2Y00 - JenaLib

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Title :   TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND PARTIAL AGONIST DOBUTAMINE (CRYSTAL DOB92)

Authors :   A. Warne, R. Moukhametzianov, J. G. Baker, R. Nehme, P. C. Edwards, A. G. G. F. X. Schertler, C. G. Tate

Date :   30 Nov 10 (Deposition) - 12 Jan 11 (Release) - 30 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

Chains :   Asym. Unit : A,B
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: A,B  (1x)

Keywords :   G Protein Coupled Receptor, Seven-Helix Receptor, Integral Membrane Protein, Thermostabilising Point Mutations, Gpcr, Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Warne, R. Moukhametzianov, J. G. Baker, R. Nehme, P. C. Edwards, A. G. W. Leslie, G. F. X. Schertler, C. G. Tate
The Structural Basis For Agonist And Partial Agonist Action On A Beta1-Adrenergic Receptor
Nature V. 469 241 2011
PubMed-ID: 21228877 | Reference-DOI: 10.1038/NATURE09746
(for further references see the PDB file header)

Molecule 1 - BETA-1 ADRENERGIC RECEPTOR
	Cell	:	ERYTHROCYTE
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	TRICHOPLUSIA NI
	Expression System Cell Line	:	HIGH FIVE
	Expression System Common	:	CABBAGE LOOPER
	Expression System Plasmid	:	PBACPAK8
	Expression System Taxid	:	7111
	Expression System Vector Type	:	BACULOVIRUS
	Fragment	:	RESIDUES 33-368
	Mutation	:	YES
	Organism Common	:	TURKEY
	Organism Scientific	:	MELEAGRIS GALLOPAVO
	Organism Taxid	:	9103
	Other Details	:	RESIDUES 3-32 AT THE N-TERMINUS AND RESIDUES 244-271 OF THE THIRD INTRACELLULAR LOOP WERE DELETED FROM THE CONSTRUCT. THE CONSTRUCT WAS TRUNCATED AFTER RESIDUE 367 AND A HEXAHIS TAG ADDED.
	Synonym	:	BETA-1 ADRENORECEPTOR, BETA-1 ADRENOCEPTOR, BETA-T

		1	2
Asymmetric Unit	:	A	B
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 17)

No.	Name	Count	Type	Full Name
1	2CV	10	Ligand/Ion	HEGA-10
2	NA	1	Ligand/Ion	SODIUM ION
3	Y00	2	Ligand/Ion	DOBUTAMINE
4	Y01	4	Ligand/Ion	CHOLESTEROL HEMISUCCINATE

Biological Unit 1 (3, 8)

No.	Name	Count	Type	Full Name
1	2CV	5	Ligand/Ion	HEGA-10
2	NA	-1	Ligand/Ion	SODIUM ION
3	Y00	1	Ligand/Ion	DOBUTAMINE
4	Y01	2	Ligand/Ion	CHOLESTEROL HEMISUCCINATE

Biological Unit 2 (3, 8)

No.	Name	Count	Type	Full Name
1	2CV	5	Ligand/Ion	HEGA-10
2	NA	-1	Ligand/Ion	SODIUM ION
3	Y00	1	Ligand/Ion	DOBUTAMINE
4	Y01	2	Ligand/Ion	CHOLESTEROL HEMISUCCINATE

Biological Unit 3 (3, 16)

No.	Name	Count	Type	Full Name
1	2CV	10	Ligand/Ion	HEGA-10
2	NA	-1	Ligand/Ion	SODIUM ION
3	Y00	2	Ligand/Ion	DOBUTAMINE
4	Y01	4	Ligand/Ion	CHOLESTEROL HEMISUCCINATE

Asymmetric Unit (16, 16)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	CYS A:133 , ARG A:157 , ILE A:161 , HOH A:2019 , ARG B:205 , ALA B:206 , ILE B:209 , 2CV B:503	BINDING SITE FOR RESIDUE Y01 A 401
02	AC2	SOFTWARE	LEU A:78 , CYS A:85 , ARG A:155 , TRP A:166	BINDING SITE FOR RESIDUE Y01 A 402
03	AC3	SOFTWARE	HIS A:180 , TRP A:181 , ASP A:184 , GLU A:185 , ASN A:204 , VAL B:160 , THR B:164 , Y01 B:401 , 2CV B:505 , HOH B:2019	BINDING SITE FOR RESIDUE 2CV A 501
04	AC4	SOFTWARE	LEU A:289	BINDING SITE FOR RESIDUE 2CV A 502
05	AC5	SOFTWARE	ARG A:205 , PHE A:315 , ARG B:148 , LEU B:152 , ARG B:157 , Y01 B:401	BINDING SITE FOR RESIDUE 2CV A 503
06	AC6	SOFTWARE	VAL A:51 , ALA A:334	BINDING SITE FOR RESIDUE 2CV A 504
07	AC7	SOFTWARE	CYS A:163 , TRP B:181 , 2CV B:501	BINDING SITE FOR RESIDUE 2CV A 505
08	AC8	SOFTWARE	LEU A:101 , VAL A:102 , TRP A:117 , ASP A:121 , PHE A:201 , SER A:211 , PHE A:306 , ASN A:310 , ASN A:329 , TRP A:330 , TYR A:333	BINDING SITE FOR RESIDUE Y00 A 601
09	AC9	SOFTWARE	CYS A:192 , ASP A:195 , CYS A:198 , HOH A:2005	BINDING SITE FOR RESIDUE NA A1359
10	BC1	SOFTWARE	ARG A:205 , ALA A:206 , ILE A:209 , 2CV A:501 , 2CV A:503 , GLU B:130 , CYS B:133 , ARG B:157 , VAL B:160 , ILE B:161 , THR B:164 , ILE B:168 , ILE B:214 , HOH B:2019	BINDING SITE FOR RESIDUE Y01 B 401
11	BC2	SOFTWARE	LEU B:78 , ARG B:155 , LYS B:159 , TRP B:166	BINDING SITE FOR RESIDUE Y01 B 402
12	BC3	SOFTWARE	VAL A:160 , THR A:164 , 2CV A:505 , HIS B:180 , TRP B:181 , ARG B:183 , ASP B:184 , GLU B:185	BINDING SITE FOR RESIDUE 2CV B 501
13	BC4	SOFTWARE	TYR B:231 , HIS B:286 , LEU B:289	BINDING SITE FOR RESIDUE 2CV B 502
14	BC5	SOFTWARE	ARG A:157 , Y01 A:401 , ARG B:205 , PHE B:315	BINDING SITE FOR RESIDUE 2CV B 503
15	BC6	SOFTWARE	GLU A:185 , 2CV A:501 , CYS B:163	BINDING SITE FOR RESIDUE 2CV B 505
16	BC7	SOFTWARE	VAL B:102 , TRP B:117 , ASP B:121 , VAL B:125 , SER B:211 , PHE B:307 , ASN B:310 , ASN B:329 , TRP B:330 , TYR B:333	BINDING SITE FOR RESIDUE Y00 B 601

Asymmetric Unit

No.	Residues
1	A:114	-	A:199
2	A:192	-	A:198
3	B:114	-	B:199
4	B:192	-	B:198

(no "Cis Peptide Bond" information available for 2Y00)

(no "SAP(SNP)/Variant" information available for 2Y00)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	ADRB1_MELGA	127-143	2	A:127-143 B:127-143

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	ADRB1_MELGA	127-143	1	A:127-143 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	ADRB1_MELGA	127-143	1	- B:127-143

Biological Unit 3 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	G_PROTEIN_RECEP_F1_1	PS00237	G-protein coupled receptors family 1 signature.	ADRB1_MELGA	127-143	2	A:127-143 B:127-143

(no "Exon" information available for 2Y00)

Asymmetric Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
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Chain A from PDB  Type:PROTEIN  Length:286
 aligned with ADRB1_MELGA | P07700 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:326
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      
          ADRB1_MELGA    33 AELLSQQWEAGMSLLMALVVLLIVAGNVLVIAAIGRTQRLQTLTNLFITSLACADLVMGLLVVPFGATLVVRGTWLWGSFLCECWTSLDVLCVTASIETLCVIAIDRYLAITSPFRYQSLMTRARAKVIICTVWAISALVSFLPIMMHWWRDEDPQALKCYQDPGCCDFVTNRAYAIASSIISFYIPLLIMIFVYLRVYREAKEQIRKIDRCEGRFYGSQEQPQPPPLPQHQPILGNGRASKRKTSRVMAMREHKALKTLGIIMGVFTLCWLPFFLVNIVNVFNRDLVPDWLFVFFNWLGYANSAFNPIIYCRSPDFRKAFKRLLC 358
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.----------------------------------------hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y00 A  33 AELLSQQWEAGMSLLMALVVLLIVAGNVLVIAAIGSTQRLQTLTNLFITSLACADLVVGLLVVPFGATLVVRGTWLWGSFLCELWTSLDVLCVTASIETLCVIAIDRYLAITSPFRYQSLMTRARAKVIICTVWAISALVSFLPIMMHWWRDEDPQALKCYQDPGCCDFVTNRAYAIASSIISFYIPLLIMIFVALRVYREAKEQ----------------------------------------SRVMLMREHKALKTLGIIMGVFTLCWLPFFLVNIVNVFNRDLVPDWLFVAFNWLGYANSAMNPIIYCRSPDFRKAFKRLLA 358
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    |    -         -         -         -     | 282       292       302       312       322       332       342       352      
                                                                                                                                                                                                                                      237                                      278

Chain B from PDB  Type:PROTEIN  Length:298
 aligned with ADRB1_MELGA | P07700 from UniProtKB/Swiss-Prot  Length:483

    Alignment length:326
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352      
          ADRB1_MELGA    33 AELLSQQWEAGMSLLMALVVLLIVAGNVLVIAAIGRTQRLQTLTNLFITSLACADLVMGLLVVPFGATLVVRGTWLWGSFLCECWTSLDVLCVTASIETLCVIAIDRYLAITSPFRYQSLMTRARAKVIICTVWAISALVSFLPIMMHWWRDEDPQALKCYQDPGCCDFVTNRAYAIASSIISFYIPLLIMIFVYLRVYREAKEQIRKIDRCEGRFYGSQEQPQPPPLPQHQPILGNGRASKRKTSRVMAMREHKALKTLGIIMGVFTLCWLPFFLVNIVNVFNRDLVPDWLFVFFNWLGYANSAFNPIIYCRSPDFRKAFKRLLC 358
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------------------------7tm_1-2y00B01 B:58-343                                                                                                                                                                                                                                                                        --------------- Pfam domains (1)
           Pfam domains (2) -------------------------7tm_1-2y00B02 B:58-343                                                                                                                                                                                                                                                                        --------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....----------------------------....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhh.hhhhhhh..hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------G_PROTEIN_RECEP_F----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2y00 B  33 AELLSQQWEAGMSLLMALVVLLIVAGNVLVIAAIGSTQRLQTLTNLFITSLACADLVVGLLVVPFGATLVVRGTWLWGSFLCELWTSLDVLCVTASIETLCVIAIDRYLAITSPFRYQSLMTRARAKVIICTVWAISALVSFLPIMMHWWRDEDPQALKCYQDPGCCDFVTNRAYAIASSIISFYIPLLIMIFVALRVYREAKEQIRKIDR----------------------------ASKRKTSRVMLMREHKALKTLGIIMGVFTLCWLPFFLVNIVNVFNRDLVPDWLFVAFNWLGYANSAMNPIIYCRSPDFRKAFKRLLA 358
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242|        -         -       272       282       292       302       312       322       332       342       352      
                                                                                                                                                                                                                                            243                          272

Legend:		→ Mismatch	(orange background)
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	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 2Y00)

(no "CATH Domain" information available for 2Y00)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GPCR_A (90)

Family: 7tm_1 (47)

Meleagris gallopavo (Common turkey) (10)

1a	7tm_1-2y00B01	B:58-343
1b	7tm_1-2y00B02	B:58-343

Asymmetric Unit(hide GO term definitions)

Chain A,B (ADRB1_MELGA | P07700)

molecular function
	GO:0004930	G-protein coupled receptor activity	Combining with an extracellular signal and transmitting the signal across the membrane by activating an associated G-protein; promotes the exchange of GDP for GTP on the alpha subunit of a heterotrimeric G-protein complex.
	GO:0005088	Ras guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Ras superfamily. Under normal cellular physiological conditions, the concentration of GTP is higher than that of GDP, favoring the replacement of GDP by GTP in association with the GTPase.
	GO:0004935	adrenergic receptor activity	Combining with epinephrine or norepinephrine and transmitting the signal across the membrane by activating the alpha-subunit of an associated heterotrimeric G-protein complex.
	GO:0004940	beta1-adrenergic receptor activity	Combining with epinephrine or norepinephrine to initiate a change in cell activity via activation of a G protein, with pharmacological characteristics of beta1-adrenergic receptors.
	GO:0008144	drug binding	Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
	GO:0004871	signal transducer activity	Conveys a signal across a cell to trigger a change in cell function or state. A signal is a physical entity or change in state that is used to transfer information in order to trigger a response.
	GO:0005057	signal transducer activity, downstream of receptor	Conveys a signal from an upstream receptor or intracellular signal transducer, converting the signal into a form where it can ultimately trigger a change in the state or activity of a cell.
	GO:0031402	sodium ion binding	Interacting selectively and non-covalently with sodium ions (Na+).
	GO:0050824	water binding	Interacting selectively and non-covalently with water (H2O).
biological process
	GO:0007186	G-protein coupled receptor signaling pathway	A series of molecular signals that proceeds with an activated receptor promoting the exchange of GDP for GTP on the alpha-subunit of an associated heterotrimeric G-protein complex. The GTP-bound activated alpha-G-protein then dissociates from the beta- and gamma-subunits to further transmit the signal within the cell. The pathway begins with receptor-ligand interaction, or for basal GPCR signaling the pathway begins with the receptor activating its G protein in the absence of an agonist, and ends with regulation of a downstream cellular process, e.g. transcription. The pathway can start from the plasma membrane, Golgi or nuclear membrane (PMID:24568158 and PMID:16902576).
	GO:0007189	adenylate cyclase-activating G-protein coupled receptor signaling pathway	The series of molecular signals generated as a consequence of a G-protein coupled receptor binding to its physiological ligand, where the pathway proceeds through activation of adenylyl cyclase activity and a subsequent increase in the concentration of cyclic AMP (cAMP).
	GO:0071880	adenylate cyclase-activating adrenergic receptor signaling pathway	The series of molecular signals generated as a consequence of an adrenergic receptor binding to its physiological ligand, where the pathway proceeds with activation of adenylyl cyclase and a subsequent increase in the concentration of cyclic AMP (cAMP).
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0030819	positive regulation of cAMP biosynthetic process	Any process that activates or increases the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of the nucleotide cAMP (cyclic AMP, adenosine 3',5'-cyclophosphate).
	GO:0043950	positive regulation of cAMP-mediated signaling	Any process which activates, maintains or increases the frequency, rate or extent of cAMP-mediated signaling, a series of molecular signals in which a cell uses cyclic AMP to convert an extracellular signal into a response.
	GO:0045823	positive regulation of heart contraction	Any process that activates or increases the frequency, rate or extent of heart contraction.
	GO:0007165	signal transduction	The cellular process in which a signal is conveyed to trigger a change in the activity or state of a cell. Signal transduction begins with reception of a signal (e.g. a ligand binding to a receptor or receptor activation by a stimulus such as light), or for signal transduction in the absence of ligand, signal-withdrawal or the activity of a constitutively active receptor. Signal transduction ends with regulation of a downstream cellular process, e.g. regulation of transcription or regulation of a metabolic process. Signal transduction covers signaling from receptors located on the surface of the cell and signaling via molecules located within the cell. For signaling between cells, signal transduction is restricted to events at and within the receiving cell.
cellular component
	GO:0005769	early endosome	A membrane-bounded organelle that receives incoming material from primary endocytic vesicles that have been generated by clathrin-dependent and clathrin-independent endocytosis; vesicles fuse with the early endosome to deliver cargo for sorting into recycling or degradation pathways.
	GO:0005768	endosome	A vacuole to which materials ingested by endocytosis are delivered.
	GO:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0005887	integral component of plasma membrane	The component of the plasma membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005886	plasma membrane	The membrane surrounding a cell that separates the cell from its external environment. It consists of a phospholipid bilayer and associated proteins.

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1dep	MEMBRANE PROTEIN, NMR, 1 STRUCTURE
2vt4	TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND CYANOPINDOLOL
2y01	TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND PARTIAL AGONIST DOBUTAMINE (CRYSTAL DOB102)
2y02	TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND AGONIST CARMOTEROL
2y03	TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND AGONIST ISOPRENALINE
2y04	TURKEY BETA1 ADRENERGIC RECEPTOR WITH STABILISING MUTATIONS AND BOUND PARTIAL AGONIST SALBUTAMOL

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 17)

Sites (16, 16)

SS Bonds (4, 4)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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Pfam Domains (1, 2)

Gene Ontology (23, 23)

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