3M8W - JenaLib

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Biological Unit 3 (Jmol Viewer)

Title :   PHOSPHOPENTOMUTASE FROM BACILLUS CEREUS

Authors :   T. D. Panosian, D. P. Nannemann, G. Watkins, B. Wadzinski, B. O. Bachman T. M. Iverson

Date :   19 Mar 10 (Deposition) - 29 Dec 10 (Release) - 23 Mar 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.85

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

Keywords :   Alkaline Phosphatase Like Core Domain, Di-Metallo Catalytic Center, Manganese Binding, Isomerase, Manganese, Metal-Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. D. Panosian, D. P. Nannemann, G. R. Watkins, V. V. Phelan, W. H. Mcdonald, B. E. Wadzinski, B. O. Bachmann, T. M. Iverson
Bacillus Cereus Phosphopentomutase Is An Alkaline Phosphatase Family Member That Exhibits An Altered Entry Point Into The Catalytic Cycle.
J. Biol. Chem. V. 286 8043 2011
PubMed-ID: 21193409 | Reference-DOI: 10.1074/JBC.M110.201350

Molecule 1 - PHOSPHOPENTOMUTASE
	Chains	:	A, B, C
	EC Number	:	5.4.2.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET28A(+)
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Expression System Vector Type	:	PLASMID
	Gene	:	BC_4087, DEOB
	Organism Scientific	:	BACILLUS CEREUS
	Organism Taxid	:	226900
	Strain	:	ATCC 14579
	Synonym	:	PHOSPHODEOXYRIBOMUTASE

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 18)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	MN	10	Ligand/Ion	MANGANESE (II) ION
3	TPO	3	Mod. Amino Acid	PHOSPHOTHREONINE
4	TRS	2	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 1 (3, 5)

No.	Name	Count	Type	Full Name
1	ACT	3	Ligand/Ion	ACETATE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 2 (2, 2)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
4	TRS	1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Biological Unit 3 (1, 1)

No.	Name	Count	Type	Full Name
1	ACT	-1	Ligand/Ion	ACETATE ION
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	TPO	1	Mod. Amino Acid	PHOSPHOTHREONINE
4	TRS	-1	Ligand/Ion	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL

Asymmetric Unit (15, 15)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	TPO A:85 , ASP A:156 , ASP A:286 , HIS A:291 , HIS A:339	BINDING SITE FOR RESIDUE MN A 395
02	AC2	SOFTWARE	ASP A:13 , TPO A:85 , ASP A:327 , HIS A:328	BINDING SITE FOR RESIDUE MN A 396
03	AC3	SOFTWARE	GLY A:27 , ASP A:28 , HIS A:334 , HOH A:589 , HOH A:935	BINDING SITE FOR RESIDUE MN A 397
04	AC4	SOFTWARE	TYR A:96 , TYR A:384 , HOH A:510 , HOH A:599	BINDING SITE FOR RESIDUE TRS A 398
05	AC5	SOFTWARE	PRO A:351 , LYS A:354 , HOH A:630 , HOH A:813	BINDING SITE FOR RESIDUE ACT A 399
06	AC6	SOFTWARE	SER A:154 , ALA A:155 , ASP A:156 , ALA A:287	BINDING SITE FOR RESIDUE ACT A 400
07	AC7	SOFTWARE	LEU A:362 , ARG A:363 , GLN A:364 , ASP A:368	BINDING SITE FOR RESIDUE ACT A 401
08	AC8	SOFTWARE	TPO B:85 , ASP B:156 , ASP B:286 , HIS B:291 , HIS B:339	BINDING SITE FOR RESIDUE MN B 395
09	AC9	SOFTWARE	ASP B:13 , TPO B:85 , ASP B:327 , HIS B:328	BINDING SITE FOR RESIDUE MN B 396
10	BC1	SOFTWARE	HOH B:703 , HOH B:704	BINDING SITE FOR RESIDUE MN B 397
11	BC2	SOFTWARE	HIS B:36 , HOH B:922 , HOH B:923 , HOH B:924 , HOH B:936	BINDING SITE FOR RESIDUE MN B 398
12	BC3	SOFTWARE	TYR B:96 , HOH B:418 , HOH B:534 , HOH B:594	BINDING SITE FOR RESIDUE TRS B 399
13	BC4	SOFTWARE	TPO C:85 , ASP C:156 , ASP C:286 , HIS C:291 , HIS C:339	BINDING SITE FOR RESIDUE MN C 395
14	BC5	SOFTWARE	ASP C:13 , TPO C:85 , ASP C:327 , HIS C:328	BINDING SITE FOR RESIDUE MN C 396
15	BC6	SOFTWARE	GLY C:27 , ASP C:28 , HIS C:334 , HOH C:435 , HOH C:456 , HOH C:930	BINDING SITE FOR RESIDUE MN C 397

(no "SS Bond" information available for 3M8W)

(no "Cis Peptide Bond" information available for 3M8W)

(no "SAP(SNP)/Variant" information available for 3M8W)

(no "PROSITE Motif" information available for 3M8W)

(no "Exon" information available for 3M8W)

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:391
 aligned with DEOB_BACCR | Q818Z9 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           DEOB_BACCR     2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee....eeee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m8w A   2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    11        21        31        41        51        61        71        81   |    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
                                                                                                              85-TPO

Chain B from PDB  Type:PROTEIN  Length:391
 aligned with DEOB_BACCR | Q818Z9 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:391
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
           DEOB_BACCR     2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee.........hhhhhh....hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhh.hhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhhh...eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee................hhhhhhhhhhhhh.........hhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3m8w B   2 NKYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    11        21        31        41        51        61        71        81   |    91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391 
                                                                                                              85-TPO

Chain C from PDB  Type:PROTEIN  Length:390
 aligned with DEOB_BACCR | Q818Z9 from UniProtKB/Swiss-Prot  Length:394

    Alignment length:390
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
           DEOB_BACCR     3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDTMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) --Metalloenzyme-3m8wC01 C:5-388                                                                                                                                                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) --Metalloenzyme-3m8wC02 C:5-388                                                                                                                                                                                                                                                                                                                                                                   ---- Pfam domains (2)
           Pfam domains (3) --Metalloenzyme-3m8wC03 C:5-388                                                                                                                                                                                                                                                                                                                                                                   ---- Pfam domains (3)
         Sec.struct. author ...eeeeeee...................hhhhhhhhhh....hhhhhhhhhhhhh.............eeeee.......hhhhhhhhhh...............hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhhhhhhhh.eeeee....eeeeeee....hhhhhhhhhhhhhhhhhhhhhh..eeeeeeeeee..eeee.....eee......hhhhhhhhh..eeeee.hhhhhh......eee...hhhhhhhhhhhhhh....eeeeeeehhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...eeeeee..................eeeeee.................hhhhhhhhhhhh.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3m8w C   3 KYKRIFLVVMDSVGIGEAPDAEQFGDLGSDTIGHIAEHMNGLQMPNMVKLGLGNIREMKGISKVEKPLGYYTKMQEKSTGKDtMTGHWEIMGLYIDTPFQVFPEGFPKELLDELEEKTGRKIIGNKPASGTEILDELGQEQMETGSLIVYTSADSVLQIAAHEEVVPLDELYKICKIARELTLDEKYMVGRVIARPFVGEPGNFTRTPNRHDYALKPFGRTVMNELKDSDYDVIAIGKISDIYDGEGVTESLRTKSNMDGMDKLVDTLNMDFTGLSFLNLVDFDALFGHRRDPQGYGEALQEYDARLPEVFAKLKEDDLLLITADHGNDPIHPGTDHTREYVPLLAYSPSMKEGGQELPLRQTFADIGATVAENFGVKMPEYGTSFLNEL 392
                                    12        22        32        42        52        62        72        82  |     92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
                                                                                                             85-TPO

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 "SCOP Domain" information available for 3M8W)

(no "CATH Domain" information available for 3M8W)

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Alk_phosphatase (47)

Family: Metalloenzyme (7)

Bacillus cereus (strain ATCC 14579 / DSM 31) (3)

1a	Metalloenzyme-3m8wC01	C:5-388
1b	Metalloenzyme-3m8wC02	C:5-388
1c	Metalloenzyme-3m8wC03	C:5-388

Asymmetric Unit(hide GO term definitions)

Chain A,B,C (DEOB_BACCR | Q818Z9)

molecular function
	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:0016853	isomerase activity	Catalysis of the geometric or structural changes within one molecule. Isomerase is the systematic name for any enzyme of EC class 5.
	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:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0008973	phosphopentomutase activity	Catalysis of the reaction: D-ribose 1-phosphate = D-ribose 5-phosphate.
biological process
	GO:0006015	5-phosphoribose 1-diphosphate biosynthetic process	The chemical reactions and pathways resulting in the formation of 5-phosphoribose 1-diphosphate, also known as 5-phosphoribosyl-1-pyrophosphate.
	GO:0043094	cellular metabolic compound salvage	Any process which produces a useful metabolic compound from derivatives of it without de novo synthesis, as carried out by individual cells.
	GO:0009264	deoxyribonucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of a deoxyribonucleotide, a compound consisting of deoxyribonucleoside (a base linked to a deoxyribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
	GO:0008152	metabolic process	The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
	GO:0009166	nucleotide catabolic process	The chemical reactions and pathways resulting in the breakdown of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
	GO:0009117	nucleotide metabolic process	The chemical reactions and pathways involving a nucleotide, a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic nucleotides (nucleoside cyclic phosphates).
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.

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	Cis Peptide Bonds
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	3m8w
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 18)

Sites (15, 15)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

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Exons (0, 0)

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Gene Ontology (14, 14)

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