5MKI | pdb_00005mki

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii

External Resource: Annotation

Domain Annotation: SCOP/SCOPe Classification
Domain Annotation: SCOP2 Classification
Domain Annotation: ECOD Classification
Domain Annotation: CATH
Gene Ontology: Gene Product Annotation
InterPro: Protein Family Classification

Domain Annotation: SCOP/SCOPe Classification SCOP-e Database Homepage

Chains	Domain Info	Class	Fold	Superfamily	Family	Domain	Species	Provenance Source (Version)
N	d5mkin_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
M	d5mkim_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
L	d5mkil_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
K	d5mkik_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
J	d5mkij_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
I	d5mkii_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
H	d5mkih_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
G	d5mkig_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
F	d5mkif_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
E	d5mkie_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
D	d5mkid_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
C	d5mkic_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
B	d5mkib_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)
A	d5mkia_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii SB ) [TaxId: 406327 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
N	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
M	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
L	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
K	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
J	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
I	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
H	SCOP2 Family	Sm motif of small nuclear ribonucleoproteins, SNRNP	8063439	4001809	SCOP2 (2022-06-29)
H	SCOP2 Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2 (2022-06-29)
G	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
F	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
E	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
D	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
C	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
A	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	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)
N	UQ_con	e5mkiN1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
M	UQ_con	e5mkiM1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
L	UQ_con	e5mkiL1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
K	UQ_con	e5mkiK1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
J	UQ_con	e5mkiJ1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
I	UQ_con	e5mkiI1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
H	UQ_con	e5mkiH1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
G	UQ_con	e5mkiG1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
F	UQ_con	e5mkiF1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
E	UQ_con	e5mkiE1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
D	UQ_con	e5mkiD1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
C	UQ_con	e5mkiC1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
B	UQ_con	e5mkiB1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)
A	UQ_con	e5mkiA1	A: a/b three-layered sandwiches	X: Periplasmic binding protein-like II	H: Rubredoxin-related	T: Tetrapyrrole methylase C-terminal domain	F: UQ_con	ECOD (v294.1)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Homology	Provenance Source (Version)
N	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
M	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
L	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
K	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
J	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
I	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
G	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.		CATH (4.3.0)

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, I, J, K, L, M, N	Like-Sm ribonucleoprotein core	RNA binding binding nucleic acid binding cation binding ion binding metal ion binding small molecule binding	-	protein-containing complex ribonucleoprotein complex

InterPro: Protein Family Classification InterPro Database Homepage

Chains	Accession	Name	Type
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR010920	LSM domain superfamily	Homologous Superfamily
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR047575	Sm domain	Domain
A, B, C, D, E A, B, C, D, E, F, G, H, I, J, K, L, M, N	IPR022901	snRNP Sm-like, putative, archaea	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. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.