3Q7U - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF MTB 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLTRANSFERASE (ISPD) COMPLEXED WITH CTP

Authors :   M. C. M. Reddy, J. B. Bruning, C. Thurman, T. R. Ioerger, J. C. Sacchettin Structural Genomics Consortium (Tbsgc)

Date :   05 Jan 11 (Deposition) - 04 May 11 (Release) - 12 Nov 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.10

Chains :   Asym./Biol. Unit : A,B

Keywords :   Tb Structural Genomics Consortium, Tbsgc, Rossmann Fold, 2-C-Methyl- D-Erythritol 4-Phosphate Cytidylyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. C. M. Reddy, J. B. Bruning, C. Thurman, T. R. Ioerger, J. C. Sacchettini
Crystal Structure Of Mycobacterium Tuberculosis 2-C-Methyl-D-Erythritol 4-Phosphate Cytidyltransferase (Ispd): A Candidate Antitubercular Drug Target
Proteins 2011
PubMed: search

Molecule 1 - 2-C-METHYL-D-ERYTHRITOL 4-PHOSPHATE CYTIDYLTRANSFERASE
	Chains	:	A, B
	EC Number	:	2.7.7.60
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28B
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector Type	:	PLASMID
	Gene	:	ISPD, RV3582C, MT3688, MTCY06G11.29C
	Organism Scientific	:	MYCOBACTERIUM TUBERCULOSIS
	Organism Taxid	:	83332
	Strain	:	H37RV
	Synonym	:	4-DIPHOSPHOCYTIDYL-2C-METHYL-D-ERYTHRITOL SYNTHASE, MEP CYTIDYLYLTRANSFERASE, MCT

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (2, 4)

No.	Name	Count	Type	Full Name
1	CTP	2	Ligand/Ion	CYTIDINE-5'-TRIPHOSPHATE
2	MG	2	Ligand/Ion	MAGNESIUM ION

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	HOH A:361 , HOH A:362 , CTP A:500	BINDING SITE FOR RESIDUE MG A 600
2	AC2	SOFTWARE	PRO A:13 , ALA A:14 , ALA A:15 , GLY A:16 , GLY A:18 , GLU A:19 , ARG A:20 , LYS A:27 , GLY A:80 , SER A:81 , ASN A:82 , ARG A:83 , THR A:86 , ASP A:107 , ALA A:108 , ALA A:109 , LYS A:215 , HOH A:233 , HOH A:243 , HOH A:264 , HOH A:306 , HOH A:308 , HOH A:368 , HOH A:387 , MG A:600	BINDING SITE FOR RESIDUE CTP A 500
3	AC3	SOFTWARE	PRO B:13 , ALA B:14 , ALA B:15 , GLY B:16 , SER B:17 , GLY B:18 , GLU B:19 , ARG B:20 , LYS B:27 , GLY B:80 , SER B:81 , ASN B:82 , ARG B:83 , THR B:86 , ASP B:107 , ALA B:108 , ALA B:109 , LYS B:215 , MG B:232 , HOH B:251 , HOH B:338 , HOH B:371 , HOH B:389	BINDING SITE FOR RESIDUE CTP B 500
4	AC4	SOFTWARE	HOH B:337 , CTP B:500	BINDING SITE FOR RESIDUE MG B 232

(no "SS Bond" information available for 3Q7U)

Asymmetric/Biological Unit

No.	Residues
1	Thr A:165	-	Pro A:166
2	Ala B:147	-	Asn B:148
3	Thr B:165	-	Pro B:166

(no "SAP(SNP)/Variant" information available for 3Q7U)

Asymmetric/Biological Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ISPD	PS01295	4-diphosphocytidyl-2C-methyl-D-erythritol synthase signature.	ISPD_MYCTO	103-110	2	A:103-110 B:103-110
1	ISPD	PS01295		ISPD_MYCTU	103-110	2	A:103-110 B:103-110

(no "Exon" information available for 3Q7U)

Asymmetric/Biological 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:222
 aligned with ISPD_MYCTO | P9WKG8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTO     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q7ua_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhh.........eeee........hhhhhhhhhhhhhh...eeeeeee...eeeee.....eee..hhh.eeee...eeeehhhhhhhhhhhh..----...hhhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q7u A   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLD----EYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175        |-   |   195       205       215       225      
                                                                                                                                                                                                            184  189

Chain A from PDB  Type:PROTEIN  Length:222
 aligned with ISPD_MYCTU | P9WKG9 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTU     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q7ua_ A: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhhh....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhh.........eeee........hhhhhhhhhhhhhh...eeeeeee...eeeee.....eee..hhh.eeee...eeeehhhhhhhhhhhh..----...hhhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q7u A   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLD----EYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175        |-   |   195       205       215       225      
                                                                                                                                                                                                            184  189

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with ISPD_MYCTO | P9WKG8 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTO     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q7ub_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --IspD-3q7uB01 B:8-231                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --IspD-3q7uB02 B:8-231                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhh.........eeee........hhhhhhhhhhhhhh...eeeeee....eeeee.....eee..hhh.eeee...eeeehhhhhhhhh....hhhhh....hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (2) -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q7u B   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

Chain B from PDB  Type:PROTEIN  Length:226
 aligned with ISPD_MYCTU | P9WKG9 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:226
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225      
           ISPD_MYCTU     6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
               SCOP domains d3q7ub_ B: automated matches                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --IspD-3q7uB01 B:8-231                                                                                                                                                                                                             Pfam domains (1)
           Pfam domains (2) --IspD-3q7uB02 B:8-231                                                                                                                                                                                                             Pfam domains (2)
         Sec.struct. author ..eeeeee............hhhh.ee..eehhhhhhhhhhh.....eeeeeehhhhhhhhhhhhhhhheeee...hhhhhhhhhhh.........eeee........hhhhhhhhhhhhhh...eeeeee....eeeee.....eee..hhh.eeee...eeeehhhhhhhhh....hhhhh....hhhhhhhh....eeee.hhhhh...hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------ISPD    ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3q7u B   6 GEVVAIVPAAGSGERLAVGVPKAFYQLDGQTLIERAVDGLLDSGVVDTVVVAVPADRTDEARQILGHRAMIVAGGSNRTDTVNLALTVLSGTAEPEFVLVHDAARALTPPALVARVVEALRDGYAAVVPVLPLSDTIKAVDANGVVLGTPERAGLRAVQTPQGFTTDLLLRSYQRGSLDLPAAEYTDDASLVEHIGGQVQVVDGDPLAFKITTKLDLLLAQAIVRG 231
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225

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/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: Nucleotide-diphospho-sugar transferases (408)

Superfamily: Nucleotide-diphospho-sugar transferases (408)

Family: automated matches (48)

Protein domain: automated matches (48)

Mycobacterium tuberculosis [TaxId: 83332] (7)

1a	d3q7ua_	A:
1b	d3q7ub_	B:

(no "CATH Domain" information available for 3Q7U)

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: GT-A (172)

Family: IspD (16)

Mycobacterium tuberculosis (4)

1a	IspD-3q7uB01	B:8-231
1b	IspD-3q7uB02	B:8-231

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (ISPD_MYCTU | P9WKG9)

molecular function
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
	GO:0002135	CTP binding	Interacting selectively and non-covalently with CTP, cytidine 5'-triphosphate.
	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:0000287	magnesium ion binding	Interacting selectively and non-covalently with magnesium (Mg) ions.
	GO:0030145	manganese ion binding	Interacting selectively and non-covalently with manganese (Mn) ions.
	GO:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	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).
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
	GO:0008270	zinc ion binding	Interacting selectively and non-covalently with zinc (Zn) ions.
biological process
	GO:0040007	growth	The increase in size or mass of an entire organism, a part of an organism or a cell.
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	GO:0051484	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway involved in terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway that contributes to terpenoid biosynthesis. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.
cellular component
	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.

Chain A,B (ISPD_MYCTO | P9WKG8)

molecular function
	GO:0050518	2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase activity	Catalysis of the reaction: 2-C-methyl-D-erythritol 4-phosphate + CTP = 4-CDP-2-C-methyl-D-erythritol + diphosphate.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0019288	isopentenyl diphosphate biosynthetic process, methylerythritol 4-phosphate pathway	The chemical reactions and pathways resulting in the formation of isopentenyl diphosphate by the mevalonate-independent pathway. Isopentenyl diphosphate (IPP) is the fundamental unit in isoprenoid biosynthesis and is biosynthesized from pyruvate and glyceraldehyde 3-phosphate via intermediates, including 1-deoxy-D-xylulose 5-phosphate.
	GO:0008299	isoprenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of any isoprenoid compound, isoprene (2-methylbuta-1,3-diene) or compounds containing or derived from linked isoprene (3-methyl-2-butenylene) residues.
	GO:0016114	terpenoid biosynthetic process	The chemical reactions and pathways resulting in the formation of terpenoids, any member of a class of compounds characterized by an isoprenoid chemical structure.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Ala B:147 - Asn B:148	[ RasMol ]
		Thr A:165 - Pro A:166	[ RasMol ]
		Thr B:165 - Pro B:166	[ RasMol ]

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	3q7u
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	ISPD_MYCTO \| P9WKG8
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	ISPD_MYCTU \| P9WKG9
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	2.7.7.60
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	ISPD_MYCTO \| P9WKG8
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UniProtKB/Swiss-Prot
	ISPD_MYCTO \| P9WKG8	:	2xwn 3okr 3q80
	ISPD_MYCTU \| P9WKG9	:	2xwn 3okr 3q80

3okr	APO MTB ISPD
3q80	MTB ISPD COMPLEXED WITH CDP-ME

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (2, 4)

Sites (4, 4)

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 (1, 2)

CATH Domains (0, 0)

Pfam Domains (1, 2)

Gene Ontology (15, 22)

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Related Entries Specified in the PDB File