Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1LS3

Crystal Structure of the Complex between Rabbit Cytosolic Serine Hydroxymethyltransferase and TriGlu-5-formyl-tetrahydrofolate

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
A	0004372	molecular_function	glycine hydroxymethyltransferase activity
A	0005521	molecular_function	lamin binding
A	0005634	cellular_component	nucleus
A	0005654	cellular_component	nucleoplasm
A	0005737	cellular_component	cytoplasm
A	0005739	cellular_component	mitochondrion
A	0005829	cellular_component	cytosol
A	0006231	biological_process	dTMP biosynthetic process
A	0006544	biological_process	glycine metabolic process
A	0006563	biological_process	L-serine metabolic process
A	0006565	biological_process	L-serine catabolic process
A	0006730	biological_process	one-carbon metabolic process
A	0009113	biological_process	purine nucleobase biosynthetic process
A	0016740	molecular_function	transferase activity
A	0017148	biological_process	negative regulation of translation
A	0019264	biological_process	glycine biosynthetic process from serine
A	0030170	molecular_function	pyridoxal phosphate binding
A	0035999	biological_process	tetrahydrofolate interconversion
A	0036094	molecular_function	small molecule binding
A	0042802	molecular_function	identical protein binding
A	0042803	molecular_function	protein homodimerization activity
A	0044281	biological_process	small molecule metabolic process
A	0046653	biological_process	tetrahydrofolate metabolic process
A	0046655	biological_process	folic acid metabolic process
A	0048027	molecular_function	mRNA 5'-UTR binding
A	0051289	biological_process	protein homotetramerization
A	0060090	molecular_function	molecular adaptor activity
A	0070905	molecular_function	serine binding
A	1904482	biological_process	cellular response to tetrahydrofolate
B	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
B	0004372	molecular_function	glycine hydroxymethyltransferase activity
B	0005521	molecular_function	lamin binding
B	0005634	cellular_component	nucleus
B	0005654	cellular_component	nucleoplasm
B	0005737	cellular_component	cytoplasm
B	0005739	cellular_component	mitochondrion
B	0005829	cellular_component	cytosol
B	0006231	biological_process	dTMP biosynthetic process
B	0006544	biological_process	glycine metabolic process
B	0006563	biological_process	L-serine metabolic process
B	0006565	biological_process	L-serine catabolic process
B	0006730	biological_process	one-carbon metabolic process
B	0009113	biological_process	purine nucleobase biosynthetic process
B	0016740	molecular_function	transferase activity
B	0017148	biological_process	negative regulation of translation
B	0019264	biological_process	glycine biosynthetic process from serine
B	0030170	molecular_function	pyridoxal phosphate binding
B	0035999	biological_process	tetrahydrofolate interconversion
B	0036094	molecular_function	small molecule binding
B	0042802	molecular_function	identical protein binding
B	0042803	molecular_function	protein homodimerization activity
B	0044281	biological_process	small molecule metabolic process
B	0046653	biological_process	tetrahydrofolate metabolic process
B	0046655	biological_process	folic acid metabolic process
B	0048027	molecular_function	mRNA 5'-UTR binding
B	0051289	biological_process	protein homotetramerization
B	0060090	molecular_function	molecular adaptor activity
B	0070905	molecular_function	serine binding
B	1904482	biological_process	cellular response to tetrahydrofolate
C	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
C	0004372	molecular_function	glycine hydroxymethyltransferase activity
C	0005521	molecular_function	lamin binding
C	0005634	cellular_component	nucleus
C	0005654	cellular_component	nucleoplasm
C	0005737	cellular_component	cytoplasm
C	0005739	cellular_component	mitochondrion
C	0005829	cellular_component	cytosol
C	0006231	biological_process	dTMP biosynthetic process
C	0006544	biological_process	glycine metabolic process
C	0006563	biological_process	L-serine metabolic process
C	0006565	biological_process	L-serine catabolic process
C	0006730	biological_process	one-carbon metabolic process
C	0009113	biological_process	purine nucleobase biosynthetic process
C	0016740	molecular_function	transferase activity
C	0017148	biological_process	negative regulation of translation
C	0019264	biological_process	glycine biosynthetic process from serine
C	0030170	molecular_function	pyridoxal phosphate binding
C	0035999	biological_process	tetrahydrofolate interconversion
C	0036094	molecular_function	small molecule binding
C	0042802	molecular_function	identical protein binding
C	0042803	molecular_function	protein homodimerization activity
C	0044281	biological_process	small molecule metabolic process
C	0046653	biological_process	tetrahydrofolate metabolic process
C	0046655	biological_process	folic acid metabolic process
C	0048027	molecular_function	mRNA 5'-UTR binding
C	0051289	biological_process	protein homotetramerization
C	0060090	molecular_function	molecular adaptor activity
C	0070905	molecular_function	serine binding
C	1904482	biological_process	cellular response to tetrahydrofolate
D	0000900	molecular_function	mRNA regulatory element binding translation repressor activity
D	0004372	molecular_function	glycine hydroxymethyltransferase activity
D	0005521	molecular_function	lamin binding
D	0005634	cellular_component	nucleus
D	0005654	cellular_component	nucleoplasm
D	0005737	cellular_component	cytoplasm
D	0005739	cellular_component	mitochondrion
D	0005829	cellular_component	cytosol
D	0006231	biological_process	dTMP biosynthetic process
D	0006544	biological_process	glycine metabolic process
D	0006563	biological_process	L-serine metabolic process
D	0006565	biological_process	L-serine catabolic process
D	0006730	biological_process	one-carbon metabolic process
D	0009113	biological_process	purine nucleobase biosynthetic process
D	0016740	molecular_function	transferase activity
D	0017148	biological_process	negative regulation of translation
D	0019264	biological_process	glycine biosynthetic process from serine
D	0030170	molecular_function	pyridoxal phosphate binding
D	0035999	biological_process	tetrahydrofolate interconversion
D	0036094	molecular_function	small molecule binding
D	0042802	molecular_function	identical protein binding
D	0042803	molecular_function	protein homodimerization activity
D	0044281	biological_process	small molecule metabolic process
D	0046653	biological_process	tetrahydrofolate metabolic process
D	0046655	biological_process	folic acid metabolic process
D	0048027	molecular_function	mRNA 5'-UTR binding
D	0051289	biological_process	protein homotetramerization
D	0060090	molecular_function	molecular adaptor activity
D	0070905	molecular_function	serine binding
D	1904482	biological_process	cellular response to tetrahydrofolate

Functional Information from PDB Data

site_id	AC1
Number of Residues	18
Details	BINDING SITE FOR RESIDUE PLP A 419A

Chain	Residue
A	SER97
A	THR226
A	HIS228
A	LYS229
A	GLY420
A	HOH506
A	HOH515
B	TYR55
B	GLY262
B	GLY263
A	GLY98
A	SER99
A	HIS126
A	THR174
A	SER175
A	ASP200
A	ALA202
A	HIS203

site_id	AC2
Number of Residues	8
Details	BINDING SITE FOR RESIDUE GLY A 420B

Chain	Residue
A	SER35
A	HIS126
A	SER175
A	LYS229
A	ARG363
A	PLP419
A	HOH515
B	TYR65

site_id	AC3
Number of Residues	16
Details	BINDING SITE FOR RESIDUE PLP C 419A

Chain	Residue
C	SER97
C	GLY98
C	SER99
C	HIS126
C	THR174
C	SER175
C	ASP200
C	ALA202
C	HIS203
C	THR226
C	HIS228
C	LYS229
C	GLY420
D	TYR55
D	GLY262
D	GLY263

site_id	AC4
Number of Residues	7
Details	BINDING SITE FOR RESIDUE GLY C 420B

Chain	Residue
C	SER35
C	SER175
C	HIS203
C	LYS229
C	ARG363
C	PLP419
D	TYR65

site_id	AC5
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP B 419A

Chain	Residue
A	TYR55
A	GLY262
A	GLY263
B	SER97
B	GLY98
B	SER99
B	HIS126
B	THR174
B	SER175
B	ASP200
B	ALA202
B	HIS203
B	THR226
B	HIS228
B	LYS229

site_id	AC6
Number of Residues	14
Details	BINDING SITE FOR RESIDUE TGF B 420C

Chain	Residue
A	GLU57
A	TYR64
A	TYR65
A	PHE257
B	LEU121
B	GLY124
B	GLY125
B	HIS126
B	LEU127
B	LYS134
B	SER175
B	ASN345
B	LEU357
B	HOH739

site_id	AC7
Number of Residues	15
Details	BINDING SITE FOR RESIDUE PLP D 419A

Chain	Residue
C	TYR55
C	GLY262
C	GLY263
D	SER97
D	GLY98
D	SER99
D	HIS126
D	THR174
D	SER175
D	ASP200
D	ALA202
D	HIS203
D	THR226
D	HIS228
D	LYS229

site_id	AC8
Number of Residues	18
Details	BINDING SITE FOR RESIDUE TGF D 420F

Chain	Residue
D	LEU127
D	LYS134
D	SER175
D	CYS176
D	GLY331
D	ASN345
D	LYS346
D	ASN347
D	ALA356
D	LEU357
D	PRO359
D	HOH740
C	GLU57
C	TYR64
C	TYR65
D	GLY124
D	GLY125
D	HIS126

site_id	AC9
Number of Residues	1
Details	BINDING SITE FOR RESIDUE GOL D 421

Chain	Residue
D	ASP182

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE GOL C 421

Chain	Residue
B	PHE418
C	ASP156
C	HOH679

site_id	BC2
Number of Residues	2
Details	BINDING SITE FOR RESIDUE GOL B 421

Chain	Residue
B	LEU181
B	ASP182

site_id	BC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE GOL B 422

Chain	Residue
A	SER49
B	ILE19
B	PRO418
B	PHE418

Functional Information from PROSITE/UniProt

site_id	PS00096
Number of Residues	17
Details	SHMT Serine hydroxymethyltransferase pyridoxal-phosphate attachment site. HVvTTTTHKTLrGCRAG

Chain	Residue	Details
A	HIS221-GLY237

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	4
Details	Active site: {"description":"Nucleophile","evidences":[{"source":"PubMed","id":"7358720","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	4
Details	Active site: {"description":"Proton donor","evidences":[{"evidenceCode":"ECO:0000250"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	4
Details	Modified residue: {"description":"N6-(pyridoxal phosphate)lysine","evidences":[{"source":"PubMed","id":"10387080","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

Catalytic Information from CSA

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

Chain	Residue	Details
A	ARG63

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

Chain	Residue	Details
D	ARG63

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

Chain	Residue	Details
C	ARG63

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

Chain	Residue	Details
B	ARG63

site_id	CSA5
Number of Residues	3
Details	Annotated By Reference To The Literature 1dfo

Chain	Residue	Details
A	THR226
A	LYS229
A	GLU57

site_id	CSA6
Number of Residues	3
Details	Annotated By Reference To The Literature 1dfo

Chain	Residue	Details
B	THR226
B	LYS229
B	GLU57

site_id	CSA7
Number of Residues	3
Details	Annotated By Reference To The Literature 1dfo

Chain	Residue	Details
C	THR226
C	LYS229
C	GLU57

site_id	CSA8
Number of Residues	3
Details	Annotated By Reference To The Literature 1dfo

Chain	Residue	Details
D	THR226
D	LYS229
D	GLU57

site_id	MCSA1
Number of Residues	6
Details	M-CSA 147

Chain	Residue	Details
A	TYR55	steric locator
A	GLU57	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
A	ASP200	electrostatic stabiliser
A	THR226	electrostatic stabiliser, hydrogen bond acceptor
A	LYS229	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
A	ARG235	electrostatic stabiliser

site_id	MCSA2
Number of Residues	6
Details	M-CSA 147

Chain	Residue	Details
B	TYR55	steric locator
B	GLU57	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
B	ASP200	electrostatic stabiliser
B	THR226	electrostatic stabiliser, hydrogen bond acceptor
B	LYS229	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
B	ARG235	electrostatic stabiliser

site_id	MCSA3
Number of Residues	6
Details	M-CSA 147

Chain	Residue	Details
C	TYR55	steric locator
C	GLU57	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
C	ASP200	electrostatic stabiliser
C	THR226	electrostatic stabiliser, hydrogen bond acceptor
C	LYS229	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
C	ARG235	electrostatic stabiliser

site_id	MCSA4
Number of Residues	6
Details	M-CSA 147

Chain	Residue	Details
D	TYR55	steric locator
D	GLU57	hydrogen bond acceptor, hydrogen bond donor, proton acceptor, proton donor
D	ASP200	electrostatic stabiliser
D	THR226	electrostatic stabiliser, hydrogen bond acceptor
D	LYS229	covalently attached, electron pair acceptor, electron pair donor, hydrogen bond donor, nucleofuge, nucleophile, proton acceptor, proton donor
D	ARG235	electrostatic stabiliser

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