1E3S - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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

Title :   RAT BRAIN 3-HYDROXYACYL-COA DEHYDROGENASE BINARY COMPLEX WITH NADH

Authors :   A. J. Powell, J. A. Read, M. J. Banfield, R. L. Brady

Date :   22 Jun 00 (Deposition) - 25 May 01 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Oxidoreductase, Dehydrogenase, Beta-Oxidation Of Fatty Acids, Steroids, Amyloid Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Powell, J. A. Read, M. J. Banfield, F. Gunn-Moore, S. D. Yan, J. Lustbader, A. R. Stern, D. M. Stern, R. L. Brady
Recognition Of Structurally Diverse Substrates By Type Ii 3-Hydroxyacyl-Coa Dehydrogenase (Hadh Ii) Amyloid-Beta Binding Alcohol Dehydrogenase (Abad)
J. Mol. Biol. V. 303 311 2000
PubMed-ID: 11023795 | Reference-DOI: 10.1006/JMBI.2000.4139

Molecule 1 - SHORT CHAIN 3-HYDROXYACYL-COA DEHYDROGENASE
	Cellular Location	:	CYTOPLASM
	Chains	:	A, B, C, D
	EC Number	:	1.1.1.35
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Cellular Location	:	CYTOPLASM
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21
	Expression System Taxid	:	511693
	Organ	:	BRAIN
	Organelle	:	MITOCHONRIA
	Organism Common	:	NORWAY RAT
	Organism Scientific	:	RATTUS NORVEGICUS
	Organism Taxid	:	10116
	Synonym	:	HADH II

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (1, 4)

No.	Name	Count	Type	Full Name
1	NAD	4	Ligand/Ion	NICOTINAMIDE-ADENINE-DINUCLEOTIDE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	GLY A:17 , SER A:20 , GLY A:21 , LEU A:22 , ASP A:41 , ALA A:63 , ASN A:64 , VAL A:65 , CYS A:91 , ALA A:92 , THR A:153 , ALA A:154 , TYR A:168 , LYS A:172 , PRO A:198 , GLY A:199 , PHE A:201 , THR A:203 , PRO A:204 , HOH A:2037 , HOH A:2107 , HOH A:2108 , HOH A:2109	BINDING SITE FOR RESIDUE NAD A 301
2	AC2	SOFTWARE	GLY B:17 , SER B:20 , GLY B:21 , LEU B:22 , ASP B:41 , VAL B:42 , ALA B:63 , ASN B:64 , VAL B:65 , CYS B:91 , ALA B:92 , GLY B:93 , THR B:153 , ALA B:154 , TYR B:168 , LYS B:172 , PRO B:198 , GLY B:199 , PHE B:201 , THR B:203 , PRO B:204 , HOH B:2127 , HOH B:2128 , HOH B:2129 , HOH B:2130	BINDING SITE FOR RESIDUE NAD B 301
3	AC3	SOFTWARE	GLY C:17 , SER C:20 , GLY C:21 , LEU C:22 , ASP C:41 , ALA C:63 , ASN C:64 , VAL C:65 , CYS C:91 , ALA C:92 , GLY C:93 , THR C:153 , ALA C:154 , TYR C:168 , LYS C:172 , PRO C:198 , GLY C:199 , PHE C:201 , THR C:203 , PRO C:204 , HOH C:2047 , HOH C:2122 , HOH C:2123 , HOH C:2124	BINDING SITE FOR RESIDUE NAD C 301
4	AC4	SOFTWARE	GLY D:17 , SER D:20 , GLY D:21 , LEU D:22 , ASP D:41 , ALA D:63 , ASN D:64 , VAL D:65 , CYS D:91 , ALA D:92 , GLY D:93 , THR D:153 , ALA D:154 , TYR D:168 , LYS D:172 , GLY D:199 , PHE D:201 , THR D:203 , PRO D:204 , HOH D:2007 , HOH D:2126 , HOH D:2127 , HOH D:2128 , HOH D:2129	BINDING SITE FOR RESIDUE NAD D 301

(no "SS Bond" information available for 1E3S)

Asymmetric/Biological Unit

No.	Residues
1	Phe A:223	-	Pro A:224
2	Phe B:223	-	Pro B:224
3	Phe C:223	-	Pro C:224
4	Phe D:223	-	Pro D:224

(no "SAP(SNP)/Variant" information available for 1E3S)

Asymmetric/Biological Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	ADH_SHORT	PS00061	Short-chain dehydrogenases/reductases family signature.	HCD2_RAT	155-183	4	A:155-183 B:155-183 C:155-183 D:155-183

(no "Exon" information available for 1E3S)

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:241
 aligned with HCD2_RAT | O70351 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:255
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
             HCD2_RAT     7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATPLLTTLPDKVRNFLASQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
               SCOP domains d1e3sa_ A: Type II 3-hydroxyacyl-CoA dehydrogenase                                                                                                                                                                                                              SCOP domains
               CATH domains 1e3sA00 A:7-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......--------------..........hhhhhhhhhhhhhhh......eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: A:155-183    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3s A   7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATP--------------SQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       | -         -  |    226       236       246       256     
                                                                                                                                                                                                                               204            219

Chain B from PDB  Type:PROTEIN  Length:241
 aligned with HCD2_RAT | O70351 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:255
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
             HCD2_RAT     7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATPLLTTLPDKVRNFLASQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
               SCOP domains d1e3sb_ B: Type II 3-hydroxyacyl-CoA dehydrogenase                                                                                                                                                                                                              SCOP domains
               CATH domains 1e3sB00 B:7-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee............hhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......--------------..........hhhhhhhhhhhhhhh......eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: B:155-183    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3s B   7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATP--------------SQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       | -         -  |    226       236       246       256     
                                                                                                                                                                                                                               204            219

Chain C from PDB  Type:PROTEIN  Length:241
 aligned with HCD2_RAT | O70351 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:255
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
             HCD2_RAT     7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATPLLTTLPDKVRNFLASQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
               SCOP domains d1e3sc_ C: Type II 3-hydroxyacyl-CoA dehydrogenase                                                                                                                                                                                                              SCOP domains
               CATH domains 1e3sC00 C:7-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhhhhhhhhhhhhhhhhhh..........eeeeee.hhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......--------------..........hhhhhhhhhhhhhhh......eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: C:155-183    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3s C   7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATP--------------SQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       | -         -  |    226       236       246       256     
                                                                                                                                                                                                                               204            219

Chain D from PDB  Type:PROTEIN  Length:241
 aligned with HCD2_RAT | O70351 from UniProtKB/Swiss-Prot  Length:261

    Alignment length:255
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256     
             HCD2_RAT     7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATPLLTTLPDKVRNFLASQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
               SCOP domains d1e3sd_ D: Type II 3-hydroxyacyl-CoA dehydrogenase                                                                                                                                                                                                              SCOP domains
               CATH domains 1e3sD00 D:7-261 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                             CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeee...hhhhhhhhhhhhhh..eeeeee....hhhhhhhhh...eeeee....hhhhhhhhhhhhhhhhh...eeee...................hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeee..hhhhhh...hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......--------------..........hhhhhhhhhhhhhhh......eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------ADH_SHORT  PDB: D:155-183    ------------------------------------------------------------------------------ PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1e3s D   7 SVKGLVAVITGGASGLGLSTAKRLVGQGATAVLLDVPNSEGETEAKKLGGNCIFAPANVTSEKEVQAALTLAKEKFGRIDVAVNCAGIAVAIKTYHEKKNQVHTLEDFQRVINVNLIGTFNVIRLVAGVMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIVGMTLPIARDLAPIGIRVVTIAPGLFATP--------------SQVPFPSRLGDPAEYAHLVQMVIENPFLNGEVIRLDGAIRMQP 261
                                    16        26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       | -         -  |    226       236       246       256     
                                                                                                                                                                                                                               204            219

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: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Type II 3-hydroxyacyl-CoA dehydrogenase (6)

Norway rat (Rattus norvegicus) [TaxId: 10116] (3)

1a	d1e3sa_	A:
1b	d1e3sb_	B:
1c	d1e3sc_	C:
1d	d1e3sd_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Norway rat (Rattus norvegicus) (18)

1a	1e3sA00	A:7-261
1b	1e3sB00	B:7-261
1c	1e3sC00	C:7-261
1d	1e3sD00	D:7-261

(no "Pfam Domain" information available for 1E3S)

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (HCD2_RAT | O70351)

molecular function
	GO:0047015	3-hydroxy-2-methylbutyryl-CoA dehydrogenase activity	Catalysis of the reaction: NAD+ + 2-methyl-3-hydroxybutyryl-CoA = NADH + H+ + 2-methylaceto-acetyl-CoA.
	GO:0003857	3-hydroxyacyl-CoA dehydrogenase activity	Catalysis of the reaction: (S)-3-hydroxyacyl-CoA + NAD+ = 3-oxoacyl-CoA + NADH + H(+).
	GO:0051287	NAD binding	Interacting selectively and non-covalently with nicotinamide adenine dinucleotide, a coenzyme involved in many redox and biosynthetic reactions; binding may be to either the oxidized form, NAD+, or the reduced form, NADH.
	GO:0018454	acetoacetyl-CoA reductase activity	Catalysis of the reaction: (R)-3-hydroxyacyl-CoA + NADP+ = 3-oxoacyl-CoA + NADPH + H+.
	GO:0001540	amyloid-beta binding	Interacting selectively and non-covalently with amyloid-beta peptide/protein and/or its precursor.
	GO:0004303	estradiol 17-beta-dehydrogenase activity	Catalysis of the reaction: estradiol-17-beta + NADP+ = estrone + NADPH + H+.
	GO:0030331	estrogen receptor binding	Interacting selectively and non-covalently with an estrogen receptor.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0016491	oxidoreductase activity	Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
	GO:0005496	steroid binding	Interacting selectively and non-covalently with a steroid, any of a large group of substances that have in common a ring system based on 1,2-cyclopentanoperhydrophenanthrene.
	GO:0030283	testosterone dehydrogenase [NAD(P)] activity	Catalysis of the reaction: testosterone + NAD(P)+ = androst-4-ene-3,17-dione + NAD(P)H + H+.
biological process
	GO:0033327	Leydig cell differentiation	The process in which a relatively unspecialized cell acquires specialized structural and/or functional features of a Leydig cell. A Leydig cell is a testosterone-secreting cell in the interstitial area, between the seminiferous tubules, in the testis.
	GO:0007569	cell aging	An aging process that has as participant a cell after a cell has stopped dividing. Cell aging may occur when a cell has temporarily stopped dividing through cell cycle arrest (GO:0007050) or when a cell has permanently stopped dividing, in which case it is undergoing cellular senescence (GO:0090398). May precede cell death (GO:0008219) and succeed cell maturation (GO:0048469).
	GO:0055114	oxidation-reduction process	A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
	GO:0051289	protein homotetramerization	The formation of a protein homotetramer, a macromolecular structure consisting of four noncovalently associated identical subunits.
	GO:0008033	tRNA processing	The process in which a pre-tRNA molecule is converted to a mature tRNA, ready for addition of an aminoacyl group.
cellular component
	GO:0005739	mitochondrion	A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
		Phe A:223 - Pro A:224	[ RasMol ]
		Phe B:223 - Pro B:224	[ RasMol ]
		Phe C:223 - Pro C:224	[ RasMol ]
		Phe D:223 - Pro D:224	[ RasMol ]

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	1e3s
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	HCD2_RAT \| O70351
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	1.1.1.35
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	HCD2_RAT \| O70351
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	HCD2_RAT \| O70351	:	1e3w 1e6w

1e3w	RAT BRAIN 3-HYDROXYACYL-COA DEHYDROGENASE BINARY COMPLEX WITH NADH AND 3-KETO BUTYRATE
2hsd	ALPHA, 20 BETA-HYDROXYSTEROID DEHYDROGENASE (HOLO FORM)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (1, 4)

Sites (4, 4)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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SCOP Domains (1, 4)

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