2DXI | PR0228 - JenaLib

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Asymmetric Unit (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   2.2 A CRYSTAL STRUCTURE OF GLUTAMYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS COMPLEXED WITH TRNA(GLU), ATP, AND L-GLUTAMOL

Authors :   S. Sekine, S. Yokoyama, Riken Structural Genomics/Proteomics Initiative (Rsgi)

Date :   28 Aug 06 (Deposition) - 31 Oct 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Ligase, Rna, Structural Genomics, Nppsfa, National Project On Protein Structural And Functional Analyses, Riken Structural Genomics/Proteomics Initiative, Rsgi, Ligase/Rna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   S. Sekine, M. Shichiri, S. Bernier, R. Chenevert, J. Lapointe, S. Yokoyama
Structural Bases Of Transfer Rna-Dependent Amino Acid Recognition And Activation By Glutamyl-Trna Synthetase
Structure V. 14 1791 2006
PubMed-ID: 17161369 | Reference-DOI: 10.1016/J.STR.2006.10.005
(for further references see the PDB file header)

Molecule 1 - TRNA
	Chains	:	C, D
	Engineered	:	YES
	Other Details	:	IN VITRO TRANSCRIPTION
	Synthetic	:	YES

Molecule 2 - GLUTAMYL-TRNA SYNTHETASE
	Chains	:	A, B
	EC Number	:	6.1.1.17
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI BL21(DE3)
	Expression System Plasmid	:	PK7
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Organism Scientific	:	THERMUS THERMOPHILUS
	Organism Taxid	:	274
	Synonym	:	GLUTAMATE--TRNA LIGASE, GLURS

		1	2	3	4
Asymmetric Unit	:	A	B	C	D
Biological Unit 1 (1x)	:	A		C
Biological Unit 2 (1x)	:		B		D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 6)

No.	Name	Count	Type	Full Name
1	ATP	2	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GAU	2	Ligand/Ion	(4S)-4-AMINO-5-HYDROXYPENTANOIC ACID
3	MG	2	Ligand/Ion	MAGNESIUM ION

Biological Unit 1 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GAU	1	Ligand/Ion	(4S)-4-AMINO-5-HYDROXYPENTANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ATP	1	Ligand/Ion	ADENOSINE-5'-TRIPHOSPHATE
2	GAU	1	Ligand/Ion	(4S)-4-AMINO-5-HYDROXYPENTANOIC ACID
3	MG	-1	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH D:1139 , HOH D:1302	BINDING SITE FOR RESIDUE MG D 902
2	AC2	SOFTWARE	SER B:9 , THR B:11 , HIS B:15 , GLY B:17 , THR B:18 , TYR B:20 , ILE B:21 , ARG B:47 , ALA B:206 , GLU B:208 , TRP B:209 , LEU B:235 , LEU B:236 , ILE B:244 , GAU B:702 , HOH B:1235 , HOH B:1268 , A D:576	BINDING SITE FOR RESIDUE ATP B 602
3	AC3	SOFTWARE	PRO A:8 , SER A:9 , THR A:11 , HIS A:15 , GLY A:17 , THR A:18 , ILE A:21 , ARG A:47 , ALA A:206 , GLU A:208 , TRP A:209 , LEU A:235 , LEU A:236 , ILE A:244 , GAU A:701 , HOH A:1040 , A C:576	BINDING SITE FOR RESIDUE ATP A 601
4	AC4	SOFTWARE	ARG A:5 , ALA A:7 , GLU A:41 , TYR A:187 , ASN A:191 , ARG A:205 , TRP A:209 , ATP A:601 , A C:576	BINDING SITE FOR RESIDUE GAU A 701
5	AC5	SOFTWARE	ARG B:5 , ALA B:7 , SER B:9 , GLU B:41 , TYR B:187 , ASN B:191 , ARG B:205 , TRP B:209 , ATP B:602 , HOH B:1268 , A D:576	BINDING SITE FOR RESIDUE GAU B 702

(no "SS Bond" information available for 2DXI)

Asymmetric Unit

No.	Residues
1	Gly A:78	-	Pro A:79
2	Arg A:152	-	Pro A:153
3	Gly B:78	-	Pro B:79
4	Arg B:152	-	Pro B:153

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYE_THET8	8-19	2	A:8-19 B:8-19

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYE_THET8	8-19	1	A:8-19 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	AA_TRNA_LIGASE_I	PS00178	Aminoacyl-transfer RNA synthetases class-I signature.	SYE_THET8	8-19	1	- B:8-19

(no "Exon" information available for 2DXI)

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:468
 aligned with SYE_THET8 | P27000 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        
           SYE_THET8      1 MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA  468
               SCOP domains d2dxia2 A:1-305 Glutamyl-tRNA synthetase (GluRS)                                                                                                                                                                                                                                                                 d2dxia1 A:306-468 C-terminal domain of glutamyl-tRNA synthetase (GluRS)                                                                                             SCOP domains
               CATH domains 2dxiA01 A:1-70,A:187-237                                              2dxiA02 A:71-186 Glutamyl-tRNA Synthetase; Domain 3                                                                 2dxiA01 A:1-70,A:187-237                           2dxiA03 A:238-322 Glutamyl-trna Synthetase; Domain 2                                 2dxiA04 A:323-370                               2dxiA05 A:371-468  [code=1.10.10.350, no name defined]                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee......eeeeee...eeeeee.hhh...eee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhh..hhhhhhhhhhh............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------AA_TRNA_LIGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2dxi A    1 MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA  468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460

Chain B from PDB  Type:PROTEIN  Length:468
 aligned with SYE_THET8 | P27000 from UniProtKB/Swiss-Prot  Length:468

    Alignment length:468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460        
           SYE_THET8      1 MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA  468
               SCOP domains d2dxib2 B:1-305 Glutamyl-tRNA synthetase (GluRS)                                                                                                                                                                                                                                                                 d2dxib1 B:306-468 C-terminal domain of glutamyl-tRNA synthetase (GluRS)                                                                                             SCOP domains
               CATH domains 2dxiB01 B:1-70,B:187-237                                              2dxiB02 B:71-186 Glutamyl-tRNA Synthetase; Domain 3                                                                 2dxiB01 B:1-70,B:187-237                           2dxiB03 B:238-322 Glutamyl-trna Synthetase; Domain 2                                 2dxiB04 B:323-370                               2dxiB05 B:371-468  [code=1.10.10.350, no name defined]                                             CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeee........hhhhhhhhhhhhhhhhhh..eeee............hhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhh..eeee..hhhhhhhhhhhhh...hhhhhhhhhhhhhhhhh....eeee......eeeeee...eeeeee.hhh...eee......hhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhh....eeeee..................hhhhhhhh..hhhhhhhhhhh............hhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhh...hhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------AA_TRNA_LIGA----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                2dxi B    1 MVVTRIAPSPTGDPHVGTAYIALFNYAWARRNGGRFIVRIEDTDRARYVPGAEERILAALKWLGLSYDEGPDVGGPHGPYRQSERLPLYQKYAEELLKRGWAYRAFETPEELEQIRKEKGGYDGRARNIPPEEAEERARRGEPHVIRLKVPRPGTTEVKDELRGVVVYDNQEIPDVVLLKSDGYPTYHLANVVDDHLMGVTDVIRAEEWLVSTPIHVLLYRAFGWEAPRFYHMPLLRNPDKTKISKRKSHTSLDWYKAEGFLPEALRNYLCLMGFSMPDGREIFTLEEFIQAFTWERVSLGGPVFDLEKLRWMNGKYIREVLSLEEVAERVKPFLREAGLSWESEAYLRRAVELMRPRFDTLKEFPEKARYLFTEDYPVSEKAQRKLEEGLPLLKELYPRLRAQEEWTEAALEALLRGFAAEKGVKLGQVAQPLRAALTGSLETPGLFEILALLGKERALRRLERALA  468
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460

Chain C from PDB  Type:RNA  Length:75
                                                                                                            
                2dxi C  501 GGCCCCAUCGUCUAGCGGUUAGGACGCGGCCCUCUCAAGGCCGAAACGGGGGUUCGAUUCCCCCUGGGGUCACCA  576
                                   510     |520A       530       540     ||551       561       571     
                                         516|  |                       546|                            
                                          518  |                        548                            
                                            520A

Chain D from PDB  Type:RNA  Length:75
                                                                                                            
                2dxi D  501 GGCCCCAUCGUCUAGCGGUUAGGACGCGGCCCUCUCAAGGCCGAAACGGGGGUUCGAUUCCCCCUGGGGUCACCA  576
                                   510     |520A       530       540     ||551       561       571     
                                         516|  |                       546|                            
                                          518  |                        548                            
                                            520A

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 '\|'

(no "Pfam Domain" information available for 2DXI)

Asymmetric Unit(hide GO term definitions)

Chain A,B (SYE_THET8 | P27000)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0004812	aminoacyl-tRNA ligase activity	Catalysis of the formation of aminoacyl-tRNA from ATP, amino acid, and tRNA with the release of diphosphate and AMP.
	GO:0004818	glutamate-tRNA ligase activity	Catalysis of the reaction: ATP + L-glutamate + tRNA(Glu) = AMP + diphosphate + L-glutamyl-tRNA(Glu).
	GO:0016874	ligase activity	Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
	GO:0016876	ligase activity, forming aminoacyl-tRNA and related compounds	Catalysis of the joining of an amino acid and a nucleic acid (usually tRNA) or poly(ribitol phosphate), with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate. The reaction forms an aminoacyl-tRNA or a related compound.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0000049	tRNA binding	Interacting selectively and non-covalently with transfer RNA.
biological process
	GO:0006424	glutamyl-tRNA aminoacylation	The process of coupling glutamate to glutamyl-tRNA, catalyzed by glutamyl-tRNA synthetase. In tRNA aminoacylation, the amino acid is first activated by linkage to AMP and then transferred to either the 2'- or the 3'-hydroxyl group of the 3'- adenosine residue of the tRNA.
	GO:0043039	tRNA aminoacylation	The chemical reactions and pathways by which the various amino acids become bonded to their corresponding tRNAs. The most common route for synthesis of aminoacyl tRNA is by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, usually catalyzed by the cognate aminoacyl-tRNA ligase. A given aminoacyl-tRNA ligase aminoacylates all species of an isoaccepting group of tRNA molecules.
	GO:0006418	tRNA aminoacylation for protein translation	The synthesis of aminoacyl tRNA by the formation of an ester bond between the 3'-hydroxyl group of the most 3' adenosine of the tRNA, to be used in ribosome-mediated polypeptide synthesis.
	GO:0006412	translation	The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		GAU	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Arg A:152 - Pro A:153	[ RasMol ]
		Arg B:152 - Pro B:153	[ RasMol ]
		Gly A:78 - Pro A:79	[ RasMol ]
		Gly B:78 - Pro B:79	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Access by PDB/NDB ID
	2dxi
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	SYE_THET8 \| P27000
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	6.1.1.17
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	SYE_THET8 \| P27000
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UniProtKB/Swiss-Prot
	SYE_THET8 \| P27000	:	1g59 1gln 1j09 1n75 1n77 1n78 2cuz 2cv0 2cv1 2cv2

1g59
1gln
1j09
1n75
1n77
1n78
2cuz	THE SAME PROTEIN COMPLEXED WITH L-GLUTAMATE
2cv0	THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), L-GLUTAMATE
2cv1	2.4 A STRUCTURE OF COMPLEX OF GLURS, TRNA(GLU), ATP, GLUTAMOL
2cv2	THE SAME PROTEIN COMPLEXED WITH TRNA(GLU), AN ENZYME INHIBITOR, GLU-AMS RELATED ID: TTK003000897.11 RELATED DB: TARGETDB

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 6)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 4)

CATH Domains (5, 10)

Pfam Domains (0, 0)

Gene Ontology (12, 12)

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