5CB5

Structural Insights into the Mechanism of Escherichia coli Ymdb

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 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 [auth R]	d5cb5r_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
B [auth A]	d5cb5a_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
C [auth B]	d5cb5b_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
D [auth C]	d5cb5c_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
E [auth D]	d5cb5d_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
G [auth F]	d5cb5f_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
H [auth G]	d5cb5g_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
I [auth H]	d5cb5h_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
J [auth I]	d5cb5i_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
K [auth J]	d5cb5j_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
L [auth K]	d5cb5k_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
N [auth M]	d5cb5m_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
O [auth N]	d5cb5n_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
P [auth O]	d5cb5o_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
Q [auth P]	d5cb5p_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
R [auth Q]	d5cb5q_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
F [auth E]	d5cb5e_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)
M [auth L]	d5cb5l_	Alpha and beta proteins (a/b)	Macro domain-like	Macro domain-like	Macro domain	automated matches	(Escherichia coli K-12 ) [TaxId: 83333 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
A [auth R]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
B [auth A]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
C [auth B]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
D [auth C]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
E [auth D]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
G [auth F]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
H [auth G]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
I [auth H]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
J [auth I]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
K [auth J]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
L [auth K]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
N [auth M]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
O [auth N]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
P [auth O]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
Q [auth P]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
R [auth Q]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
F [auth E]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	SCOP2B (2022-06-29)
M [auth L]	SCOP2B Superfamily	Macro domain-like	8041651	3000458	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 [auth R]	Macro	e5cb5R1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
B [auth A]	Macro	e5cb5A1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
C [auth B]	Macro	e5cb5B1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
D [auth C]	Macro	e5cb5C1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
E [auth D]	Macro	e5cb5D1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
G [auth F]	Macro	e5cb5F1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
H [auth G]	Macro	e5cb5G1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
I [auth H]	Macro	e5cb5H1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
J [auth I]	Macro	e5cb5I1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
K [auth J]	Macro	e5cb5J1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
L [auth K]	Macro	e5cb5K1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
N [auth M]	Macro	e5cb5M1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
O [auth N]	Macro	e5cb5N1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
P [auth O]	Macro	e5cb5O1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
Q [auth P]	Macro	e5cb5P1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
R [auth Q]	Macro	e5cb5Q1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
F [auth E]	Macro	e5cb5E1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)
M [auth L]	Macro	e5cb5L1	A: a/b three-layered sandwiches	X: Macro domain-like (From Topology)	H: Macro domain-like (From Topology)	T: Macro domain-like	F: Macro	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A [auth R]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
B [auth A]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
C [auth B]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
D [auth C]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
E [auth D]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
G [auth F]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
H [auth G]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
I [auth H]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
J [auth I]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
K [auth J]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
L [auth K]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
N [auth M]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
O [auth N]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
P [auth O]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
Q [auth P]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
R [auth Q]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
F [auth E]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)
M [auth L]	3.40.220.10	Alpha Beta	3-Layer(aba) Sandwich	Leucine Aminopeptidase, subunit E	domain 1	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q]	PF01661	Macro domain (Macro)	Macro domain	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently ...	The Macro or A1pp domain is a module of about 180 amino acids which can bind ADP-ribose (an NAD metabolite) or related ligands. Binding to ADP-ribose could be either covalent or non-covalent [1]: in certain cases it is believed to bind non-covalently [2]; while in other cases (such as Aprataxin) it appears to bind both non-covalently through a zinc finger motif, and covalently through a separate region of the protein [3]. This domain is found in a number of otherwise unrelated proteins. It is found at the C-terminus of the macro-H2A histone protein 4 and also in the non-structural proteins of several types of ssRNA viruses such as NSP3 from alpha-viruses and coronaviruses. This domain is also found on its own in a family of proteins from bacteria, archaebacteria and eukaryotes. The 3D structure of the SARS-CoV Macro domain has a mixed alpha/beta fold consisting of a central seven-stranded twisted mixed beta sheet sandwiched between two alpha helices on one face, and three on the other. The final alpha-helix, located on the edge of the central beta-sheet, forms the C terminus of the protein [4]. The crystal structure of AF1521 (a Macro domain-only protein from Archaeoglobus fulgidus) has also been reported and compared with other Macro domain containing proteins. Several Macro domain only proteins are shorter than AF1521, and appear to lack either the first strand of the beta-sheet or the C-terminal helix 5. Well conserved residues form a hydrophobic cleft and cluster around the AF1521-ADP-ribose binding site [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q]	O-acetyl-ADP-ribose deacetylase	enzyme regulator activity molecular function inhibitor activity molecular function regulator activity nuclease inhibitor activity enzyme inhibitor activity endoribonuclease inhibitor activity ribonuclease inhibitor activity binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding purine nucleoside binding small molecule binding enzyme regulator activity molecular function inhibitor activity molecular function regulator activity nuclease inhibitor activity enzyme inhibitor activity endoribonuclease inhibitor activity ribonuclease inhibitor activity binding organic cyclic compound binding nucleoside binding heterocyclic compound binding carbohydrate derivative binding purine nucleoside binding small molecule binding protein binding enzyme binding deacetylase activity O-acetyl-ADP-ribose deacetylase activity hydrolase activity catalytic activity	nucleobase-containing compound metabolic process glycosyl compound metabolic process nucleobase-containing small molecule metabolic process carbohydrate derivative metabolic process metabolic process small molecule metabolic process primary metabolic process purine nucleoside metabolic process nucleoside metabolic process purine-containing compound metabolic process cell aggregation regulation of biological process biofilm formation regulation of cellular process nucleobase-containing compound metabolic process glycosyl compound metabolic process nucleobase-containing small molecule metabolic process carbohydrate derivative metabolic process metabolic process small molecule metabolic process primary metabolic process purine nucleoside metabolic process nucleoside metabolic process purine-containing compound metabolic process cell aggregation regulation of biological process biofilm formation regulation of cellular process regulation of single-species biofilm formation on inanimate substrate biological process involved in intraspecies interaction between organisms biological regulation single-species biofilm formation on inanimate substrate single-species biofilm formation aggregation of unicellular organisms submerged biofilm formation regulation of single-species biofilm formation cellular process single-species submerged biofilm formation response to stimulus response to chemical response to antibiotic	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q]	IPR024900	O-acetyl-ADP-ribose deacetylase	Family
A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q]	IPR043472	Macro domain-like	Homologous Superfamily
A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], A [auth R], B [auth A], C [auth B], D [auth C], E [auth D], F [auth E], G [auth F], H [auth G], I [auth H], J [auth I], K [auth J], L [auth K], M [auth L], N [auth M], O [auth N], P [auth O], Q [auth P], R [auth Q]	IPR002589	Macro 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.