2V58 - JenaLib

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 1

Authors :   I. Mochalkin, J. R. Miller

Date :   02 Oct 08 (Deposition) - 13 Jan 09 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

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

Keywords :   Fatty Acid Biosynthesis, Biotin Carboxylase, Nucleotide-Binding, Atp-Binding, Antibacterial, Lipid Synthesis, Fas, Ligase, Biotin, Bacterial, Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. R. Miller, S. Dunham, I. Mochalkin, C. Banotai, M. Bowman, S. Buist, B. Dunkle, D. Hanna, H. J. Harwood, M. D. Huband, A. Karnovsky, M. Kuhn, C. Limberakis, J. Y. Liu, S. Mehrens, W. T. Mueller, L. Narasimhan, A. Ogden, J. Ohren, J. V. Prasad, J. A. Shelly, L. Skerlos, M. Sulavik, V. H. Thomas, S. Vanderroest, L. Wang, Z. Wang, A. Whitton, T. Zhu, C. K. Stover
A Class Of Selective Antibacterials Derived From A Protein Kinase Inhibitor Pharmacophore.
Proc. Natl. Acad. Sci. Usa V. 106 1737 2009
PubMed-ID: 19164768 | Reference-DOI: 10.1073/PNAS.0811275106

Molecule 1 - BIOTIN CARBOXYLASE
	Chains	:	A, B
	EC Number	:	6.3.4.14
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	ACETYL-COA CARBOXYLASE SUBUNIT A

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CL	2	Ligand/Ion	CHLORIDE ION
2	LZJ	2	Ligand/Ion	6-(2,6-DIBROMOPHENYL)PYRIDO[2,3-D]PYRIMIDINE-2,7-DIAMINE

Biological Unit 1 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LZJ	1	Ligand/Ion	6-(2,6-DIBROMOPHENYL)PYRIDO[2,3-D]PYRIMIDINE-2,7-DIAMINE

Biological Unit 2 (1, 1)

No.	Name	Count	Type	Full Name
1	CL	-1	Ligand/Ion	CHLORIDE ION
2	LZJ	1	Ligand/Ion	6-(2,6-DIBROMOPHENYL)PYRIDO[2,3-D]PYRIMIDINE-2,7-DIAMINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ILE A:157 , LYS A:159 , GLU A:201 , LYS A:202 , TYR A:203 , LEU A:204 , HIS A:209 , GLN A:233 , HIS A:236 , LEU A:278 , ILE A:437	BINDING SITE FOR RESIDUE LZJ A1448
2	AC2	SOFTWARE	ILE B:157 , LYS B:159 , MET B:169 , GLU B:201 , LYS B:202 , TYR B:203 , LEU B:204 , HIS B:209 , GLN B:233 , HIS B:236 , LEU B:278 , ILE B:437	BINDING SITE FOR RESIDUE LZJ B1447
3	AC3	SOFTWARE	ARG A:292 , GLN A:294 , VAL A:295 , HOH A:2103	BINDING SITE FOR RESIDUE CL A1449
4	AC4	SOFTWARE	ARG B:292 , GLN B:294 , VAL B:295	BINDING SITE FOR RESIDUE CL B1448

(no "SS Bond" information available for 2V58)

Asymmetric Unit

No.	Residues
1	Tyr A:154	-	Pro A:155
2	Ala A:243	-	Pro A:244
3	Tyr B:154	-	Pro B:155
4	Ala B:243	-	Pro B:244

(no "SAP(SNP)/Variant" information available for 2V58)

Asymmetric Unit (3, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BC	PS50979	Biotin carboxylation domain profile.	ACCC_ECOLI	1-445	2	A:1-445 B:1-445
2	CPSASE_1	PS00866	Carbamoyl-phosphate synthase subdomain signature 1.	ACCC_ECOLI	154-168	2	A:154-168 B:154-168
3	CPSASE_2	PS00867	Carbamoyl-phosphate synthase subdomain signature 2.	ACCC_ECOLI	286-293	2	A:286-293 B:286-293

Biological Unit 1 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BC	PS50979	Biotin carboxylation domain profile.	ACCC_ECOLI	1-445	1	A:1-445 -
2	CPSASE_1	PS00866	Carbamoyl-phosphate synthase subdomain signature 1.	ACCC_ECOLI	154-168	1	A:154-168 -
3	CPSASE_2	PS00867	Carbamoyl-phosphate synthase subdomain signature 2.	ACCC_ECOLI	286-293	1	A:286-293 -

Biological Unit 2 (3, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	BC	PS50979	Biotin carboxylation domain profile.	ACCC_ECOLI	1-445	1	- B:1-445
2	CPSASE_1	PS00866	Carbamoyl-phosphate synthase subdomain signature 1.	ACCC_ECOLI	154-168	1	- B:154-168
3	CPSASE_2	PS00867	Carbamoyl-phosphate synthase subdomain signature 2.	ACCC_ECOLI	286-293	1	- B:286-293

(no "Exon" information available for 2V58)

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:447
 aligned with ACCC_ECOLI | P24182 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:447
                                    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       
           ACCC_ECOLI     1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGLQ 447
               SCOP domains d2v58a1 A:1-114 Biotin carboxylase (BC), N-terminal domain                                                        d2v58a2 A:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d2v58a3 A:331-447 Biotin carboxylase (BC), C-domain                                                                   SCOP domains
               CATH domains 2v58A01 A:1-85  [code=3.40.50.20, no name defined]                                   ---------------------------------------------2v58A03 A:131-203 ATP-grasp fold, A domain                               ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhhh..eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeeeeeee..eeeeee.hhhhhhhhhhhhhhhhhhhhh...eeeee.....eeeeeeeee.....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhhh.....hhhhh....eeeeeeee...........ee..eee......eeeee......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BC  PDB: A:1-445 UniProt: 1-445                                                                                                                                                                                                                                                                                                                                                                                                                              -- PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------------------------------------------------------------------------CPSASE_2---------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v58 A   1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGLQ 447
                                    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

Chain B from PDB  Type:PROTEIN  Length:446
 aligned with ACCC_ECOLI | P24182 from UniProtKB/Swiss-Prot  Length:449

    Alignment length:446
                                    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      
           ACCC_ECOLI     1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGL 446
               SCOP domains d2v58b1 B:1-114 Biotin carboxylase (BC), N-terminal domain                                                        d2v58b2 B:115-330 Biotin carboxylase (BC), domain 2                                                                                                                                                                     d2v58b3 B:331-446 Biotin carboxylase (BC), C-domain                                                                  SCOP domains
               CATH domains 2v58B01 B:1-85  [code=3.40.50.20, no name defined]                                   ---------------------------------------------2v58B03 B:131-203 ATP-grasp fold, A domain                               --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) CPSase_L_chain-2v58B05 B:1-110                                                                                ----CPSase_L_D2-2v58B01 B:115-324                                                                                                                                                                                     -----------Biotin_carb_C-2v58B03 B:336-441                                                                           ----- Pfam domains (1)
           Pfam domains (2) CPSase_L_chain-2v58B06 B:1-110                                                                                ----CPSase_L_D2-2v58B02 B:115-324                                                                                                                                                                                     -----------Biotin_carb_C-2v58B04 B:336-441                                                                           ----- Pfam domains (2)
         Sec.struct. author ...eeee..hhhhhhhhhhhhhhh..eeeeeee.hhh.hhhhhhh.eeeeee..hhhhh..hhhhhhhhhhhh...eee........hhhhhhhhhhh..ee...hhhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhh..eeeee........eeee....hhhhhhhhhhhhhhhhhh...eeeee.....eeeeeeeeee....eeeeeeeeeeeee..eeeeeee.....hhhhhhhhhhhhhhhhhhh..eeeeeeeeeee..eeeeeeee.....hhhhhhhhhh.hhhhhhhhhhh......hhhhh....eeeeeeee...........ee..eee......eeeee......ee......eeeeeeeee.hhhhhhhhhhhhhhhheee....hhhhhhhhhhhhhhhhh....hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) BC  PDB: B:1-445 UniProt: 1-445                                                                                                                                                                                                                                                                                                                                                                                                                              - PROSITE (1)
                PROSITE (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------CPSASE_1       ---------------------------------------------------------------------------------------------------------------------CPSASE_2--------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2v58 B   1 MLDKIVIANRGEIALRILRACKELGIKTVAVHSSADRDLKHVLLADETVCIGPAPSVKSYLNIPAIISAAEITGAVAIHPGYGFLSENANFAEQVERSGFIFIGPKAETIRLMGDKVSAIAAMKKAGVPCVPGSDGPLGDDMDKNRAIAKRIGYPVIIKASGGGGGRGMRVVRGDAELAQSISMTRAEAKAAFSNDMVYMEKYLENPRHVEIQVLADGQGNAIYLAERDCSMQRRHQKVVEEAPAPGITPELRRYIGERCAKACVDIGYRGAGTFEFLFENGEFYFIEMNTRIQVEHPVTEMITGVDLIKEQLRIAAGQPLSIKQEEVHVRGHAVECRINAEDPNTFLPSPGKITRFHAPGGFGVRWESHIYAGYTVPPYYDSMIGKLICYGENRDVAIARMKNALQELIIDGIKTNVDLQIRIMNDENFQHGGTNIHYLEKKLGL 446
                                    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

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(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Dna Ligase; domain 1 (375)

Homologous Superfamily: ATP-grasp fold, A domain (109)

Escherichia coli. Organism_taxid: 562. (21)

1a	2v58A03	A:131-203
1b	2v58B03	B:131-203

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: [code=3.40.50.20, no name defined] (85)

Escherichia coli. Organism_taxid: 562. (17)

2a	2v58A01	A:1-85
2b	2v58B01	B:1-85

Asymmetric Unit(hide GO term definitions)

Chain A,B (ACCC_ECOLI | P24182)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003989	acetyl-CoA carboxylase activity	Catalysis of the reaction: ATP + acetyl-CoA + HCO3- = ADP + phosphate + malonyl-CoA.
	GO:0004075	biotin carboxylase activity	Catalysis of the reaction: ATP + biotin-carboxyl-carrier protein + CO2 = ADP + phosphate + carboxybiotin-carboxyl-carrier protein.
	GO:0003824	catalytic activity	Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	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: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:0006633	fatty acid biosynthetic process	The chemical reactions and pathways resulting in the formation of a fatty acid, any of the aliphatic monocarboxylic acids that can be liberated by hydrolysis from naturally occurring fats and oils. Fatty acids are predominantly straight-chain acids of 4 to 24 carbon atoms, which may be saturated or unsaturated; branched fatty acids and hydroxy fatty acids also occur, and very long chain acids of over 30 carbons are found in waxes.
	GO:0006631	fatty acid metabolic process	The chemical reactions and pathways involving fatty acids, aliphatic monocarboxylic acids liberated from naturally occurring fats and oils by hydrolysis.
	GO:0006629	lipid metabolic process	The chemical reactions and pathways involving lipids, compounds soluble in an organic solvent but not, or sparingly, in an aqueous solvent. Includes fatty acids; neutral fats, other fatty-acid esters, and soaps; long-chain (fatty) alcohols and waxes; sphingoids and other long-chain bases; glycolipids, phospholipids and sphingolipids; and carotenes, polyprenols, sterols, terpenes and other isoprenoids.
	GO:2001295	malonyl-CoA biosynthetic process	The chemical reactions and pathways resulting in the formation of malonyl-CoA, the S-malonyl derivative of coenzyme A.
	GO:0045717	negative regulation of fatty acid biosynthetic process	Any process that stops, prevents, or reduces the frequency, rate or extent of the chemical reactions and pathways resulting in the formation of fatty acids.
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.

Asymmetric Unit
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	Cis Peptide Bonds
		Ala A:243 - Pro A:244	[ RasMol ]
		Ala B:243 - Pro B:244	[ RasMol ]
		Tyr A:154 - Pro A:155	[ RasMol ]
		Tyr B:154 - Pro B:155	[ RasMol ]

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	2v58
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1bnc
1dv1	STRUCTURE OF BIOTIN CARBOXYLASE (APO)
1dv2	THE STRUCTURE OF BIOTIN CARBOXYLASE, MUTANT E288K, COMPLEXED WITH ATP
1k69	MODEL INTERACTION BETWEEN BCCP AND ATP-BOUND CARBOXYLASESUBUNIT OF ACETYL COA CARBOXYLASE
2gps	CRYSTAL STRUCTURE OF THE BIOTIN CARBOXYLASE SUBUNIT, E23RMUTANT, OF ACETYL-COA CARBOXYLASE FROM ESCHERICHIA COLI.
2gpw	CRYSTAL STRUCTURE OF THE BIOTIN CARBOXYLASE SUBUNIT, F363AMUTANT, OF ACETYL-COA CARBOXYLASE FROM ESCHERICHIA COLI.
2j9g	CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX WITH AMPPNP AND ADP
2v59	CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 2
2v5a	CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E.COLI IN COMPLEX WITH POTENT INHIBITOR 3
2vr1	CRYSTAL STRUCTURE OF BIOTIN CARBOXYLASE FROM E. COLI IN COMPLEX WITH ATP ANALOG, ADPCF2P.

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (3, 6)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

CATH Domains (2, 4)

Pfam Domains (3, 6)

Gene Ontology (15, 15)

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