3AH2 - JenaLib

Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Title :   HA1 SUBCOMPONENT OF BOTULINUM TYPE C PROGENITOR TOXIN COMPLEXED WITH N-ACETYLGALACTOSAMINE

Authors :   T. Nakamura, T. Tonozuka, A. Ide, T. Yuzawa, K. Oguma, A. Nishikawa

Date :   13 Apr 10 (Deposition) - 28 Apr 10 (Release) - 28 Apr 10 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Toxin, Beta Trefoil, Hemagglutinin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Nakamura, T. Tonozuka, A. Ide, T. Yuzawa, K. Oguma, A. Nishikawa
Sugar-Binding Sites Of The Ha1 Subcomponent Of Clostridium Botulinum Type C Progenitor Toxin
J. Mol. Biol. V. 376 854 2008
PubMed-ID: 18178224 | Reference-DOI: 10.1016/J.JMB.2007.12.031
(for further references see the PDB file header)

Molecule 1 - MAIN HEMAGGLUTININ COMPONENT
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PMAL-2X FLAG-HA1
	Expression System Strain	:	JM109
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	CLOSTRIDIUM BOTULINUM
	Organism Taxid	:	1491
	Strain	:	TYPE C
	Synonym	:	HA1 SUBCOMPONENT OF BOTULINUM TYPE C PROGENITOR TOXIN, HEMAGGLUTININ COMPONENT HA1, HA 33 KDA SUBUNIT, HA1

		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 (1, 1)

No.	Name	Count	Type	Full Name
1	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 1 (0, 0)

No.	Name	Count	Type	Full Name
1	NGA	-1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	NGA	1	Ligand/Ion	N-ACETYL-D-GALACTOSAMINE

Asymmetric Unit (1, 1)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:39 , GLU A:203 , SER B:165 , LYS B:166 , ASN B:167 , LEU B:168 , TRP B:176 , PHE B:179 , ARG B:183 , HOH B:401 , HOH B:752	BINDING SITE FOR RESIDUE NGA B 2000

(no "SS Bond" information available for 3AH2)

Asymmetric Unit

No.	Residues
1	Ala A:75	-	Pro A:76
2	Ala B:75	-	Pro B:76

Asymmetric Unit (13, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_HA33_CLOBO_001 *	N	22	S	HA33_CLOBO	---	---	A/B	N	22	S
02	UniProt	VAR_HA33_CLOBO_002 *	K	60	T	HA33_CLOBO	---	---	A/B	K	60	T
03	UniProt	VAR_HA33_CLOBO_003 *	N	74	D	HA33_CLOBO	---	---	A/B	N	74	D
04	UniProt	VAR_HA33_CLOBO_004 *	N	98	D	HA33_CLOBO	---	---	A/B	N	98	D
05	UniProt	VAR_HA33_CLOBO_005 *	I	106	L	HA33_CLOBO	---	---	A/B	I	106	L
06	UniProt	VAR_HA33_CLOBO_006 *	I	120	T	HA33_CLOBO	---	---	A/B	I	120	T
07	UniProt	VAR_HA33_CLOBO_007 *	M	125	I	HA33_CLOBO	---	---	A/B	M	125	I
08	UniProt	VAR_HA33_CLOBO_008 *	S	131	N	HA33_CLOBO	---	---	A/B	S	131	N
09	UniProt	VAR_HA33_CLOBO_009 *	S	133	N	HA33_CLOBO	---	---	A/B	S	133	N
10	UniProt	VAR_HA33_CLOBO_010 *	I	187	L	HA33_CLOBO	---	---	A/B	I	187	L
11	UniProt	VAR_HA33_CLOBO_011 *	I	187	T	HA33_CLOBO	---	---	A/B	I	187	T
12	UniProt	VAR_HA33_CLOBO_012 *	I	262	T	HA33_CLOBO	---	---	A/B	I	262	T
13	UniProt	VAR_HA33_CLOBO_013 *	H	267	N	HA33_CLOBO	---	---	A/B	H	267	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_HA33_CLOBO_001 *	N	22	S	HA33_CLOBO	---	---	A	N	22	S
02	UniProt	VAR_HA33_CLOBO_002 *	K	60	T	HA33_CLOBO	---	---	A	K	60	T
03	UniProt	VAR_HA33_CLOBO_003 *	N	74	D	HA33_CLOBO	---	---	A	N	74	D
04	UniProt	VAR_HA33_CLOBO_004 *	N	98	D	HA33_CLOBO	---	---	A	N	98	D
05	UniProt	VAR_HA33_CLOBO_005 *	I	106	L	HA33_CLOBO	---	---	A	I	106	L
06	UniProt	VAR_HA33_CLOBO_006 *	I	120	T	HA33_CLOBO	---	---	A	I	120	T
07	UniProt	VAR_HA33_CLOBO_007 *	M	125	I	HA33_CLOBO	---	---	A	M	125	I
08	UniProt	VAR_HA33_CLOBO_008 *	S	131	N	HA33_CLOBO	---	---	A	S	131	N
09	UniProt	VAR_HA33_CLOBO_009 *	S	133	N	HA33_CLOBO	---	---	A	S	133	N
10	UniProt	VAR_HA33_CLOBO_010 *	I	187	L	HA33_CLOBO	---	---	A	I	187	L
11	UniProt	VAR_HA33_CLOBO_011 *	I	187	T	HA33_CLOBO	---	---	A	I	187	T
12	UniProt	VAR_HA33_CLOBO_012 *	I	262	T	HA33_CLOBO	---	---	A	I	262	T
13	UniProt	VAR_HA33_CLOBO_013 *	H	267	N	HA33_CLOBO	---	---	A	H	267	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (13, 13)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_HA33_CLOBO_001 *	N	22	S	HA33_CLOBO	---	---	B	N	22	S
02	UniProt	VAR_HA33_CLOBO_002 *	K	60	T	HA33_CLOBO	---	---	B	K	60	T
03	UniProt	VAR_HA33_CLOBO_003 *	N	74	D	HA33_CLOBO	---	---	B	N	74	D
04	UniProt	VAR_HA33_CLOBO_004 *	N	98	D	HA33_CLOBO	---	---	B	N	98	D
05	UniProt	VAR_HA33_CLOBO_005 *	I	106	L	HA33_CLOBO	---	---	B	I	106	L
06	UniProt	VAR_HA33_CLOBO_006 *	I	120	T	HA33_CLOBO	---	---	B	I	120	T
07	UniProt	VAR_HA33_CLOBO_007 *	M	125	I	HA33_CLOBO	---	---	B	M	125	I
08	UniProt	VAR_HA33_CLOBO_008 *	S	131	N	HA33_CLOBO	---	---	B	S	131	N
09	UniProt	VAR_HA33_CLOBO_009 *	S	133	N	HA33_CLOBO	---	---	B	S	133	N
10	UniProt	VAR_HA33_CLOBO_010 *	I	187	L	HA33_CLOBO	---	---	B	I	187	L
11	UniProt	VAR_HA33_CLOBO_011 *	I	187	T	HA33_CLOBO	---	---	B	I	187	T
12	UniProt	VAR_HA33_CLOBO_012 *	I	262	T	HA33_CLOBO	---	---	B	I	262	T
13	UniProt	VAR_HA33_CLOBO_013 *	H	267	N	HA33_CLOBO	---	---	B	H	267	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (13, 26)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
01	UniProt	VAR_HA33_CLOBO_001 *	N	22	S	HA33_CLOBO	---	---	A/B	N	22	S
02	UniProt	VAR_HA33_CLOBO_002 *	K	60	T	HA33_CLOBO	---	---	A/B	K	60	T
03	UniProt	VAR_HA33_CLOBO_003 *	N	74	D	HA33_CLOBO	---	---	A/B	N	74	D
04	UniProt	VAR_HA33_CLOBO_004 *	N	98	D	HA33_CLOBO	---	---	A/B	N	98	D
05	UniProt	VAR_HA33_CLOBO_005 *	I	106	L	HA33_CLOBO	---	---	A/B	I	106	L
06	UniProt	VAR_HA33_CLOBO_006 *	I	120	T	HA33_CLOBO	---	---	A/B	I	120	T
07	UniProt	VAR_HA33_CLOBO_007 *	M	125	I	HA33_CLOBO	---	---	A/B	M	125	I
08	UniProt	VAR_HA33_CLOBO_008 *	S	131	N	HA33_CLOBO	---	---	A/B	S	131	N
09	UniProt	VAR_HA33_CLOBO_009 *	S	133	N	HA33_CLOBO	---	---	A/B	S	133	N
10	UniProt	VAR_HA33_CLOBO_010 *	I	187	L	HA33_CLOBO	---	---	A/B	I	187	L
11	UniProt	VAR_HA33_CLOBO_011 *	I	187	T	HA33_CLOBO	---	---	A/B	I	187	T
12	UniProt	VAR_HA33_CLOBO_012 *	I	262	T	HA33_CLOBO	---	---	A/B	I	262	T
13	UniProt	VAR_HA33_CLOBO_013 *	H	267	N	HA33_CLOBO	---	---	A/B	H	267	N
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	HA33_CLOBO	12-140 180-284	4	A:12-140 B:12-140 A:180-284 B:180-284

Biological Unit 1 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	HA33_CLOBO	12-140 180-284	2	A:12-140 - A:180-284 -

Biological Unit 2 (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	HA33_CLOBO	12-140 180-284	2	- B:12-140 - B:180-284

Biological Unit 3 (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	RICIN_B_LECTIN	PS50231	Lectin domain of ricin B chain profile.	HA33_CLOBO	12-140 180-284	4	A:12-140 B:12-140 A:180-284 B:180-284

(no "Exon" information available for 3AH2)

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:283
 aligned with HA33_CLOBO | P46084 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           HA33_CLOBO     4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
               SCOP domains d3ah2a1 A:4-148 Hemagglutinin component Ha1                                                                                                      d3ah2a2 A:149-286 Hemagglutinin component Ha1                                                                                              SCOP domains
               CATH domains 3ah2A01 A:4-141  [code=2.80.10.50, no name defined]                                                                                       3ah2A02 A:142-286  [code=2.80.10.50, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.....eeeee.....eeeee...hhhh.eeeeee....eeeeee......eeee......eeee....hhhh.eeeee......eeeee.....eeeee.....eeeee...hhhh.eeeeehhhhhhh.eeeeeee......eeee......eeee....hhhh.eeeeee....eeeeee....eeeee.......eeee....hhhh.eeeeee..eeeeeeeee.....eeeee.hhh......eeeee...hhhh.eeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------S-------------------------------------T-------------D-----------------------D-------L-------------T----I-----N-N-----------------------------------------------------L--------------------------------------------------------------------------T----N------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------RICIN_B_LECTIN  PDB: A:12-140 UniProt: 12-140                                                                                    ---------------------------------------RICIN_B_LECTIN  PDB: A:180-284 UniProt: 180-284                                                          -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ah2 A   4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283

Chain B from PDB  Type:PROTEIN  Length:283
 aligned with HA33_CLOBO | P46084 from UniProtKB/Swiss-Prot  Length:286

    Alignment length:283
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283   
           HA33_CLOBO     4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
               SCOP domains d3ah2b1 B:4-148 Hemagglutinin component Ha1                                                                                                      d3ah2b2 B:149-286 Hemagglutinin component Ha1                                                                                              SCOP domains
               CATH domains 3ah2B01 B:4-141  [code=2.80.10.50, no name defined]                                                                                       3ah2B02 B:142-286  [code=2.80.10.50, no name defined]                                                                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeee.....eeeee.....eeeee...hhhh.eeeeee....eeeeee......eeee......eeee....hhhh.eeeee......eeeee.....eeeee.....eeeee...hhhh.eeeeehhhhhhh.eeeeeee......eeee......eeee....hhhh.eeeeee....eeeeee.....eeee.......eeee....hhhh.eeeeee..eeeeeeeee.....eeeee.hhh......eeeee...hhhh.eeeee. Sec.struct. author
             SAPs(SNPs) (1) ------------------S-------------------------------------T-------------D-----------------------D-------L-------------T----I-----N-N-----------------------------------------------------L--------------------------------------------------------------------------T----N------------------- SAPs(SNPs) (1)
             SAPs(SNPs) (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------T--------------------------------------------------------------------------------------------------- SAPs(SNPs) (2)
                    PROSITE --------RICIN_B_LECTIN  PDB: B:12-140 UniProt: 12-140                                                                                    ---------------------------------------RICIN_B_LECTIN  PDB: B:180-284 UniProt: 180-284                                                          -- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ah2 B   4 TNANDLRNNEVFFISPSNNTNKVLDKISQSEVKLWNKLSGANQKWRLIYDTNKQAYKIKVMDNTSLILTWNAPLSSVSVKTDTNGDNQYWYLLQNYISRNVIIRNYMNPNLVLQYNIDDTLMVSTQTSSSNQFFKFSNCIYEALNNRNCKLQTQLNSDRFLSKNLNSQIIVLWQWFDSSRQKWIIEYNETKSAYTLKCQENNRYLTWIQNSNNYVETYQSTDSLIQYWNINYLDNDASKYILYNLQDTNRVLDVYNSQIANGTHVIVDSYHGNTNQQWIINLI 286
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283

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 beta proteins (24004)

Fold: beta-Trefoil (385)

Superfamily: Ricin B-like lectins (91)

Family: Ricin B-like (65)

Protein domain: Hemagglutinin component Ha1 (4)

Clostridium botulinum [TaxId: 1491] (3)

1a	d3ah2a1	A:4-148
1b	d3ah2a2	A:149-286
1c	d3ah2b1	B:4-148
1d	d3ah2b2	B:149-286

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Trefoil (289)

Topology: Trefoil (Acidic Fibroblast Growth Factor, subunit A) (289)

Homologous Superfamily: [code=2.80.10.50, no name defined] (289)

Clostridium botulinum. Organism_taxid: 1491. Strain: type c. (3)

1a	3ah2A01	A:4-141
1b	3ah2B01	B:4-141
1c	3ah2A02	A:142-286
1d	3ah2B02	B:142-286

(no "Pfam Domain" information available for 3AH2)

Asymmetric Unit(hide GO term definitions)

Chain A,B (HA33_CLOBO | P46084)

molecular function
	GO:0030246		carbohydrate binding		Interacting selectively and non-covalently with any carbohydrate, which includes monosaccharides, oligosaccharides and polysaccharides as well as substances derived from monosaccharides by reduction of the carbonyl group (alditols), by oxidation of one or more hydroxy groups to afford the corresponding aldehydes, ketones, or carboxylic acids, or by replacement of one or more hydroxy group(s) by a hydrogen atom. Cyclitols are generally not regarded as carbohydrates.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:75 - Pro A:76	[ RasMol ]
		Ala B:75 - Pro B:76	[ RasMol ]

Biological Units
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		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
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Access by PDB/NDB ID
	3ah2
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	HA33_CLOBO \| P46084
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		Domain Information	:	XDom
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	HA33_CLOBO \| P46084
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UniProtKB/Swiss-Prot
	HA33_CLOBO \| P46084	:	1qxm 2e4m 3ah1 3ah4 3aj5 3aj6

1qxm	THE SAME PROTEIN IN THE UNLIGANDED FORM
3ah1	THE SAME PROTEIN COMPLEXED WITH SIALIC ACID
3ah4	THE SAME PROTEIN COMPLEXED WITH GALACTOSE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 1)

Sites (1, 1)

SS Bonds (0, 0)

Cis Peptide Bonds (2, 2)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (13, 26)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 4)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (1, 1)

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Databases

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Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File