1IXO - JenaLib

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Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   ENZYME-ANALOGUE SUBSTRATE COMPLEX OF PYRIDOXINE 5'-PHOSPHATE SYNTHASE

Authors :   M. Garrido-Franco, B. Laber, R. Huber, T. Clausen

Date :   28 Jun 02 (Deposition) - 11 Feb 03 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Tim Barrel, Enzyme-Ligand Complex, Open-Closed Transition, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Garrido-Franco, B. Laber, R. Huber, T. Clausen
Enzyme-Ligand Complexes Of Pyridoxine 5'-Phosphate Synthase Implications For Substrate Binding And Catalysis
J. Mol. Biol. V. 321 601 2002
PubMed-ID: 12206776 | Reference-DOI: 10.1016/S0022-2836(02)00695-2
(for further references see the PDB file header)

Molecule 1 - PYRIDOXINE 5'-PHOSPHATE SYNTHASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PASK-IBA3
	Expression System Strain	:	JM83
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PDXJ
	Organism Scientific	:	ESCHERICHIA COLI
	Organism Taxid	:	562
	Synonym	:	PYRIDOXAL PHOSPHATE BIOSYNTHETIC PROTEIN PDXJ

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (1, 5)

No.	Name	Count	Type	Full Name
1	G3P	5	Ligand/Ion	SN-GLYCEROL-3-PHOSPHATE

Biological Unit 1 (1, 10)

No.	Name	Count	Type	Full Name
1	G3P	10	Ligand/Ion	SN-GLYCEROL-3-PHOSPHATE

Biological Unit 2 (1, 2)

No.	Name	Count	Type	Full Name
1	G3P	2	Ligand/Ion	SN-GLYCEROL-3-PHOSPHATE

Biological Unit 3 (1, 2)

No.	Name	Count	Type	Full Name
1	G3P	2	Ligand/Ion	SN-GLYCEROL-3-PHOSPHATE

Biological Unit 4 (1, 2)

No.	Name	Count	Type	Full Name
1	G3P	2	Ligand/Ion	SN-GLYCEROL-3-PHOSPHATE

Asymmetric Unit (5, 5)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASN A:9 , ARG A:20 , THR A:43 , GLU A:72 , HIS A:193 , GLY A:194 , ASN A:213 , ILE A:214 , GLY A:215 , HIS A:216 , HOH A:1025 , HOH A:1034 , HOH A:1054	BINDING SITE FOR RESIDUE G3P A 1001
2	AC2	SOFTWARE	ASN B:9 , GLU B:72 , GLU B:153 , HIS B:193 , GLY B:194 , ASN B:213 , ILE B:214 , GLY B:215 , HIS B:216 , HOH B:1024 , HOH B:1030 , HOH B:1047 , HOH B:1069 , HOH B:1073 , ARG C:20	BINDING SITE FOR RESIDUE G3P B 1002
3	AC3	SOFTWARE	ARG B:20 , ASN C:9 , THR C:43 , GLU C:72 , HIS C:193 , GLY C:194 , ASN C:213 , ILE C:214 , GLY C:215 , HIS C:216 , G3P C:1005 , HOH C:1016 , HOH C:1036	BINDING SITE FOR RESIDUE G3P C 1003
4	AC4	SOFTWARE	ASN D:9 , ARG D:20 , GLU D:72 , GLU D:153 , HIS D:193 , GLY D:194 , ASN D:213 , ILE D:214 , GLY D:215 , HIS D:216 , HOH D:1014 , HOH D:1017 , HOH D:1026	BINDING SITE FOR RESIDUE G3P D 1004
5	AC5	SOFTWARE	ARG B:20 , ASP C:11 , HIS C:12 , HIS C:45 , ARG C:47 , HIS C:52 , GLU C:72 , HIS C:193 , G3P C:1003	BINDING SITE FOR RESIDUE G3P C 1005

(no "SS Bond" information available for 1IXO)

Asymmetric Unit

No.	Residues
1	Tyr A:24	-	Pro A:25
2	Tyr B:24	-	Pro B:25
3	Tyr C:24	-	Pro C:25
4	Tyr D:24	-	Pro D:25

Asymmetric Unit (1, 4)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	A/B/C/D	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (1, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	A/B/C/D	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	B/C	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	A	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_PDXJ_ECOLI_001 *	G	194	S	PDXJ_ECOLI	---	---	D	G	194	S
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

(no "PROSITE Motif" information available for 1IXO)

(no "Exon" information available for 1IXO)

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:235
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ixoa_ A: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ixoA00 A:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhh......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeeee..-------........hhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh..eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixo A   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPE-------EGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91    |    -  |    111       121       131       141       151       161       171       181       191       201       211       221       231       241  
                                                                                                                         96     104

Chain B from PDB  Type:PROTEIN  Length:235
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ixob_ B: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ixoB00 B:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhh......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...-------.....hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhh..eeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixo B   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPE-------EGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91    |    -  |    111       121       131       141       151       161       171       181       191       201       211       221       231       241  
                                                                                                                         96     104

Chain C from PDB  Type:PROTEIN  Length:235
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ixoc_ C: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ixoC00 C:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhh.......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeeee.hhhhhhhhhhhh..eeeee..-------.....hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeeeehhhhhhh.hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixo C   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPE-------EGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91    |    -  |    111       121       131       141       151       161       171       181       191       201       211       221       231       241  
                                                                                                                         96     104

Chain D from PDB  Type:PROTEIN  Length:235
 aligned with PDXJ_ECOLI | P0A794 from UniProtKB/Swiss-Prot  Length:243

    Alignment length:242
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241  
           PDXJ_ECOLI     2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPEKRQEVTTEGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
               SCOP domains d1ixod_ D: Pyridoxine 5'-phosphate synthase                                                                                                                                                                                                        SCOP domains
               CATH domains 1ixoD00 D:2-243 Aldolase class I                                                                                                                                                                                                                   CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeehhhhhhhhhh......hhhhhhhhhhh....eeeee........hhhhhhhhhhhh...eeeee..hhhhhhhhhhhh..eeee...-------.....hhhhhhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhh...eeeeehhhhhh..hhhhhhhhhhhhhhhhhhhhhh..eeeee......hhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------S------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ixo D   2 AELLLGVNIDHIATLRNARGTAYPDPVQAAFIAEQAGADGITVHLREDRRHITDRDVRILRQTLDTRMNLEMAVTEEMLAIAVETKPHFCCLVPE-------EGGLDVAGQRDKMRDACKRLADAGIQVSLFIDADEEQIKAAAEVGAPFIEIHTGCYADAKTDAEQAQELARIAKAATFAASLGLKVNAGHGLTYHNVKAIAAIPEMHELNIGHAIIGRAVMTGLKDAVAEMKRLMLEARG 243
                                    11        21        31        41        51        61        71        81        91    |    -  |    111       121       131       141       151       161       171       181       191       201       211       221       231       241  
                                                                                                                         96     104

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 '\|'

Asymmetric Unit

Classes(

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Folds(

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Superfamilies( (-)

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Families(

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Protein Domains( (-)

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Organisms( (-)

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

Fold: TIM beta/alpha-barrel (3956)

Superfamily: Pyridoxine 5'-phosphate synthase (11)

Family: Pyridoxine 5'-phosphate synthase (8)

Protein domain: Pyridoxine 5'-phosphate synthase (7)

Escherichia coli [TaxId: 562] (7)

1a	d1ixoa_	A:
1b	d1ixob_	B:
1c	d1ixoc_	C:
1d	d1ixod_	D:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: Alpha-Beta Barrel (2994)

Topology: TIM Barrel (2806)

Homologous Superfamily: Aldolase class I (887)

Escherichia coli. Organism_taxid: 562. (43)

1a	1ixoA00	A:2-243
1b	1ixoB00	B:2-243
1c	1ixoC00	C:2-243
1d	1ixoD00	D:2-243

(no "Pfam Domain" information available for 1IXO)

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (PDXJ_ECOLI | P0A794)

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:0033856	pyridoxine 5'-phosphate synthase activity	Catalysis of the reaction: 1-deoxy-D-xylulose 5-phosphate + 3-amino-2-oxopropyl phosphate = 2 H(2)O + H(+) + phosphate + pyridoxine 5'-phosphate.
	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:0016769	transferase activity, transferring nitrogenous groups	Catalysis of the transfer of a nitrogenous group from one compound (donor) to another (acceptor).
biological process
	GO:0008615	pyridoxine biosynthetic process	The chemical reactions and pathways resulting in the formation of pyridoxine, 2-methyl-3-hydroxy-4,5-bis(hydroxymethyl)pyridine, one of the vitamin B6 compounds.
cellular component
	GO:0005737	cytoplasm	All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
	GO:0005829	cytosol	The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.

Asymmetric Unit
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	1ixo
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UniProtKB/Swiss-Prot
	PDXJ_ECOLI \| P0A794	:	1ho1 1ho4 1ixn 1ixp 1ixq 1m5w

1ho1	1HO1 CONTAINS PYRIDOXINE 5'-PHOSPHATE SYNTHASE
1ho4	1HO4 CONTAINS PYRIDOXINE 5'-PHOSPHATE SYNTHASE COMPLEXED WITH INORGANIC PHOSPHATE
1ixn	1IXN CONTAINS ENZYME-SUBSTRATE COMPLEX OF PYRIDOXINE 5'- PHOSPHATE SYNTHASE
1ixp	1IXP CONTAINS ENZYME-PHOSPHATE COMPLEX OF PYRIDOXINE 5'- PHOSPHATE SYNTHASE
1ixq	1IXQ CONTAINS ENZYME-PHOSPHATE2 COMPLEX OF PYRIDOXINE 5'- PHOSPHATE SYNTHASE

Description

Compounds

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Ligands, Modified Residues, Ions (1, 5)

Sites (5, 5)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

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