6CD1

Crystal structure of Medicago truncatula serine hydroxymethyltransferase 3 (MtSHMT3), complexes with reaction intermediates

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d6cd1a_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
B	d6cd1b_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
C	d6cd1c_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
F	d6cd1f_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
D	d6cd1d_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
E	d6cd1e_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
G	d6cd1g_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)
H	d6cd1h_	Alpha and beta proteins (a/b)	PLP-dependent transferase-like	PLP-dependent transferases	GABA-aminotransferase-like	automated matches	Barrel medic (Medicago truncatula ) [TaxId: 3880 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)
B	SCOP2 Family	GABA-aminotransferase-like	8073322	4000675	SCOP2 (2022-06-29)
B	SCOP2 Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2 (2022-06-29)
C	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	PLP-dependent transferases	8073323	3000954	SCOP2B (2022-06-29)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	SHMT	e6cd1A2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
A	Aminotran_5_N	e6cd1A1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
B	SHMT	e6cd1B2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
B	Aminotran_5_N	e6cd1B1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
C	SHMT	e6cd1C2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
C	Aminotran_5_N	e6cd1C1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
F	SHMT	e6cd1F2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
F	Aminotran_5_N	e6cd1F1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
D	SHMT	e6cd1D2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
D	Aminotran_5_N	e6cd1D1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
E	SHMT	e6cd1E1	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
E	Aminotran_5_N	e6cd1E2	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
G	SHMT	e6cd1G2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
G	Aminotran_5_N	e6cd1G1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)
H	SHMT	e6cd1H2	A: a+b two layers	X: C-terminal domain in some PLP-dependent transferases (From Topology)	H: C-terminal domain in some PLP-dependent transferases (From Topology)	T: C-terminal domain in some PLP-dependent transferases	F: SHMT	ECOD (1.6)
H	Aminotran_5_N	e6cd1H1	A: a/b three-layered sandwiches	X: PLP-dependent transferases (From Topology)	H: PLP-dependent transferases (From Topology)	T: PLP-dependent transferases	F: Aminotran_5_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, F	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase	-	Domain
E, G, H	PF00464	Serine hydroxymethyltransferase (SHMT)	Serine hydroxymethyltransferase	-	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, F	Serine hydroxymethyltransferase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding glycine hydroxymethyltransferase activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding glycine hydroxymethyltransferase activity hydroxymethyl-, formyl- and related transferase activity	folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process methylation tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process methylation tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process glycine biosynthetic process from serine small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle
E, G, H	Serine hydroxymethyltransferase	transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding glycine hydroxymethyltransferase activity transferase activity, transferring one-carbon groups transferase activity methyltransferase activity catalytic activity vitamin binding vitamin B6 binding pyridoxal phosphate binding ion binding binding organic cyclic compound binding anion binding heterocyclic compound binding small molecule binding glycine hydroxymethyltransferase activity hydroxymethyl-, formyl- and related transferase activity	folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process methylation tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process folic acid-containing compound metabolic process cellular metabolic process metabolic process cellular process tetrahydrofolate metabolic process pteridine-containing compound metabolic process cellular modified amino acid metabolic process methylation tetrahydrofolate interconversion small molecule metabolic process one-carbon metabolic process serine family amino acid metabolic process oxoacid metabolic process cellular biosynthetic process amino acid metabolic process organic acid metabolic process organic acid biosynthetic process alpha-amino acid metabolic process carboxylic acid biosynthetic process glycine metabolic process glycine biosynthetic process glycine biosynthetic process from serine small molecule biosynthetic process carboxylic acid metabolic process primary metabolic process L-amino acid biosynthetic process L-serine metabolic process L-amino acid metabolic process proteinogenic amino acid metabolic process amino acid biosynthetic process biosynthetic process proteinogenic amino acid biosynthetic process serine family amino acid biosynthetic process alpha-amino acid biosynthetic process	membrane-bounded organelle intracellular organelle intracellular anatomical structure mitochondrion organelle cytoplasm cellular anatomical entity intracellular membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, F	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
A, B, C, D, F	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
A, B, C, D, F	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
A, B, C, D, F	IPR001085	Serine hydroxymethyltransferase	Family
A, B, C, D, F	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
A, B, C, D, F	IPR049943	Serine hydroxymethyltransferase-like	Family
A, B, C, D, F	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site
E, G, H	IPR015421	Pyridoxal phosphate-dependent transferase, major domain	Homologous Superfamily
E, G, H	IPR015422	Pyridoxal phosphate-dependent transferase, small domain	Homologous Superfamily
E, G, H	IPR039429	Serine hydroxymethyltransferase-like domain	Domain
E, G, H	IPR001085	Serine hydroxymethyltransferase	Family
E, G, H	IPR015424	Pyridoxal phosphate-dependent transferase	Homologous Superfamily
E, G, H	IPR049943	Serine hydroxymethyltransferase-like	Family
E, G, H	IPR019798	Serine hydroxymethyltransferase, pyridoxal phosphate binding site	Binding Site

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, G, H	LLP	Parent Component: LYS RESID: AA0119 PSI-MOD : N6-pyridoxal phosphate-L-lysine MOD:00128

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.