4PEF - JenaLib

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Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Biological Unit 5 (Jmol Viewer)

Title :   DBR1 IN COMPLEX WITH SULFATE

Authors :   E. J. Montemayor, A. Katolik, N. E. Clark, A. B. Taylor, J. P. Schuermann D. J. Combs, R. Johnsson, S. P. Holloway, S. W. Stevens, M. J. Damha, P. J

Date :   23 Apr 14 (Deposition) - 27 Aug 14 (Release) - 01 Oct 14 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.96

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A  (1x)
Biol. Unit 2: B  (1x)
Biol. Unit 3: C  (1x)
Biol. Unit 4: D  (1x)
Biol. Unit 5: E  (1x)

Keywords :   Nuclease, Phosphodiesterase, Metallohydrolase, Metallophosphoesterase, Lariat Rna, Hydrolase, Metalloenzyme (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   E. J. Montemayor, A. Katolik, N. E. Clark, A. B. Taylor, J. P. Schuermann, D. J. Combs, R. Johnsson, S. P. Holloway, S. W. Stevens, M. J. Damha, P. J. Hart
Structural Basis Of Lariat Rna Recognition By The Intron Debranching Enzyme Dbr1.
Nucleic Acids Res. V. 42 10845 2014
PubMed-ID: 25123664 | Reference-DOI: 10.1093/NAR/GKU725

Molecule 1 - RNA LARIAT DEBRANCHING ENZYME, PUTATIVE
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21 STAR(DE3)PLYSS
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	EHI_062730
	Organism Scientific	:	ENTAMOEBA HISTOLYTICA
	Organism Taxid	:	5759

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A
Biological Unit 2 (1x)	:		B
Biological Unit 3 (1x)	:			C
Biological Unit 4 (1x)	:				D
Biological Unit 5 (1x)	:					E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 18)

No.	Name	Count	Type	Full Name
1	GOL	3	Ligand/Ion	GLYCEROL
2	MN	5	Ligand/Ion	MANGANESE (II) ION
3	SO4	10	Ligand/Ion	SULFATE ION

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 4 (2, 3)

No.	Name	Count	Type	Full Name
1	GOL	1	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Biological Unit 5 (1, 2)

No.	Name	Count	Type	Full Name
1	GOL	-1	Ligand/Ion	GLYCEROL
2	MN	-1	Ligand/Ion	MANGANESE (II) ION
3	SO4	2	Ligand/Ion	SULFATE ION

Asymmetric Unit (18, 18)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASP A:45 , ASN A:90 , HIS A:180 , HIS A:230 , SO4 A:403 , HOH A:614	binding site for residue MN A 401
02	AC2	SOFTWARE	ARG A:50 , ASN A:95 , HIS A:99 , PRO A:146 , HOH A:509 , HOH A:520 , HOH A:662	binding site for residue SO4 A 402
03	AC3	SOFTWARE	HIS A:16 , ASP A:45 , ASN A:90 , HIS A:91 , HIS A:230 , HIS A:232 , MN A:401 , HOH A:614 , HOH A:672 , HOH A:701	binding site for residue SO4 A 403
04	AC4	SOFTWARE	SER A:38 , ASN A:122 , LYS A:266 , THR A:267 , HOH A:691	binding site for residue GOL A 404
05	AC5	SOFTWARE	ASP B:45 , ASN B:90 , HIS B:180 , HIS B:230 , SO4 B:403 , HOH B:516	binding site for residue MN B 401
06	AC6	SOFTWARE	ARG B:50 , ASN B:95 , HIS B:99 , PRO B:146 , HOH B:591 , HOH B:603 , HOH B:628 , HOH B:682	binding site for residue SO4 B 402
07	AC7	SOFTWARE	HIS B:16 , ASP B:45 , ASN B:90 , HIS B:91 , HIS B:230 , HIS B:232 , MN B:401 , HOH B:516 , HOH B:640 , HOH B:713	binding site for residue SO4 B 403
08	AC8	SOFTWARE	SER B:38 , ASN B:122 , LYS B:266 , THR B:267 , HOH B:680 , HOH B:728	binding site for residue GOL B 404
09	AC9	SOFTWARE	ASP C:45 , ASN C:90 , HIS C:180 , HIS C:230 , SO4 C:403 , HOH C:709	binding site for residue MN C 401
10	AD1	SOFTWARE	ARG C:50 , ASN C:95 , HIS C:99 , HOH C:508 , HOH C:512 , HOH C:648 , HOH C:699	binding site for residue SO4 C 402
11	AD2	SOFTWARE	HIS C:16 , ASP C:45 , ASN C:90 , HIS C:91 , HIS C:230 , HIS C:232 , MN C:401 , HOH C:709	binding site for residue SO4 C 403
12	AD3	SOFTWARE	ASP D:45 , ASN D:90 , HIS D:180 , HIS D:230 , SO4 D:403 , HOH D:542	binding site for residue MN D 401
13	AD4	SOFTWARE	ARG D:50 , ASN D:95 , HIS D:99 , PRO D:146 , HOH D:505 , HOH D:643	binding site for residue SO4 D 402
14	AD5	SOFTWARE	HIS D:16 , ASP D:45 , ASN D:90 , HIS D:91 , HIS D:230 , HIS D:232 , MN D:401 , HOH D:542	binding site for residue SO4 D 403
15	AD6	SOFTWARE	GLY D:68 , ASP D:69 , HIS D:71	binding site for residue GOL D 404
16	AD7	SOFTWARE	ASP E:45 , ASN E:90 , HIS E:180 , HIS E:230 , SO4 E:403 , HOH E:614	binding site for residue MN E 401
17	AD8	SOFTWARE	ARG E:50 , ASN E:95 , HIS E:99 , PRO E:146 , HOH E:540 , HOH E:636 , HOH E:695	binding site for residue SO4 E 402
18	AD9	SOFTWARE	HIS E:16 , ASP E:45 , ASN E:90 , HIS E:91 , HIS E:230 , HIS E:232 , MN E:401 , HOH E:614 , HOH E:644 , HOH E:674	binding site for residue SO4 E 403

(no "SS Bond" information available for 4PEF)

Asymmetric Unit

No.	Residues
1	Tyr A:144	-	Pro A:145
2	Phe A:292	-	Pro A:293
3	Tyr B:144	-	Pro B:145
4	Phe B:292	-	Pro B:293
5	Tyr C:144	-	Pro C:145
6	Phe C:292	-	Pro C:293
7	Tyr D:144	-	Pro D:145
8	Phe D:292	-	Pro D:293
9	Tyr E:144	-	Pro E:145
10	Phe E:292	-	Pro E:293

(no "SAP(SNP)/Variant" information available for 4PEF)

(no "PROSITE Motif" information available for 4PEF)

(no "Exon" information available for 4PEF)

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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhh........hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pef A   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Chain B from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pef B   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Chain C from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhhhh......hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pef C   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Chain D from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhh.......hhhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.....hhh.eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhhh.hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pef D   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Chain E from PDB  Type:PROTEIN  Length:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee.....hhhhhhhhhhhhhhhhh..eeeeee........hhhhhhhh..hhhhh...hhhhhhh........eee......hhhhhhhh...eeee..eee...eeeeee..eeeeee....hhhhh...ee...hhhhh........hhhhhhh.........eeee.....hhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhh..eeee......eeeee..eeeee.........eeeeeee.......eehhhhhhhhhhhhhhhh...ee.....hhhhhhh..hhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4pef E   5 QIQHIAIVGCVHGKYREMYRQLSEYEKSTGKEISFVICTGDMQTLRYEADLVYLKVPPKYKQMGDFHLYYEGKEKAPYLTLFIGGNHESSNVLLHLYNGGFVCFNMYYLGVCSCININGLRIVGVSGIYKSFDEKKPYTYPPSPNDVVSLFHTRNYVIQMLSNLSQSSQIDISLSHDWPQGIVMKGNYKQLYRFQPGFKKDGASLGSPINKVILNTLKPKYWISGHMHCEYHAEEGPTHFIALGKIGYKNAISYLDLPLKQKTDLEYDKDWVCNLIMTWPAFSNKAQFPDLSYSISELLSKRTKELDKKIIELWEKYIGLKIIYDSDTFDIQFTSRRFYIEKIYNELNI 353
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
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	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 4PEF)

(no "CATH Domain" information available for 4PEF)

(no "Pfam Domain" information available for 4PEF)

Asymmetric Unit(hide GO term definitions)

Asymmetric Unit
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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Phe A:292 - Pro A:293	[ RasMol ]
		Phe B:292 - Pro B:293	[ RasMol ]
		Phe C:292 - Pro C:293	[ RasMol ]
		Phe D:292 - Pro D:293	[ RasMol ]
		Phe E:292 - Pro E:293	[ RasMol ]
		Tyr A:144 - Pro A:145	[ RasMol ]
		Tyr B:144 - Pro B:145	[ RasMol ]
		Tyr C:144 - Pro C:145	[ RasMol ]
		Tyr D:144 - Pro D:145	[ RasMol ]
		Tyr E:144 - Pro E:145	[ RasMol ]

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (10, 10)

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