3P6A - JenaLib

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF THE DH/PH DOMAINS OF P115-RHOGEF (R399E MUTANT)

Authors :   Z. Chen, L. Guo, S. R. Sprang, P. C. Sternweis

Date :   11 Oct 10 (Deposition) - 05 Jan 11 (Release) - 05 Jan 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Regulation Of Rhoa Gtpase, Rhogef, Dh, Ph, Rho, Signaling Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   Z. Chen, L. Guo, S. R. Sprang, P. C. Sternweis
Modulation Of A Gef Switch: Autoinhibition Of The Intrinsic Guanine Nucleotide Exchange Activity Of P115-Rhoref
Protein Sci. V. 20 107 2011
PubMed: search

Molecule 1 - RHO GUANINE NUCLEOTIDE EXCHANGE FACTOR 1
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PGEX-KG
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Fragment	:	UNP RESIDUES 377-748
	Gene	:	ARHGEF1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Synonym	:	115 KDA GUANINE NUCLEOTIDE EXCHANGE FACTOR, P115-RHOGEF, P115RHOGEF, SUB1.5

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

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 3P6A)

(no "Site" information available for 3P6A)

(no "SS Bond" information available for 3P6A)

Asymmetric Unit

No.	Residues
1	Pro A:411	-	Lys A:412
2	Lys A:639	-	Asn A:640
3	Ala A:735	-	Gln A:736
4	Lys B:639	-	Asn B:640
5	His B:690	-	Ser B:691
6	Ala B:735	-	Gln B:736

(no "SAP(SNP)/Variant" information available for 3P6A)

Asymmetric Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DH_2	PS50010	Dbl homology (DH) domain profile.	ARHG1_HUMAN	416-605	2	A:416-605 B:416-605
2	PH_DOMAIN	PS50003	PH domain profile.	ARHG1_HUMAN	647-760	2	A:647-760 B:647-760

Biological Unit 1 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DH_2	PS50010	Dbl homology (DH) domain profile.	ARHG1_HUMAN	416-605	1	A:416-605 -
2	PH_DOMAIN	PS50003	PH domain profile.	ARHG1_HUMAN	647-760	1	A:647-760 -

Biological Unit 2 (2, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DH_2	PS50010	Dbl homology (DH) domain profile.	ARHG1_HUMAN	416-605	1	- B:416-605
2	PH_DOMAIN	PS50003	PH domain profile.	ARHG1_HUMAN	647-760	1	- B:647-760

Asymmetric Unit (11, 22)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.1b	ENST00000354532	1b	ENSE00001053104	chr19:42387267-42387356	90	ARHG1_HUMAN	-	0	0	-	-
1.3	ENST00000354532	3	ENSE00002160017	chr19:42392135-42392177	43	ARHG1_HUMAN	1-8	8	0	-	-
1.4	ENST00000354532	4	ENSE00001796026	chr19:42392263-42392349	87	ARHG1_HUMAN	9-37	29	0	-	-
1.5	ENST00000354532	5	ENSE00001629400	chr19:42392823-42392936	114	ARHG1_HUMAN	38-75	38	0	-	-
1.6	ENST00000354532	6	ENSE00001605951	chr19:42396096-42396194	99	ARHG1_HUMAN	76-108	33	0	-	-
1.7	ENST00000354532	7	ENSE00001614868	chr19:42396402-42396444	43	ARHG1_HUMAN	109-123	15	0	-	-
1.8	ENST00000354532	8	ENSE00001706685	chr19:42396674-42396920	247	ARHG1_HUMAN	123-205	83	0	-	-
1.9	ENST00000354532	9	ENSE00001771138	chr19:42397345-42397374	30	ARHG1_HUMAN	205-215	11	0	-	-
1.10	ENST00000354532	10	ENSE00001613938	chr19:42398280-42398379	100	ARHG1_HUMAN	215-248	34	0	-	-
1.11	ENST00000354532	11	ENSE00001731644	chr19:42398524-42398620	97	ARHG1_HUMAN	249-281	33	0	-	-
1.12	ENST00000354532	12	ENSE00001712166	chr19:42398699-42398734	36	ARHG1_HUMAN	281-293	13	0	-	-
1.13	ENST00000354532	13	ENSE00001682337	chr19:42399422-42399559	138	ARHG1_HUMAN	293-339	47	0	-	-
1.14a	ENST00000354532	14a	ENSE00000492791	chr19:42400450-42400555	106	ARHG1_HUMAN	339-374	36	0	-	-
1.15d	ENST00000354532	15d	ENSE00000708622	chr19:42402591-42402736	146	ARHG1_HUMAN	374-423	50	2	A:411-423 B:411-423	13 13
1.16	ENST00000354532	16	ENSE00000708620	chr19:42406037-42406183	147	ARHG1_HUMAN	423-472	50	2	A:423-472 B:423-472	50 50
1.17	ENST00000354532	17	ENSE00000708617	chr19:42406424-42406506	83	ARHG1_HUMAN	472-499	28	2	A:472-499 (gaps) B:472-499 (gaps)	28 28
1.18	ENST00000354532	18	ENSE00000708615	chr19:42406683-42406808	126	ARHG1_HUMAN	500-541	42	2	A:500-541 B:500-541	42 42
1.19	ENST00000354532	19	ENSE00000708613	chr19:42406934-42407048	115	ARHG1_HUMAN	542-580	39	2	A:542-580 B:542-580	39 39
1.20	ENST00000354532	20	ENSE00000708611	chr19:42407457-42407557	101	ARHG1_HUMAN	580-613	34	2	A:580-613 B:580-613	34 34
1.22	ENST00000354532	22	ENSE00000708609	chr19:42407859-42407936	78	ARHG1_HUMAN	614-639	26	2	A:614-639 B:614-639	26 26
1.23	ENST00000354532	23	ENSE00000708607	chr19:42408187-42408262	76	ARHG1_HUMAN	640-665	26	2	A:640-665 B:640-665	26 26
1.24	ENST00000354532	24	ENSE00000708605	chr19:42408368-42408535	168	ARHG1_HUMAN	665-721	57	2	A:665-721 (gaps) B:665-721 (gaps)	57 57
1.25	ENST00000354532	25	ENSE00000708603	chr19:42409101-42409188	88	ARHG1_HUMAN	721-750	30	2	A:721-750 B:721-750	30 30
1.26	ENST00000354532	26	ENSE00000708602	chr19:42409327-42409413	87	ARHG1_HUMAN	750-779	30	2	A:750-765 B:750-765	16 16
1.27	ENST00000354532	27	ENSE00000708601	chr19:42409912-42409979	68	ARHG1_HUMAN	779-802	24	0	-	-
1.28	ENST00000354532	28	ENSE00000708600	chr19:42410091-42410177	87	ARHG1_HUMAN	802-831	30	0	-	-
1.29	ENST00000354532	29	ENSE00000708599	chr19:42410609-42410772	164	ARHG1_HUMAN	831-885	55	0	-	-
1.30	ENST00000354532	30	ENSE00001660749	chr19:42410855-42410955	101	ARHG1_HUMAN	886-912	27	0	-	-
1.31	ENST00000354532	31	ENSE00001691041	chr19:42411257-42411597	341	ARHG1_HUMAN	-	0	0	-	-

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
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:344
 aligned with ARHG1_HUMAN | Q92888 from UniProtKB/Swiss-Prot  Length:912

    Alignment length:355
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760     
          ARHG1_HUMAN   411 PKSQVKRQEVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPLEELQNIFPSLDELIEVHSLFLDRLMKRRQESGYLIEEIGDVLLARFDGAEGSWFQKISSRFCSRQSFALEQLKAKQRKDPRFCAFVQEAESRPRCRRLQLKDMIPTEMQRLTKYPLLLQSIGQNTEEPTEREKVELAAECCREILHHVNQAVRDMEDLLRLKDYQRRLDLSHLRQSSDPMLSEFKNLDITKKKLVHEGPLTWRVTKDKAVEVHVLLLDDLLLLLQRQDERLLLKSHSRTLTPTPDGKTMLRPVLRLTSAMTREVATDHKAFYVLFTWDQEAQIYELVAQTVSERKNWCALITETAGSLKVP 765
               SCOP domains d3p6aa1 A:411-623 automated matches                                                                                                                                                                                  d3p6aa2 A:624-765 automated matches                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh--....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhh.hhhhh...........eeeeeeeeee.....eeeeeeeee..eeeeeeee..eee......---------.....eee...eeeee......eeeeee.......eeeee..hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DH_2  PDB: A:416-605 UniProt: 416-605                                                                                                                                                         -----------------------------------------PH_DOMAIN  PDB: A:647-760 UniProt: 647-760                                                                        ----- PROSITE
           Transcript 1 (1) Exon 1.15d   ------------------------------------------------Exon 1.17 UniProt: 472-499  Exon 1.18  PDB: A:500-541 UniProt: 500-541Exon 1.19  PDB: A:542-580              ---------------------------------Exon 1.22  PDB: A:614-639 Exon 1.23  PDB: A:640-665 -------------------------------------------------------Exon 1.25  PDB: A:721-750     --------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.16  PDB: A:423-472 UniProt: 423-472        -----------------------------------------------------------------------------------------------------------Exon 1.20  PDB: A:580-613         ---------------------------------------------------Exon 1.24  PDB: A:665-721 (gaps) UniProt: 665-721        ----------------------------Exon 1.26        Transcript 1 (2)
                 3p6a A 411 PKSQVKRQEVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPLEELQNIFPSLDELIEVHSLFLDRLMKRRQES--LIEEIGDVLLARFDGAEGSWFQKISSRFCSRQSFALEQLKAKQRKDPRFCAFVQEAESRPRCRRLQLKDMIPTEMQRLTKYPLLLQSIGQNTEEPTEREKVELAAECCREILHHVNQAVRDMEDLLRLKDYQRRLDLSHLRQSSDPMLSEFKNLDITKKKLVHEGPLTWRVTKDKAVEVHVLLLDDLLLLLQRQDERLLLKSHSR---------TMLRPVLRLTSAMTREVATDHKAFYVLFTWDQEAQIYELVAQTVSERKNWCALITETAGSLKVP 765
                                   420       430       440       450       460       470       480    |  490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690 |       - |     710       720       730       740       750       760     
                                                                                                    485  |                                                                                                                                                                                                         692       702                                                               
                                                                                                       488

Chain B from PDB  Type:PROTEIN  Length:343
 aligned with ARHG1_HUMAN | Q92888 from UniProtKB/Swiss-Prot  Length:912

    Alignment length:355
                                   420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690       700       710       720       730       740       750       760     
          ARHG1_HUMAN   411 PKSQVKRQEVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPLEELQNIFPSLDELIEVHSLFLDRLMKRRQESGYLIEEIGDVLLARFDGAEGSWFQKISSRFCSRQSFALEQLKAKQRKDPRFCAFVQEAESRPRCRRLQLKDMIPTEMQRLTKYPLLLQSIGQNTEEPTEREKVELAAECCREILHHVNQAVRDMEDLLRLKDYQRRLDLSHLRQSSDPMLSEFKNLDITKKKLVHEGPLTWRVTKDKAVEVHVLLLDDLLLLLQRQDERLLLKSHSRTLTPTPDGKTMLRPVLRLTSAMTREVATDHKAFYVLFTWDQEAQIYELVAQTVSERKNWCALITETAGSLKVP 765
               SCOP domains d3p6ab1 B:411-623 automated matches                                                                                                                                                                                  d3p6ab2 B:624-765 automated matches                                                                                                            SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) ---------RhoGEF-3p6aB01 B:420-604                                                                                                                                                                 ---------------------------------------------------------------------------------------          ---------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) ---------RhoGEF-3p6aB02 B:420-604                                                                                                                                                                 ---------------------------------------------------------------------------------------          ---------------------------------------------------------------- Pfam domains (2)
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh--....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhheehhhhhhh.hhhhhhhh........eeeeeeeeeeee..eeeeeeeeee..eeeeeeee..eee.....----------.....eee...eeeee......eeeeee.......eeeee..hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----DH_2  PDB: B:416-605 UniProt: 416-605                                                                                                                                                         -----------------------------------------PH_DOMAIN  PDB: B:647-760 UniProt: 647-760                                                                        ----- PROSITE
           Transcript 1 (1) Exon 1.15d   ------------------------------------------------Exon 1.17 UniProt: 472-499  Exon 1.18  PDB: B:500-541 UniProt: 500-541Exon 1.19  PDB: B:542-580              ---------------------------------Exon 1.22  PDB: B:614-639 Exon 1.23  PDB: B:640-665 -------------------------------------------------------Exon 1.25  PDB: B:721-750     --------------- Transcript 1 (1)
           Transcript 1 (2) ------------Exon 1.16  PDB: B:423-472 UniProt: 423-472        -----------------------------------------------------------------------------------------------------------Exon 1.20  PDB: B:580-613         ---------------------------------------------------Exon 1.24  PDB: B:665-721 (gaps) UniProt: 665-721        ----------------------------Exon 1.26        Transcript 1 (2)
                 3p6a B 411 PKSQVKRQEVISELLVTEAAHVRMLRVLHDLFFQPMAECLFFPLEELQNIFPSLDELIEVHSLFLDRLMKRRQES--LIEEIGDVLLARFDGAEGSWFQKISSRFCSRQSFALEQLKAKQRKDPRFCAFVQEAESRPRCRRLQLKDMIPTEMQRLTKYPLLLQSIGQNTEEPTEREKVELAAECCREILHHVNQAVRDMEDLLRLKDYQRRLDLSHLRQSSDPMLSEFKNLDITKKKLVHEGPLTWRVTKDKAVEVHVLLLDDLLLLLQRQDERLLLKSHS----------TMLRPVLRLTSAMTREVATDHKAFYVLFTWDQEAQIYELVAQTVSERKNWCALITETAGSLKVP 765
                                   420       430       440       450       460       470       480    |  490       500       510       520       530       540       550       560       570       580       590       600       610       620       630       640       650       660       670       680       690|        - |     710       720       730       740       750       760     
                                                                                                    485  |                                                                                                                                                                                                        691        702                                                               
                                                                                                       488

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	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 '\|'

Asymmetric Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All alpha proteins (14657)

Fold: DBL homology domain (DH-domain) (22)

Superfamily: DBL homology domain (DH-domain) (22)

Family: automated matches (3)

Protein domain: automated matches (3)

Human (Homo sapiens) [TaxId: 9606] (2)

1a	d3p6aa1	A:411-623
1b	d3p6ab1	B:411-623

Class: All beta proteins (24004)

Fold: PH domain-like barrel (258)

Superfamily: PH domain-like (257)

Family: automated matches (50)

Protein domain: automated matches (50)

Human (Homo sapiens) [TaxId: 9606] (30)

2a	d3p6aa2	A:624-765
2b	d3p6ab2	B:624-765

(no "CATH Domain" information available for 3P6A)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: RhoGEF] (22)

Family: RhoGEF (22)

Homo sapiens (Human) (16)

1a	RhoGEF-3p6aB01	B:420-604
1b	RhoGEF-3p6aB02	B:420-604

Asymmetric Unit(hide GO term definitions)

Chain A,B (ARHG1_HUMAN | Q92888)

molecular function
	GO:0005096	GTPase activator activity	Binds to and increases the activity of a GTPase, an enzyme that catalyzes the hydrolysis of GTP.
	GO:0005089	Rho guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase of the Rho family. 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:0005085	guanyl-nucleotide exchange factor activity	Stimulates the exchange of guanyl nucleotides associated with a GTPase. 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:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
biological process
	GO:0007266	Rho protein signal transduction	A series of molecular signals within the cell that are mediated by a member of the Rho family of proteins switching to a GTP-bound active state.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0050771	negative regulation of axonogenesis	Any process that stops, prevents, or reduces the frequency, rate or extent of axonogenesis.
	GO:0043547	positive regulation of GTPase activity	Any process that activates or increases the activity of a GTPase.
	GO:0035023	regulation of Rho protein signal transduction	Any process that modulates the frequency, rate or extent of Rho protein signal transduction.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
	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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:735 - Gln A:736	[ RasMol ]
		Ala B:735 - Gln B:736	[ RasMol ]
		His B:690 - Ser B:691	[ RasMol ]
		Lys A:639 - Asn A:640	[ RasMol ]
		Lys B:639 - Asn B:640	[ RasMol ]
		Pro A:411 - Lys A:412	[ RasMol ]

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	3p6a
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	ARHG1_HUMAN \| Q92888	:	1iap 1shz 3ab3 3odo 3odw 3odx

1txd	CRYSTAL STRUCTURE OF THE DH/PH DOMAINS OF LEUKEMIA- ASSOCIATED RHOGEF
1x86	CRYSTAL STRUCTURE OF THE DH/PH DOMAINS OF LEUKEMIA- ASSOCIATED RHOGEF IN COMPLEX WITH RHOA
1xcg	CRYSTAL STRUCTURE OF THE DH/PH DOMAINS OF PDZ-RHOGEF IN COMPLEX WITH RHOA
3odo	CRYSTAL STRUCTURE OF THE DH/PH DOMAINS OF P115-RHOGEF
3odw	CRYSTAL STRUCTURE OF THE LINKER-DH/PH DOMAINS OF P115-RHOGEF
3odx	CRYSTAL STRUCTURE OF THE N-TERMINALLY TRUNCATED LINKER-DH/ PH DOMAINS OF P115-RHOGEF

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (6, 6)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (2, 4)

Exons (11, 22)

Sequences/Alignments

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SCOP Domains (2, 4)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (13, 13)

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