3LGX | pdb_00003lgx

Structure of probable D-alanine-poly(phosphoribitol) ligase subunit-1 from Streptococcus pyogenes with ATP

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	d3lgxa1	Multi-domain proteins (alpha and beta)	Acetyl-CoA synthetase-like	Acetyl-CoA synthetase-like	automated matches	automated matches	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
A	d3lgxa2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
B	d3lgxb1	Multi-domain proteins (alpha and beta)	Acetyl-CoA synthetase-like	Acetyl-CoA synthetase-like	automated matches	automated matches	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
B	d3lgxb2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
C	d3lgxc1	Multi-domain proteins (alpha and beta)	Acetyl-CoA synthetase-like	Acetyl-CoA synthetase-like	automated matches	automated matches	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
C	d3lgxc2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
D	d3lgxd1	Multi-domain proteins (alpha and beta)	Acetyl-CoA synthetase-like	Acetyl-CoA synthetase-like	automated matches	automated matches	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	SCOPe (2.08)
D	d3lgxd2	Artifacts	Tags	Tags	Tags	N-terminal Tags	(Streptococcus pyogenes M1 GAS ) [TaxId: 160490 ],	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	Ank_2, Ank_4, Ank_5	e3lgxA9	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
B	Ank_2, Ank_4, Ank_5	e3lgxB9	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
C	Ank_2, Ank_4, Ank_5	e3lgxC9	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)
D	Ank_2, Ank_4, Ank_5	e3lgxD9	A: a/b three-layered sandwiches	X: Subtilisin-like	H: Subtilisin-like	T: Subtilisin-like	F: Ank_2, Ank_4, Ank_5	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
A	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
B	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
B	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
C	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
C	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)
D	3.40.50.12780	Alpha Beta	3-Layer(aba) Sandwich	Rossmann fold	ANL, N-terminal domain	CATH (4.3.0)
D	3.30.300.30	Alpha Beta	2-Layer Sandwich	GMP Synthetase	Chain A, domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00501	AMP-binding enzyme (AMP-binding)	AMP-binding enzyme	-	Family
A, B, C, D	PF13193	AMP-binding enzyme C-terminal domain (AMP-binding_C)	AMP-binding enzyme C-terminal domain	This is a small domain that is found C terminal to Pfam:PF00501. It has a central beta sheet core that is flanked by alpha helices.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	D-alanine--poly(phosphoribitol) ligase subunit 1	binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding binding adenyl ribonucleotide binding nucleotide binding purine ribonucleotide binding purine ribonucleoside triphosphate binding nucleoside phosphate binding ion binding purine nucleotide binding anion binding adenyl nucleotide binding ATP binding heterocyclic compound binding carbohydrate derivative binding ribonucleotide binding small molecule binding ligase activity, forming carbon-sulfur bonds D-alanine [D-alanyl carrier protein] ligase activity catalytic activity acid-thiol ligase activity ligase activity	carbohydrate derivative biosynthetic process teichoic acid biosynthetic process peptidoglycan-based cell wall biogenesis small molecule biosynthetic process cell wall organization or biogenesis carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process macromolecule biosynthetic process cellular component biogenesis cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process lipoteichoic acid biosynthetic process carbohydrate derivative biosynthetic process teichoic acid biosynthetic process peptidoglycan-based cell wall biogenesis small molecule biosynthetic process cell wall organization or biogenesis carbohydrate derivative metabolic process organic acid biosynthetic process organic acid metabolic process macromolecule biosynthetic process cellular component biogenesis cell wall biogenesis biosynthetic process cell wall macromolecule biosynthetic process lipoteichoic acid biosynthetic process cellular process metabolic process small molecule metabolic process cellular component organization or biogenesis macromolecule metabolic process teichoic acid metabolic process cell wall macromolecule metabolic process	cellular anatomical structure intracellular anatomical structure cytoplasm

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR020845	AMP-binding, conserved site	Conserved Site
A, B, C, D	IPR042099	ANL, N-terminal domain	Homologous Superfamily
A, B, C, D	IPR045851	AMP-binding enzyme domain superfamily	Homologous Superfamily
A, B, C, D	IPR025110	AMP-binding enzyme, C-terminal domain	Domain
A, B, C, D	IPR000873	AMP-dependent synthetase/ligase domain	Domain
A, B, C, D	IPR010072	D-alanine--D-alanyl carrier protein ligase	Family
A, B, C, D	IPR044507	D-alanine:D-alanyl carrier protein ligase-like	Family
A, B, C, D	IPR010071	Amino acid adenylation domain	Domain

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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.