3M9D | pdb_00003m9d

Crystal structure of the prokaryotic ubiquintin-like protein Pup complexed with the hexameric proteasomal ATPase Mpa which includes the amino terminal coiled coil domain and the inter domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
O	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091036	3000354	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	HypC/PAN OB-fold domain-like	8091037	3000354	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)
O	Prot_ATP_ID_OB_C	e3m9dO3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
O	Prot_ATP_ID_OB_N	e3m9dO2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
N	Prot_ATP_ID_OB_C	e3m9dN3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
N	Prot_ATP_ID_OB_N	e3m9dN2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
M	Prot_ATP_ID_OB_C	e3m9dM3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
M	Prot_ATP_ID_OB_N	e3m9dM2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
L	Prot_ATP_ID_OB_C	e3m9dL3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
L	Prot_ATP_ID_OB_N	e3m9dL2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
K	Prot_ATP_ID_OB_C	e3m9dK3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
K	Prot_ATP_ID_OB_N	e3m9dK2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
J	Prot_ATP_ID_OB_C	e3m9dJ3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
J	Prot_ATP_ID_OB_N	e3m9dJ2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
F	Prot_ATP_ID_OB_C	e3m9dF3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
F	Prot_ATP_ID_OB_N	e3m9dF2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
E	Prot_ATP_ID_OB_C	e3m9dE3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
E	Prot_ATP_ID_OB_N	e3m9dE2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
D	Prot_ATP_ID_OB_C	e3m9dD3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
D	Prot_ATP_ID_OB_N	e3m9dD2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
C	Prot_ATP_ID_OB_C	e3m9dC3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
C	Prot_ATP_ID_OB_N	e3m9dC2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
B	Prot_ATP_ID_OB_C	e3m9dB3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
B	Prot_ATP_ID_OB_N	e3m9dB2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)
A	Prot_ATP_ID_OB_C	e3m9dA3	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_C	ECOD (1.6)
A	Prot_ATP_ID_OB_N	e3m9dA2	A: beta barrels	X: OB-fold	H: Nucleic acid-binding proteins (From Topology)	T: Nucleic acid-binding proteins	F: Prot_ATP_ID_OB_N	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	PF16450	Proteasomal ATPase OB C-terminal domain (Prot_ATP_ID_OB_C)	Proteasomal ATPase OB C-terminal domain	This is the C-terminal interdomain (ID) or oligonucleotide binding (OB) domain of proteasomal ATPase [1-2]	Domain
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	PF17758	Proteasomal ATPase OB N-terminal domain (Prot_ATP_ID_OB_N)	Proteasomal ATPase OB N-terminal domain	This is N-terminal interdomain (ID), oligonucleotide binding (OB) domain of proteasomal ATPase [1-2].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
G, H, I, P, Q G, H, I, P, Q, R	Prokaryotic ubiquitin-like protein pup	protein tag activity molecular tag activity molecular adaptor activity protein-containing complex binding binding proteasome binding	catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process peptidyl-lysine modification macromolecule modification catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process cellular process macromolecule metabolic process protein metabolic process peptidyl-lysine modification macromolecule modification protein pupylation peptidyl-amino acid modification protein modification process post-translational protein modification protein modification by small protein conjugation protein modification by small protein conjugation or removal proteasomal protein catabolic process	-
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	Proteasome-associated ATPase	protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity 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 protein-macromolecule adaptor activity ubiquitin-like protein reader activity molecular adaptor activity 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 pyrophosphatase activity ATP hydrolysis activity ribonucleoside triphosphate phosphatase activity hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides hydrolase activity hydrolase activity, acting on acid anhydrides catalytic activity ATP-dependent activity ATP-dependent peptidase activity peptidase activity catalytic activity, acting on a protein identical protein binding protein binding	catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteasomal ubiquitin-independent protein catabolic process catabolic process proteolysis involved in protein catabolic process proteasomal protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process proteolysis metabolic process cellular process protein metabolic process macromolecule metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteasomal ubiquitin-independent protein catabolic process protein unfolding response to nitrosative stress response to stimulus response to stress symbiont-mediated perturbation of host defense response cellular response to stimulus biological process involved in interspecies interaction between organisms symbiont-mediated perturbation of host immune response cellular response to oxidative stress cellular response to chemical stress biological process involved in interaction with host biological process involved in symbiotic interaction response to oxidative stress cellular response to chemical stimulus cellular response to stress symbiont-mediated perturbation of host process response to chemical symbiont defense to host-produced reactive oxygen species symbiont-mediated perturbation of host innate immune response modulation of process of another organism cellular response to nitrogen compound response to oxygen-containing compound response to nitrogen compound cellular response to oxygen-containing compound cellular response to nitric oxide response to nitric oxide cellular response to reactive nitrogen species response to other organism symbiont-mediated perturbation of host defenses symbiont-mediated response to host defenses response to external stimulus response to biotic stimulus response to host response to external biotic stimulus	cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall proteasome accessory complex protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome complex endopeptidase complex cell periphery cellular anatomical structure plasma membrane membrane external encapsulating structure cell wall peptidoglycan-based cell wall proteasome accessory complex protein-containing complex intracellular anatomical structure catalytic complex peptidase complex proteasome complex endopeptidase complex proteasome-activating nucleotidase complex intracellular protein-containing complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
G, H, I, P, Q G, H, I, P, Q, R	IPR008515	Prokaryotic ubiquitin-like protein Pup	Family
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR041626	Proteasomal ATPase, N-terminal OB domain	Domain
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR003593	AAA+ ATPase domain	Domain
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR003959	ATPase, AAA-type, core	Domain
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR027417	P-loop containing nucleoside triphosphate hydrolase	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR050168	AAA ATPase domain-containing protein	Family
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR032501	Proteasomal ATPase, second OB domain	Domain
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR022482	Proteasome ATPase	Family
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR003960	ATPase, AAA-type, conserved site	Conserved Site
A, B, C, D, E A, B, C, D, E, F, J, K, L, M, N, O	IPR012340	Nucleic acid-binding, OB-fold	Homologous Superfamily

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Crystal structure of the prokaryotic ubiquintin-like protein Pup complexed with the hexameric proteasomal ATPase Mpa which includes the amino terminal coiled coil domain and the inter domain

External Resource: Annotation

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

3M9D | pdb_00003m9d