3DWK

Identification of Dynamic Structural Motifs Involved in Peptidoglycan Glycosyltransfer

External Resource: Annotation

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

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

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
A	d3dwka1	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	PBP transglycosylase domain-like	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
A	d3dwka2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
B	d3dwkb1	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	PBP transglycosylase domain-like	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
B	d3dwkb2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
C	d3dwkc1	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	PBP transglycosylase domain-like	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
C	d3dwkc2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
D	d3dwkd1	Alpha and beta proteins (a+b)	Lysozyme-like	Lysozyme-like	PBP transglycosylase domain-like	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)
D	d3dwkd2	Multi-domain proteins (alpha and beta)	beta-lactamase/transpeptidase-like	beta-lactamase/transpeptidase-like	beta-Lactamase/D-ala carboxypeptidase	Penicillin-binding protein 2, PBP2	(Staphylococcus aureus subsp. aureus COL ) [TaxId: 93062 ],	SCOPe (2.08)

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	Transpeptidase_1st_1	e3dwkA1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st_1	ECOD (1.6)
A	Transpeptidase_2nd	e3dwkA2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd	ECOD (1.6)
A	Transgly	e3dwkA3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transgly	ECOD (1.6)
B	Transpeptidase_1st_1	e3dwkB1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st_1	ECOD (1.6)
B	Transpeptidase_2nd	e3dwkB2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd	ECOD (1.6)
B	Transgly	e3dwkB3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transgly	ECOD (1.6)
C	Transpeptidase_1st_1	e3dwkC1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st_1	ECOD (1.6)
C	Transpeptidase_2nd	e3dwkC2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd	ECOD (1.6)
C	Transgly	e3dwkC3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transgly	ECOD (1.6)
D	Transpeptidase_1st_1	e3dwkD1	A: alpha complex topology	X: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	H: alpha-helical domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: alpha-helical domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_1st_1	ECOD (1.6)
D	Transpeptidase_2nd	e3dwkD2	A: a+b three layers	X: Profilin-like	H: a+b domain in beta-lactamase/transpeptidase-like proteins (From Topology)	T: a+b domain in beta-lactamase/transpeptidase-like proteins	F: Transpeptidase_2nd	ECOD (1.6)
D	Transgly	e3dwkD3	A: a+b complex topology	X: Lysozyme-like (From Homology)	H: Lysozyme-like	T: Lysozyme-like	F: Transgly	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.90.1310.20	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)		CATH (4.3.0)
A	1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	CATH (4.3.0)
A	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
B	3.90.1310.20	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)		CATH (4.3.0)
B	1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	CATH (4.3.0)
B	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
C	3.90.1310.20	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)		CATH (4.3.0)
C	1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	CATH (4.3.0)
C	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)
D	3.90.1310.20	Alpha Beta	Alpha-Beta Complex	Penicillin-binding protein 2a (Domain 2)		CATH (4.3.0)
D	1.10.3810.10	Mainly Alpha	Orthogonal Bundle	Penicillin binding protein transpeptidase fold	Biosynthetic peptidoglycan transglycosylase-like	CATH (4.3.0)
D	3.40.710.10	Alpha Beta	3-Layer(aba) Sandwich	Beta-lactamase	DD-peptidase/beta-lactamase superfamily	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00912	Transglycosylase (Transgly)	Transglycosylase	-	Family
A, B, C, D	PF00905	Penicillin binding protein transpeptidase domain (Transpeptidase)	Penicillin binding protein transpeptidase domain	The active site serine (residue 337 in Swiss:P14677) is conserved in all members of this family.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Penicillin-binding protein 2	amide binding organic acid binding binding ion binding organic cyclic compound binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding serine-type exopeptidase activity peptidase activity amide binding organic acid binding binding ion binding organic cyclic compound binding anion binding penicillin binding carboxylic acid binding heterocyclic compound binding monocarboxylic acid binding small molecule binding sulfur compound binding serine-type exopeptidase activity peptidase activity catalytic activity, acting on a protein serine hydrolase activity hydrolase activity serine-type D-Ala-D-Ala carboxypeptidase activity serine-type carboxypeptidase activity serine-type peptidase activity exopeptidase activity catalytic activity carboxypeptidase activity peptidoglycan glycosyltransferase activity glycosyltransferase activity transferase activity hexosyltransferase activity	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane cellular anatomical entity

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR001264	Glycosyl transferase, family 51	Domain
A, B, C, D	IPR012338	Beta-lactamase/transpeptidase-like	Homologous Superfamily
A, B, C, D	IPR036950	Penicillin binding protein transglycosylase domain	Homologous Superfamily
A, B, C, D	IPR001460	Penicillin-binding protein, transpeptidase	Domain
A, B, C, D	IPR023346	Lysozyme-like domain superfamily	Homologous Superfamily

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.