_id	AC2
Number of Residues	3
Details	binding site for residue EDO A 303

Chain	Residue
A	LYS241
B	HOH476
C	EDO303

site_id	AC3
Number of Residues	4
Details	binding site for residue CL A 304

Chain	Residue
B	ARG116
C	ARG116
A	ARG116
A	HOH494

site_id	AC4
Number of Residues	5
Details	binding site for residue CL A 305

Chain	Residue
A	THR93
A	ASN195
A	MET196
A	THR197
A	OS5307

site_id	AC5
Number of Residues	5
Details	binding site for residue ACY A 306

Chain	Residue
A	THR118
A	MET119
B	MET119
C	THR118
C	MET119

site_id	AC6
Number of Residues	19
Details	binding site for residue OS5 A 307

Chain	Residue
A	GLY16
A	THR18
A	THR92
A	ALA94
A	CYS95
A	GLY96
A	PHE177
A	ILE194
A	ASN195
A	THR219
A	ASP220
A	ASP222
A	VAL236
A	LEU240
A	CL305
A	HOH420
A	HOH473
C	HIS137
C	LEU279

site_id	AC7
Number of Residues	3
Details	binding site for residue EDO B 301

Chain	Residue
A	PHE276
A	EDO301
B	ASP234

site_id	AC8
Number of Residues	5
Details	binding site for residue CL B 302

Chain	Residue
B	THR93
B	ASN195
B	MET196
B	THR197
B	OS5303

site_id	AC9
Number of Residues	20
Details	binding site for residue OS5 B 303

Chain	Residue
A	HIS137
A	LEU279
B	GLY16
B	THR18
B	PRO69
B	ALA94
B	CYS95
B	GLY96
B	PHE177
B	ILE194
B	ASN195
B	MET196
B	THR219
B	ASP220
B	ASP222
B	LEU240
B	ALA244
B	CL302
B	HOH406
B	HOH418

site_id	AD1
Number of Residues	3
Details	binding site for residue EDO C 301

Chain	Residue
C	THR261
C	GLU262
C	EDO302

site_id	AD2
Number of Residues	6
Details	binding site for residue EDO C 302

Chain	Residue
A	EDO301
B	LYS241
C	EDO301
C	EDO304
C	EDO306
C	HOH464

site_id	AD3
Number of Residues	3
Details	binding site for residue EDO C 303

Chain	Residue
A	EDO303
C	LEU280
C	EDO305

site_id	AD4
Number of Residues	2
Details	binding site for residue EDO C 304

Chain	Residue
C	EDO302
C	EDO306

site_id	AD5
Number of Residues	4
Details	binding site for residue EDO C 305

Chain	Residue
A	ASP234
C	PHE276
C	VAL278
C	EDO303

site_id	AD6
Number of Residues	2
Details	binding site for residue EDO C 306

Chain	Residue
C	EDO302
C	EDO304

site_id	AD7
Number of Residues	5
Details	binding site for residue CL C 307

Chain	Residue
C	THR93
C	ASN195
C	MET196
C	THR197
C	OS5308

site_id	AD8
Number of Residues	17
Details	binding site for residue OS5 C 308

Chain	Residue
C	GLY96
C	PHE177
C	ILE194
C	ASN195
C	THR219
C	ASP220
C	ASP222
C	LEU240
C	ALA244
C	CL307
C	HOH417
B	HIS137
B	LEU279
C	THR18
C	THR93
C	ALA94
C	CYS95

Functional Information from PROSITE/UniProt

site_id	PS01240
Number of Residues	41
Details	PNP_MTAP_2 Purine and other phosphorylases family 2 signature. LarhGrqHtImpskVnyqAn.IwAlkeeGcth.VIvtTAcGSL

Chain	Residue	Details
A	LEU58-LEU98

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	18
Details	BINDING:

Chain	Residue	Details
A	THR18
B	MET196
B	THR197
B	ASP220
C	THR18
C	ARG60
C	THR93
C	MET196
C	THR197
C	ASP220
A	ARG60
A	THR93
A	MET196
A	THR197
A	ASP220
B	THR18
B	ARG60
B	THR93

site_id	SWS_FT_FI2
Number of Residues	6
Details	SITE: Important for substrate specificity

Chain	Residue	Details
A	SER178
A	VAL233
B	SER178
B	VAL233
C	SER178
C	VAL233

site_id	SWS_FT_FI3
Number of Residues	3
Details	MOD_RES: N6-acetyllysine => ECO:0000250\|UniProtKB:Q9CQ65

Chain	Residue	Details
A	LYS51
B	LYS51
C	LYS51

Catalytic Information from CSA

site_id	MCSA1
Number of Residues	2
Details	M-CSA 244

Chain	Residue	Details
A	ASP220	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	ASP222	electrostatic stabiliser

site_id	MCSA2
Number of Residues	2
Details	M-CSA 244

Chain	Residue	Details
B	ASP220	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	ASP222	electrostatic stabiliser

site_id	MCSA3
Number of Residues	2
Details	M-CSA 244

Chain	Residue	Details
C	ASP220	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	ASP222	electrostatic stabiliser

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