5MKN | pdb_00005mkn

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
Protein Family Annotation
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)
Y [auth Z]	d5mknz_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
X [auth Y]	d5mkny_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
W [auth X]	d5mknx_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
V [auth W]	d5mknw_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
U [auth V]	d5mknv_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
T [auth U]	d5mknu_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
S [auth T]	d5mknt_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
R	d5mknr_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
Q	d5mknq_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
P	d5mknp_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
O	d5mkno_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
N	d5mknn_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
M	d5mknm_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
L	d5mknl_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
K	d5mknk_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
J	d5mknj_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
I	d5mkni_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
H	d5mknh_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
G	d5mkng_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
F	d5mknf_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
E	d5mkne_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
D	d5mknd_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
C	d5mknc_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
B	d5mknb_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)
A	d5mkna_	All beta proteins	Sm-like fold	Sm-like ribonucleoproteins	automated matches	automated matches	(Methanococcus vannielii ) [TaxId: 2187 ],	SCOPe (2.08)

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Chains	Type	Family Name	Domain Identifier	Family Identifier	Provenance Source (Version)
Z [auth a]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
Y [auth Z]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
X [auth Y]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
W [auth X]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
V [auth W]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
U [auth V]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
T [auth U]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
S [auth T]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
R	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
Q	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
P	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
O	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
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	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (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)
BA [auth d]	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
B	SCOP2B Superfamily	Sm-like ribonucleoproteins	8063440	3000419	SCOP2B (2022-06-29)
AA [auth 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)
Z [auth a]	LSM	e5mkna1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
Y [auth Z]	LSM	e5mknZ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
X [auth Y]	LSM	e5mknY1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
W [auth X]	LSM	e5mknX1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
V [auth W]	LSM	e5mknW1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
U [auth V]	LSM	e5mknV1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
T [auth U]	LSM	e5mknU1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
S [auth T]	LSM	e5mknT1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
R	LSM	e5mknR1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
Q	LSM	e5mknQ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
P	LSM	e5mknP1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
O	LSM	e5mknO1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
N	LSM	e5mknN1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
M	LSM	e5mknM1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
L	LSM	e5mknL1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
K	LSM	e5mknK1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
J	LSM	e5mknJ1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
I	LSM	e5mknI1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
H	LSM	e5mknH1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
G	LSM	e5mknG1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
F	LSM	e5mknF1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
E	LSM	e5mknE1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
D	LSM	e5mknD1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
C	LSM	e5mknC1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
BA [auth d]	LSM	e5mknd1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
B	LSM	e5mknB1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
AA [auth b]	LSM	e5mknb1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)
A	LSM	e5mknA1	A: beta barrels	X: SH3	H: SH3	T: SH3	F: LSM	ECOD (1.6)

Domain Annotation: CATH CATH Database Homepage

Chain	Domain	Class	Architecture	Topology	Provenance Source (Version)
Z [auth a]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
Y [auth Z]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
X [auth Y]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
W [auth X]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
V [auth W]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
U [auth V]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
T [auth U]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
S [auth T]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
R	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
Q	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
P	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
O	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
N	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
M	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
L	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
K	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
J	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
I	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
H	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
G	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
F	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
E	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
D	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
C	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
BA [auth d]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
B	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
AA [auth b]	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)
A	2.30.30.100	Mainly Beta	Roll	SH3 type barrels.	CATH (utative)

Protein Family Annotation Pfam Database Homepage

Chains	Accession	Name	Description	Comments	Source
A, AA [auth b], B, BA [auth d], C, A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	PF01423	LSM domain (LSM)	LSM domain	The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) i ...	The LSM domain contains Sm proteins as well as other related LSM (Like Sm) proteins. The U1, U2, U4/U6, and U5 small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing contain seven Sm proteins (B/B', D1, D2, D3, E, F and G) in common, which assemble around the Sm site present in four of the major spliceosomal small nuclear RNAs. The U6 snRNP binds to the LSM (Like Sm) proteins [3]. Sm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Sm proteins. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. This family also includes the bacterial Hfq (host factor Q) proteins. Hfq are also RNA-binding proteins, that form hexameric rings.	Domain

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

Chains	Polymer	Molecular Function	Biological Process	Cellular Component
A, AA [auth b], B, BA [auth d], C, A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	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, AA [auth b], B, BA [auth d], C, A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR001163	Sm domain, eukaryotic/archaea-type	Domain
A, AA [auth b], B, BA [auth d], C, A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR010920	LSM domain superfamily	Homologous Superfamily
A, AA [auth b], B, BA [auth d], C, A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR047575	Sm domain	Domain
A, AA [auth b], B, BA [auth d], C, A, AA [auth b], B, BA [auth d], C, D, E, F, G, H, I, J, K, L, M, N, O, P, Q, R, S [auth T], T [auth U], U [auth V], V [auth W], W [auth X], X [auth Y], Y [auth Z], Z [auth a]	IPR022901	snRNP Sm-like, putative, archaea	Family

Prepare Data

Validate Data

Deposit Data

Help and Resources

.id_divider{ color: #ccc; padding: 0 10px 0 10px; } .extended_id_info{ color: #ccc; font-size: 18px; position: relative; top: -10px; left: 4px; } 5MKN | pdb_00005mkn

Crystal structure of SmAP (LSm) protein from Methanococcus vannielii

External Resource: Annotation

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

Domain Annotation: SCOP2 Classification SCOP2 Database Homepage

Domain Annotation: ECOD Classification ECOD Database Homepage

Domain Annotation: CATH CATH Database Homepage

Protein Family Annotation Pfam Database Homepage

Gene Ontology: Gene Product Annotation Gene Ontology Database Homepage

InterPro: Protein Family Classification InterPro Database Homepage

5MKN | pdb_00005mkn