7NPI

Crystal structure of Mindy2 (C266A) in complex with Lys48-linked penta-ubiquitin (K48-Ub5)

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
EA [auth e]	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
G	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
KA [auth k]	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
S	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
Y	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Cysteine proteinases	8103488	3001808	SCOP2B (2022-06-29)
AA [auth a]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
BA [auth b]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
CA [auth c]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
DA [auth d]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
FA [auth f]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
GA [auth g]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
H	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
HA [auth h]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
IA [auth i]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
JA [auth j]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
LA [auth l]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
MA [auth m]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
N	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
NA [auth n]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
OA [auth o]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
T	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
U	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
V	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
W	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
X	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
Z	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
PA [auth p]	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Ubiquitin-like	8043829	3000157	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)
EA [auth e]	PF04424	e7npie1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
G	PF04424	e7npiG1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
KA [auth k]	PF04424	e7npik1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
M	PF04424	e7npiM1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
S	PF04424	e7npiS1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
Y	PF04424	e7npiY1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
A	PF04424	e7npiA1	A: a+b complex topology	X: Cysteine proteinases-like	H: Cysteine proteinases (From Topology)	T: Cysteine proteinases	F: PF04424	ECOD (1.6)
AA [auth a]	PF00240	e7npia1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
B	PF00240	e7npiB1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
BA [auth b]	PF00240	e7npib1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
C	PF00240	e7npiC1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
CA [auth c]	PF00240	e7npic1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
D	PF00240	e7npiD1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
DA [auth d]	PF00240	e7npid1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
E	PF00240	e7npiE1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
F	PF00240	e7npiF1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
FA [auth f]	PF00240	e7npif1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
GA [auth g]	PF00240	e7npig1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
H	PF00240	e7npiH1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
HA [auth h]	PF00240	e7npih1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
I	PF00240	e7npiI1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
IA [auth i]	PF00240	e7npii1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
J	PF00240	e7npiJ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
JA [auth j]	PF00240	e7npij1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
K	PF00240	e7npiK1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
LA [auth l]	PF00240	e7npil1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
MA [auth m]	PF00240	e7npim1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
N	PF00240	e7npiN1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
NA [auth n]	PF00240	e7npin1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
O	PF00240	e7npiO1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
OA [auth o]	PF00240	e7npio1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
P	PF00240	e7npiP1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
R	PF00240	e7npiR1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
T	PF00240	e7npiT1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
U	PF00240	e7npiU1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
V	PF00240	e7npiV1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
W	PF00240	e7npiW1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
X	PF00240	e7npiX1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
Z	PF00240	e7npiZ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
L	PF00240	e7npiL1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
PA [auth p]	PF00240	e7npip1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)
Q	PF00240	e7npiQ1	A: a+b two layers	X: beta-Grasp	H: Ubiquitin-related	T: Ubiquitin-like	F: PF00240	ECOD (1.6)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, EA [auth e], G, KA [auth k], M, A, EA [auth e], G, KA [auth k], M, S, Y	PF04424	MINDY deubiquitinase (MINDY_DUB)	MINDY deubiquitinase	-	Family
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	PF00240	Ubiquitin family (ubiquitin)	Ubiquitin family	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry ...	This family contains a number of ubiquitin-like proteins: SUMO (smt3 homologue) (see Swiss:Q02724), Nedd8 (see Swiss:P29595), Elongin B (see Swiss:Q15370), Rub1 (see Swiss:Q9SHE7), and Parkin (see Swiss:O60260). A number of them are thought to carry a distinctive five-residue motif termed the proteasome-interacting motif (PIM), which may have a biologically significant role in protein delivery to proteasomes and recruitment of proteasomes to transcription sites [5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, EA [auth e], G, KA [auth k], M, A, EA [auth e], G, KA [auth k], M, S, Y	Ubiquitin carboxyl-terminal hydrolase MINDY-2	cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding K48-linked deubiquitinase activity cysteine-type peptidase activity ubiquitin-like protein peptidase activity peptidase activity cysteine-type deubiquitinase activity catalytic activity, acting on a protein hydrolase activity catalytic activity deubiquitinase activity polyubiquitin modification-dependent protein binding protein binding binding K48-linked polyubiquitin modification-dependent protein binding modification-dependent protein binding K48-linked deubiquitinase activity K6-linked polyubiquitin modification-dependent protein binding K63-linked polyubiquitin modification-dependent protein binding K11-linked polyubiquitin modification-dependent protein binding cysteine-type carboxypeptidase activity cysteine-type exopeptidase activity exopeptidase activity carboxypeptidase activity	organic substance metabolic process organonitrogen compound metabolic process proteolysis metabolic process primary metabolic process protein metabolic process macromolecule metabolic process	membrane-bounded organelle intracellular anatomical structure nucleus membrane-enclosed lumen intracellular membrane-bounded organelle cellular anatomical entity intracellular organelle lumen intracellular organelle nucleoplasm organelle lumen organelle nuclear lumen
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	Polyubiquitin-C	protein binding binding enzyme binding protease binding protein tag activity molecular tag activity ubiquitin protein ligase binding ubiquitin-like protein ligase binding RNA binding organic cyclic compound binding nucleic acid binding	organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organonitrogen compound catabolic process organonitrogen compound metabolic process catabolic process proteolysis involved in protein catabolic process primary metabolic process protein catabolic process macromolecule catabolic process organic substance metabolic process modification-dependent macromolecule catabolic process modification-dependent protein catabolic process proteolysis metabolic process protein metabolic process macromolecule metabolic process organic substance catabolic process protein ubiquitination macromolecule modification post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm membrane-bounded organelle intracellular anatomical structure membrane intracellular vesicle cellular anatomical entity intracellular membrane-bounded organelle intracellular organelle cytoplasmic vesicle membrane bounding membrane of organelle cytoplasmic vesicle vesicle membrane organelle endocytic vesicle membrane cytoplasm vesicle organelle membrane endocytic vesicle extracellular exosome extracellular vesicle extracellular organelle extracellular region extracellular space extracellular membrane-bounded organelle cytosol endosome membrane endosome endomembrane system mitochondrial membrane mitochondrion organelle outer membrane organelle envelope mitochondrial envelope mitochondrial outer membrane outer membrane cell periphery plasma membrane nucleus membrane-enclosed lumen intracellular organelle lumen nucleoplasm organelle lumen nuclear lumen organelle subcompartment endoplasmic reticulum subcompartment nuclear outer membrane-endoplasmic reticulum membrane network endoplasmic reticulum endoplasmic reticulum membrane

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, EA [auth e], G, KA [auth k], M, A, EA [auth e], G, KA [auth k], M, S, Y	IPR007518	MINDY deubiquitinase	Family
A, EA [auth e], G, KA [auth k], M, A, EA [auth e], G, KA [auth k], M, S, Y	IPR033979	MINDY deubiquitinase domain	Domain
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	IPR019954	Ubiquitin conserved site	Conserved Site
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	IPR000626	Ubiquitin-like domain	Domain
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	IPR019956	Ubiquitin domain	Domain
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	IPR029071	Ubiquitin-like domain superfamily	Homologous Superfamily

Pharos: Disease Associations Pharos Homepage Annotation

Chains	Drug Target	Associated Disease
A, EA [auth e], G, KA [auth k], M, A, EA [auth e], G, KA [auth k], M, S, Y	Pharos: Q8NBR6	Alzheimer disease osteosarcoma psoriasis Gaucher disease ovarian cancer spina bifida medulloblastoma pancreatic intraductal papillary-mucinous neoplasm
AA [auth a], B, BA [auth b], C, CA [auth c], AA [auth a], B, BA [auth b], C, CA [auth c], D, DA [auth d], E, F, FA [auth f], GA [auth g], H, HA [auth h], I, IA [auth i], J, JA [auth j], K, L, LA [auth l], MA [auth m], N, NA [auth n], O, OA [auth o], P, PA [auth p], Q, R, T, U, V, W, X, Z	Pharos: P0CG48	acute myeloid leukemia heart disease myocardial infarction pancreatic ductal adenocarcinoma astrocytic tumor lung cancer osteosarcoma renal cell carcinoma glioblastoma malignant pancreatic neoplasm ovarian cancer