5IZN | pdb_00005izn

The crystal structure of 50S ribosomal protein L25 from Vibrio vulnificus CMCP6

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)
H	SCOP2 Family	Ribosomal protein L25-like	8100113	4002376	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Ribosomal protein L25-like	8100114	3001161	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)
H	Ribosomal_L25p	e5iznH1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
G	Ribosomal_L25p	e5iznG1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
F	Ribosomal_L25p	e5iznF1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
E	Ribosomal_L25p	e5iznE1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
D	Ribosomal_L25p	e5iznD1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
C	Ribosomal_L25p	e5iznC1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
B	Ribosomal_L25p	e5iznB1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)
A	Ribosomal_L25p	e5iznA1	A: beta barrels	X: Ribosomal protein L25-like	H: Ribosomal protein L25-like (From Topology)	T: Ribosomal protein L25-like	F: Ribosomal_L25p	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
H	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
G	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
F	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
E	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
D	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
C	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
B	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)
A	2.40.240.10	Mainly Beta	Beta Barrel	Ribosomal Protein L25	Chain P	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D, E A, B, C, D, E, F, G, H	PF01386	Ribosomal L25p family (Ribosomal_L25p)	Ribosomal L25p family	Ribosomal protein L25 is an RNA binding protein, that binds 5S rRNA. This family includes Ctc from B. subtilis Swiss:P14194, which is induced by stress.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D, E A, B, C, D, E, F, G, H	50S ribosomal protein L25	RNA binding binding rRNA binding 5S rRNA binding nucleic acid binding structural molecule activity structural constituent of ribosome	biosynthetic process metabolic process cellular process primary metabolic process protein metabolic process macromolecule metabolic process translation gene expression protein biosynthetic process macromolecule biosynthetic process	protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol protein-containing complex intracellular anatomical structure intracellular membraneless organelle intracellular organelle ribosomal subunit cytosolic large ribosomal subunit cellular anatomical structure cytosolic ribosome organelle ribonucleoprotein complex membraneless organelle ribosome cytoplasm cytosol large ribosomal subunit

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H	IPR011035	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, anti-codon-binding domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020055	Ribosomal protein bL25, short-form	Family
A, B, C, D, E A, B, C, D, E, F, G, H	IPR029751	Large ribosomal subunit protein bL25, L25 domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020056	Large ribosomal subunit protein bL25/Gln-tRNA synthetase, N-terminal	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H	IPR020930	Large ribosomal subunit protein uL5, bacteria	Family

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.