2GMJ - JenaLib

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Title :   STRUCTURE OF PORCINE ELECTRON TRANSFER FLAVOPROTEIN-UBIQUINONE OXIDOREDUCTASE

Authors :   J. Zhang, F. E. Frerman, J. -J. P. Kim

Date :   06 Apr 06 (Deposition) - 17 Oct 06 (Release) - 31 Mar 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Electron Transfer, Flavoprotein, Oxidoreductase, Ubiquinone (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   J. Zhang, F. E. Frerman, J. J. Kim
Structure Of Electron Transfer Flavoprotein-Ubiquinone Oxidoreductase And Electron Transfer To The Mitochondrial Ubiquinone Pool.
Proc. Natl. Acad. Sci. Usa V. 103 16212 2006
PubMed-ID: 17050691 | Reference-DOI: 10.1073/PNAS.0604567103
(for further references see the PDB file header)

Molecule 1 - ELECTRON TRANSFER FLAVOPROTEIN-UBIQUINONE OXIDOREDUCTASE
	Chains	:	A, B
	EC Number	:	1.5.5.1
	Organism Common	:	PIG
	Organism Scientific	:	SUS SCROFA
	Organism Taxid	:	9823
	Synonym	:	ETF-QO, ETF-UBIQUINONE OXIDOREDUCTASE, ETF DEHYDROGENASE, ELECTRON-TRANSFERRING-FLAVOPROTEIN DEHYDROGENASE, FRAGMENT

		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 (3, 10)

No.	Name	Count	Type	Full Name
1	FAD	2	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SF4	2	Ligand/Ion	IRON/SULFUR CLUSTER
3	TBU	6	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Biological Unit 1 (3, 6)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER
3	TBU	4	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	FAD	1	Ligand/Ion	FLAVIN-ADENINE DINUCLEOTIDE
2	SF4	1	Ligand/Ion	IRON/SULFUR CLUSTER
3	TBU	2	Ligand/Ion	TERTIARY-BUTYL ALCOHOL

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	LEU A:504 , CYS A:528 , PRO A:529 , CYS A:553 , VAL A:554 , CYS A:556 , LYS A:557 , CYS A:559 , TRP A:570	BINDING SITE FOR RESIDUE SF4 A 610
02	AC2	SOFTWARE	GLY A:42 , GLY A:44 , PRO A:45 , ALA A:46 , GLU A:71 , LYS A:72 , HIS A:79 , SER A:82 , GLY A:83 , ALA A:84 , CYS A:85 , ALA A:167 , ALA A:212 , GLU A:213 , GLY A:214 , HIS A:218 , PHE A:275 , LEU A:333 , GLY A:353 , CYS A:354 , ILE A:364 , LYS A:365 , GLY A:366 , THR A:367 , HOH A:706 , HOH A:719 , HOH A:801	BINDING SITE FOR RESIDUE FAD A 611
03	AC3	SOFTWARE	LEU B:504 , CYS B:528 , PRO B:529 , VAL B:532 , CYS B:553 , VAL B:554 , CYS B:556 , LYS B:557 , CYS B:559	BINDING SITE FOR RESIDUE SF4 B 612
04	AC4	SOFTWARE	GLY B:42 , GLY B:44 , PRO B:45 , ALA B:46 , GLU B:71 , LYS B:72 , HIS B:79 , SER B:82 , GLY B:83 , ALA B:84 , CYS B:85 , ALA B:167 , GLU B:213 , GLY B:214 , HIS B:218 , PHE B:275 , TYR B:277 , ARG B:331 , LEU B:333 , GLY B:353 , CYS B:354 , ILE B:364 , LYS B:365 , GLY B:366 , THR B:367 , VAL B:572	BINDING SITE FOR RESIDUE FAD B 613
05	AC5	SOFTWARE	ILE A:364 , HOH A:788	BINDING SITE FOR RESIDUE TBU A 621
06	AC6	SOFTWARE	TYR A:271 , THR A:438 , TBU A:623	BINDING SITE FOR RESIDUE TBU A 622
07	AC7	SOFTWARE	LEU A:131 , TBU A:622	BINDING SITE FOR RESIDUE TBU A 623
08	AC8	SOFTWARE	LYS A:324 , LEU A:491	BINDING SITE FOR RESIDUE TBU A 624
09	AC9	SOFTWARE	TBU B:626	BINDING SITE FOR RESIDUE TBU B 625
10	BC1	SOFTWARE	GLY B:273 , TBU B:625	BINDING SITE FOR RESIDUE TBU B 626

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

Asymmetric Unit

No.	Residues
1	Val A:6	-	Pro A:7
2	Trp A:264	-	Pro A:265
3	Trp B:264	-	Pro B:265

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

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	ETFD_PIG	577-606	2	A:544-573 B:544-573

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	ETFD_PIG	577-606	1	A:544-573 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	4FE4S_FER_2	PS51379	4Fe-4S ferredoxin-type iron-sulfur binding domain profile.	ETFD_PIG	577-606	1	- B:544-573

(no "Exon" information available for 2GMJ)

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:581
 aligned with ETFD_PIG | P55931 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:581
                                    46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576       586       596       606       616 
             ETFD_PIG    37 CKVPRITTHYTIYPRDQDKRWEGVNMERFAEEADVVIVGAGPAGLSAATRLKQLAAQHEKDLRVCLVEKAAHIGAHTLSGACLDPRAFEELFPDWKEKGAPLNTPVTEDRFGILTEKYRIPVPILPGLPMNNHGNYVVRLGHLVSWMGEQAEALGVEVYPGYAAAEILFHEDGSVKGIATNDVGIQKDGAPKTTFERGLELHAKVTIFAEGCHGHLAKQLYKKFDLRANCEPQTYGIGLKELWVIDEKKWKPGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLLALGFVVGLDYQNPYLSPFREFQRWKHHPSIKPTLEGGKRIAYGARALNEGGFQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGTLAAESIFNQLTSENLQSKTIGLHVTEYEDNLKNSWVWKELYSVRNIRPSCHGILGVYGGMIYTGIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQGDGFRLQINAQNCVHCKTCDIKDPSQNINWVVPEGGGGPAYNGM 617
               SCOP domains d2gmja1 A:4-236,A:336-482 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                                                                                                                                               d2gmja2 A:237-335 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                 d2gmja1 A:4-236,A:336-482 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                                                         d2gmja3 A:483-584 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................hhhhh.......eee..eeee..hhhhhhhhhhhhhhhhhh.....eeeee.............ee.hhhhhhhh.hhhhhh....ee..ee..eee....eee..............ee.hhhhhhhhhhhhhhhhh.eeee...eeeeee.....eeeeee..eee.....eeeeee...eee..eeee.....hhhhhhhhhhh..........eeeeeeeeee.hhhhh...eeeeeee........eeeeeee......eeeeeeeee........hhhhhhhhhh....hhhhhh..eeeeeeeeeee.hhhhhh...ee..eee..............hhhhhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhh..hhhhhhh.hhhhhhhhhhhhhh...............hhhhhh.hhhhh..............hhhhhhhh............eee...hhhhhhhhhhh..hhhhhh....eeeee......eeeee.hhhh...hhhhhhh....eee.............. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------4FE4S_FER_2  PDB: A:544-573   ----------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gmj A   4 CKVPRITTHYTIYPRDQDKRWEGVNMERFAEEADVVIVGAGPAGLSAATRLKQLAAQHEKDLRVCLVEKAAHIGAHTLSGACLDPRAFEELFPDWKEKGAPLNTPVTEDRFGILTEKYRIPVPILPGLPMNNHGNYVVRLGHLVSWMGEQAEALGVEVYPGYAAAEILFHEDGSVKGIATNDVGIQKDGAPKTTFERGLELHAKVTIFAEGCHGHLAKQLYKKFDLRANCEPQTYGIGLKELWVIDEKKWKPGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLLALGFVVGLDYQNPYLSPFREFQRWKHHPSIKPTLEGGKRIAYGARALNEGGFQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGTLAAESIFNQLTSENLQSKTIGLHVTEYEDNLKNSWVWKELYSVRNIRPSCHGILGVYGGMIYTGIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQGDGFRLQINAQNCVHCKTCDIKDPSQNINWVVPEGGGGPAYNGM 584
                                    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       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583

Chain B from PDB  Type:PROTEIN  Length:578
 aligned with ETFD_PIG | P55931 from UniProtKB/Swiss-Prot  Length:617

    Alignment length:578
                                    49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369       379       389       399       409       419       429       439       449       459       469       479       489       499       509       519       529       539       549       559       569       579       589       599       609        
             ETFD_PIG    40 PRITTHYTIYPRDQDKRWEGVNMERFAEEADVVIVGAGPAGLSAATRLKQLAAQHEKDLRVCLVEKAAHIGAHTLSGACLDPRAFEELFPDWKEKGAPLNTPVTEDRFGILTEKYRIPVPILPGLPMNNHGNYVVRLGHLVSWMGEQAEALGVEVYPGYAAAEILFHEDGSVKGIATNDVGIQKDGAPKTTFERGLELHAKVTIFAEGCHGHLAKQLYKKFDLRANCEPQTYGIGLKELWVIDEKKWKPGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLLALGFVVGLDYQNPYLSPFREFQRWKHHPSIKPTLEGGKRIAYGARALNEGGFQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGTLAAESIFNQLTSENLQSKTIGLHVTEYEDNLKNSWVWKELYSVRNIRPSCHGILGVYGGMIYTGIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQGDGFRLQINAQNCVHCKTCDIKDPSQNINWVVPEGGGGPAYNGM 617
               SCOP domains d2gmjb1 B:7-236,B:336-482 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                                                                                                                                            d2gmjb2 B:237-335 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                 d2gmjb1 B:7-236,B:336-482 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                                                         d2gmjb3 B:483-584 Electron transfer flavoprotein-ubiquinone oxidoreductase, EFT-QO                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhh............eeee..hhhhhhhhhhhhhhhhhhh....eeee..............ee...hhhhhh..hhhhh........eeeeeee....eee..............ee.hhhhhhhhhhhhhhh...eee....eeeeee.....eeeeee...................eee..eeee.....hhhhhhhhhhhh.........eeeeeeeeee.hhhhh...eeeeeee........eeeeeee......eeeeeeeee........hhhhhhhhhh....hhhhhh..eeeeeeeeeee.hhhhhh...ee..eee..............hhhhhhhhhhhhhhhhhhhhh............hhhhhhhhh.hhhhhhhhhh...hhhhh..hhhhhhhhhhh...................hhhhh....................hhhhhhhh............eee...hhhhhhhhhhhhhhhhh......eeee........eeee........hhhhhhh....eee.............. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------4FE4S_FER_2  PDB: B:544-573   ----------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2gmj B   7 PRITTHYTIYPRDQDKRWEGVNMERFAEEADVVIVGAGPAGLSAATRLKQLAAQHEKDLRVCLVEKAAHIGAHTLSGACLDPRAFEELFPDWKEKGAPLNTPVTEDRFGILTEKYRIPVPILPGLPMNNHGNYVVRLGHLVSWMGEQAEALGVEVYPGYAAAEILFHEDGSVKGIATNDVGIQKDGAPKTTFERGLELHAKVTIFAEGCHGHLAKQLYKKFDLRANCEPQTYGIGLKELWVIDEKKWKPGRVDHTVGWPLDRHTYGGSFLYHLNEGEPLLALGFVVGLDYQNPYLSPFREFQRWKHHPSIKPTLEGGKRIAYGARALNEGGFQSIPKLTFPGGLLIGCSPGFMNVPKIKGTHTAMKSGTLAAESIFNQLTSENLQSKTIGLHVTEYEDNLKNSWVWKELYSVRNIRPSCHGILGVYGGMIYTGIFYWIFRGMEPWTLKHKGSDSDQLKPAKDCTPIEYPKPDGQISFDLLSSVALSGTNHEHDQPAHLTLKDDSVPVNRNLSIYDGPEQRFCPAGVYEFVPLEQGDGFRLQINAQNCVHCKTCDIKDPSQNINWVVPEGGGGPAYNGM 584
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506       516       526       536       546       556       566       576

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 "CATH Domain" information available for 2GMJ)

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

Asymmetric Unit(hide GO term definitions)

Chain A,B (ETFD_PIG | P55931)

molecular function
	GO:0051539	4 iron, 4 sulfur cluster binding	Interacting selectively and non-covalently with a 4 iron, 4 sulfur (4Fe-4S) cluster; this cluster consists of four iron atoms, with the inorganic sulfur atoms found between the irons and acting as bridging ligands.
	GO:0009055	electron carrier activity	Any molecular entity that serves as an electron acceptor and electron donor in an electron transport chain. An electron transport chain is a process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0004174	electron-transferring-flavoprotein dehydrogenase activity	Catalysis of the reaction: reduced ETF + ubiquinone = ETF + ubiquinol.
	GO:0050660	flavin adenine dinucleotide binding	Interacting selectively and non-covalently with FAD, flavin-adenine dinucleotide, the coenzyme or the prosthetic group of various flavoprotein oxidoreductase enzymes, in either the oxidized form, FAD, or the reduced form, FADH2.
	GO:0051536	iron-sulfur cluster binding	Interacting selectively and non-covalently with an iron-sulfur cluster, a combination of iron and sulfur atoms.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0043783	oxidoreductase activity, oxidizing metal ions with flavin as acceptor	Catalysis of an oxidation-reduction in which the oxidation state of metal ion is altered and flavin acts as an electron acceptor.
	GO:0048039	ubiquinone binding	Interacting selectively and non-covalently with ubiquinone, a quinone derivative with a tail of isoprene units.
biological process
	GO:0022900	electron transport chain	A process in which a series of electron carriers operate together to transfer electrons from donors to any of several different terminal electron acceptors to generate a transmembrane electrochemical gradient.
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0006979	response to oxidative stress	Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of oxidative stress, a state often resulting from exposure to high levels of reactive oxygen species, e.g. superoxide anions, hydrogen peroxide (H2O2), and hydroxyl radicals.
cellular component
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0005743	mitochondrial inner membrane	The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric Unit
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	Cis Peptide Bonds
		Trp A:264 - Pro A:265	[ RasMol ]
		Trp B:264 - Pro B:265	[ RasMol ]
		Val A:6 - Pro A:7	[ RasMol ]

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	ETFD_PIG \| P55931	:	2gmh

2gmh	STRUCTURE OF PORCINE ELECTRON TRANSFER FLAVOPROTEIN- UBIQUINONE OXIDOREDUCTASE IN COMPLEXED WITH UBIQUINONE

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 10)

Sites (10, 10)

SS Bonds (0, 0)

Cis Peptide Bonds (3, 3)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (1, 2)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (3, 6)

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Gene Ontology (15, 15)

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