4ODM

Structure of SlyD from Thermus thermophilus in complex with S2-W23A peptide

External Resource: Annotation

Domain Annotation: ECOD Classification
Domain Annotation: CATH
Protein Family Annotation
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification
Protein Modification Annotation

Domain Annotation: ECOD Classification ECOD Database Homepage

Chains	Family Name	Domain Identifier	Architecture	Possible Homology	Homology	Topology	Family	Provenance Source (Version)
A	FKBP_C	e4odmA2	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
A	SlpA_1	e4odmA1	A: a+b two layers	X: FKBP-like	H: Archaeal FKBP insertion domain (From Topology)	T: Archaeal FKBP insertion domain	F: SlpA_1	ECOD (1.6)
B	FKBP_C	e4odmB1	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
B	SlpA_1	e4odmB2	A: a+b two layers	X: FKBP-like	H: Archaeal FKBP insertion domain (From Topology)	T: Archaeal FKBP insertion domain	F: SlpA_1	ECOD (1.6)
C	FKBP_C	e4odmC2	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
C	SlpA_1	e4odmC1	A: a+b two layers	X: FKBP-like	H: Archaeal FKBP insertion domain (From Topology)	T: Archaeal FKBP insertion domain	F: SlpA_1	ECOD (1.6)
D	FKBP_C	e4odmD2	A: a+b two layers	X: FKBP-like	H: FKBP-like	T: FKBP-like	F: FKBP_C	ECOD (1.6)
D	SlpA_1	e4odmD1	A: a+b two layers	X: FKBP-like	H: Archaeal FKBP insertion domain (From Topology)	T: Archaeal FKBP insertion domain	F: SlpA_1	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
A	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
B	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
C	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)
D	3.10.50.40	Alpha Beta	Roll	Chitinase A	domain 3	CATH (4.3.0)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, B, C, D	PF00254	FKBP-type peptidyl-prolyl cis-trans isomerase (FKBP_C)	FKBP-type peptidyl-prolyl cis-trans isomerase	-	Domain
E, F, G, H, I E, F, G, H, I, J, K, L, M	PF00318	Ribosomal protein S2 (Ribosomal_S2)	Ribosomal protein S2	-	Family

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, B, C, D	Peptidyl-prolyl cis-trans isomerase SlyD	isomerase activity catalytic activity, acting on a protein peptidyl-prolyl cis-trans isomerase activity catalytic activity cis-trans isomerase activity cation binding ion binding binding metal ion binding small molecule binding	protein refolding organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein refolding organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process primary metabolic process gene expression macromolecule biosynthetic process protein maturation organic substance metabolic process protein folding biosynthetic process organic substance biosynthetic process metabolic process cellular process protein metabolic process macromolecule metabolic process	-
E, F, G, H, I E, F, G, H, I, J, K, L, M	30S ribosomal protein S2	cation binding transition metal ion binding zinc ion binding ion binding binding metal ion binding small molecule binding structural molecule activity structural constituent of ribosome	ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly ribonucleoprotein complex biogenesis organelle assembly protein-containing complex organization non-membrane-bounded organelle assembly ribosomal small subunit assembly protein-RNA complex assembly ribosomal small subunit biogenesis cellular component organization cellular component biogenesis ribosome biogenesis organelle organization protein-RNA complex organization cellular component assembly protein-containing complex assembly cellular process cellular component organization or biogenesis ribosome assembly organonitrogen compound metabolic process cellular biosynthetic process cellular metabolic process organonitrogen compound biosynthetic process primary metabolic process translation gene expression macromolecule biosynthetic process organic substance metabolic process biosynthetic process organic substance biosynthetic process cytoplasmic translation metabolic process protein metabolic process macromolecule metabolic process	cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit cellular anatomical entity intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome cytoplasm cytosol cytosolic small ribosomal subunit protein-containing complex intracellular anatomical structure small ribosomal subunit cellular anatomical entity intracellular organelle ribosomal subunit cytosolic ribosome organelle ribonucleoprotein complex intracellular non-membrane-bounded organelle ribosome cytoplasm cytosol non-membrane-bounded organelle

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D	IPR046357	Peptidyl-prolyl cis-trans isomerase domain superfamily	Homologous Superfamily
A, B, C, D	IPR001179	FKBP-type peptidyl-prolyl cis-trans isomerase domain	Domain
E, F, G, H, I E, F, G, H, I, J, K, L, M	IPR005706	Small ribosomal subunit protein uS2, bacteria/mitochondria/plastid	Family
E, F, G, H, I E, F, G, H, I, J, K, L, M	IPR023591	Small ribosomal subunit protein uS2, flavodoxin-like domain superfamily	Homologous Superfamily
E, F, G, H, I E, F, G, H, I, J, K, L, M	IPR018130	Small ribosomal subunit protein uS2, conserved site	Conserved Site
E, F, G, H, I E, F, G, H, I, J, K, L, M	IPR001865	Small ribosomal subunit protein uS2	Family

Protein Modification Annotation

Modified Residue(s)
Chain	Residue(s)	Description
E, F, G, H, I E, F, G, H, I, J, K, L, M	NH2	RESID: AA0081 , AA0083 , AA0084 , AA0086 , AA0087 , AA0088 , AA0090 , AA0091 , AA0092 , AA0093 , AA0095 , AA0096 , AA0097 , AA0098 , AA0099 , AA0100 PSI-MOD : L-alanine amide MOD:00090 , L-asparagine amide MOD:00092 , L-aspartic acid 1-amide MOD:00093 , L-glutamine amide MOD:00095 , L-glutamic acid 1-amide MOD:00096 , glycine amide MOD:00097 , L-isoleucine amide MOD:00099 , L-leucine amide MOD:00100 , L-lysine amide MOD:00101 , L-methionine amide MOD:00102 , L-proline amide MOD:00104 , L-serine amide MOD:00105 , L-threonine amide MOD:00106 , L-tryptophan amide MOD:00107 , L-tyrosine amide MOD:00108 , L-valine amide MOD:00109

RCSB PDB Core Operations are funded by the National Science Foundation (DBI-1832184), 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 R01GM133198.