5NKZ | pdb_00005nkz

Crystal structure of H. polymorpha ubiquitin conjugating enzyme Pex4p in complex with soluble domain of Pex22p

External Resource: Annotation

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: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
D [auth B]	SCOP2B Superfamily	UBC-like	8059994	3000570	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	UBC-like	8059994	3000570	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)
C	UNK_F_TYPE	e5nkzC1	A: a/b three-layered sandwiches	X: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase (From Topology)	H: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase (From Topology)	T: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase	F: UNK_F_TYPE	ECOD (1.6)
B [auth D]	UNK_F_TYPE	e5nkzD1	A: a/b three-layered sandwiches	X: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase (From Topology)	H: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase (From Topology)	T: NadA-like/4-hydroxy-3-methylbut-2-enyl diphosphate reductase	F: UNK_F_TYPE	ECOD (1.6)
D [auth B]	UQ_con	e5nkzB1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)
A	UQ_con	e5nkzA1	A: a+b two layers	X: UBC-like	H: UBC-like (From Topology)	T: UBC-like	F: UQ_con	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
D [auth B]	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)
A	3.10.110.10	Alpha Beta	Roll	Ubiquitin Conjugating Enzyme	Ubiquitin Conjugating Enzyme	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, D [auth B]	PF00179	Ubiquitin-conjugating enzyme (UQ_con)	Ubiquitin-conjugating enzyme	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cystein ...	Proteins destined for proteasome-mediated degradation may be ubiquitinated. Ubiquitination follows conjugation of ubiquitin to a conserved cysteine residue of UBC homologues. TSG101 is one of several UBC homologues that lacks this active site cysteine [4, 5].	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
B [auth D], C	Peroxin 22	-	cellular component organization peroxisome organization organelle organization cellular process cellular component organization or biogenesis	membrane-bounded organelle intracellular anatomical structure membrane peroxisome intracellular membrane-bounded organelle microbody membrane intracellular organelle cellular anatomical structure bounding membrane of organelle organelle peroxisomal membrane microbody cytoplasm organelle membrane
A, D [auth B]	Ubiquitin-conjugating enzyme E2-21 kDa	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 aminoacyltransferase activity ubiquitin-like protein transferase activity catalytic activity, acting on a protein acyltransferase activity transferase activity catalytic activity ubiquitin-protein transferase activity ubiquitin conjugating enzyme activity ubiquitin-like protein conjugating enzyme activity	cellular component organization peroxisome organization organelle organization cellular process cellular component organization or biogenesis primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation cellular component organization peroxisome organization organelle organization cellular process cellular component organization or biogenesis primary metabolic process protein ubiquitination macromolecule modification metabolic process protein metabolic process macromolecule metabolic process post-translational protein modification protein modification process protein modification by small protein conjugation protein modification by small protein conjugation or removal	-

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
B [auth D], C	IPR024359	Peroxisome assembly protein 22	Family
B [auth D], C	IPR038613	Peroxin 22, C-terminal domain superfamiliy	Homologous Superfamily
A, D [auth B]	IPR050113	Ubiquitin-conjugating enzyme	Family
A, D [auth B]	IPR016135	Ubiquitin-conjugating enzyme/RWD-like	Homologous Superfamily
A, D [auth B]	IPR000608	Ubiquitin-conjugating (UBC), catalytic core domain	Domain
A, D [auth B]	IPR023313	Ubiquitin-conjugating enzyme, active site	Active Site

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.