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Asym./Biol. Unit (Jmol Viewer)

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

Title :   CRYSTAL STRUCTURES OF NK1-HEPARIN COMPLEXES REVEAL THE BASIS FOR NK1 ACTIVITY AND ENABLE ENGINEERING OF POTENT AGONISTS OF THE MET RECEPTOR

Authors :   D. Lietha, D. Y. Chirgadze, B. Mulloy, T. L. Blundell, E. Gherardi

Date :   19 Sep 01 (Deposition) - 02 Oct 01 (Release) - 12 Jul 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.30

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

Keywords :   Hgf/Sf, Hormone/Growth Factor, Hormone-Growth Factor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   D. Lietha, D. Y. Chirgadze, B. Mulloy, T. L. Blundell, E. Gherardi
Crystal Structures Of Nk1-Heparin Complexes Reveal The Basi For Nk1 Activity And Enable Engineering Of Potent Agonists Of The Met Receptor
Embo J. V. 20 5543 2001
PubMed-ID: 11597998 | Reference-DOI: 10.1093/EMBOJ/20.20.5543

Molecule 1 - HEPATOCYTE GROWTH FACTOR
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	PICHIA PASTORIS
	Expression System Plasmid	:	PPIC-9K
	Expression System Strain	:	GS115
	Expression System Taxid	:	4922
	Expression System Vector	:	YEAST
	Fragment	:	NK1
	Mutation	:	YES
	Organism Common	:	HUMAN
	Organism Scientific	:	HOMO SAPIENS
	Organism Taxid	:	9606
	Other Details	:	NK1 DIMER IN COMPLEX WITH HEPARIN MOLECULE
	Synonym	:	SCATTER FACTOR, SF, HEPATOPOEITIN A

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 7)

No.	Name	Count	Type	Full Name
1	EPE	2	Ligand/Ion	4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
2	IDS	3	Ligand/Ion	2-O-SULFO-ALPHA-L-IDOPYRANURONIC ACID
3	SGN	2	Ligand/Ion	N,O6-DISULFO-GLUCOSAMINE

Asymmetric Unit (3, 3)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:58 , PHE A:162 , GLU A:183 , GLU A:184 , GLY A:185 , GLY A:186 , TRP A:188 , PHE A:190 , ARG A:197 , TYR A:198 , IDS A:301	binding site for residue EPE A 306
2	AC2	SOFTWARE	SER B:161 , PHE B:162 , GLU B:184 , GLY B:185 , GLY B:186 , TRP B:188 , PHE B:190 , ARG B:197 , TYR B:198 , VAL B:200 , HOH B:407	binding site for residue EPE B 301
3	AC3	SOFTWARE	LYS A:58 , LYS A:60 , THR A:61 , LYS A:62 , LYS A:63 , ARG A:73 , LYS A:78 , GLY A:79 , LYS A:132 , ARG A:181 , GLY A:182 , GLU A:183 , EPE A:306	binding site for Poly-Saccharide residues IDS A 301 through IDS A 305

Asymmetric/Biological Unit

No.	Residues
1	A:74	-	A:84
2	A:128	-	A:206
3	A:149	-	A:189
4	A:177	-	A:201
5	B:128	-	B:206
6	B:149	-	B:189
7	B:177	-	B:201

Asymmetric/Biological Unit

No.	Residues
1	Ile A:156	-	Pro A:157
2	Ile B:156	-	Pro B:157

Asymmetric/Biological Unit (1, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_014570	S	153	I	HGF_HUMAN	Polymorphism	17566	A/B	S	153	I

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

Asymmetric/Biological Unit (2, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	KRINGLE_2	PS50070	Kringle domain profile.	HGF_HUMAN	127-206 210-288 304-383 390-469	2	A:127-206 B:127-206 - - -
2	KRINGLE_1	PS00021	Kringle domain signature.	HGF_HUMAN	176-189 259-271 353-365 439-452	2	A:176-189 B:176-189 - - -

Asymmetric/Biological Unit (5, 9)

	ENSEMBL					UniProtKB			PDB
No.	Transcript ID	Exon	Exon ID	Genome Location	Length	ID	Location	Length	Count	Location	Length
1.2a	ENST00000222390	2a	ENSE00001949645	chr7:81399514-81399200	315	HGF_HUMAN	1-30	30	0	-	-
1.3b	ENST00000222390	3b	ENSE00000698746	chr7:81392188-81392023	166	HGF_HUMAN	30-85	56	2	A:38-85 B:42-85 (gaps)	48 44
1.4b	ENST00000222390	4b	ENSE00001790262	chr7:81388120-81388008	113	HGF_HUMAN	85-123	39	2	A:85-123 B:85-123 (gaps)	39 39
1.5b	ENST00000222390	5b	ENSE00000698725	chr7:81386619-81386505	115	HGF_HUMAN	123-161	39	2	A:123-161 B:123-161	39 39
1.6a	ENST00000222390	6a	ENSE00000698723	chr7:81381578-81381436	143	HGF_HUMAN	161-209	49	2	A:161-208 B:161-209	48 49
1.7	ENST00000222390	7	ENSE00000698721	chr7:81374436-81374316	121	HGF_HUMAN	209-249	41	1	- B:209-210	- 2
1.8	ENST00000222390	8	ENSE00000698671	chr7:81372787-81372669	119	HGF_HUMAN	249-289	41	0	-	-
1.10	ENST00000222390	10	ENSE00000698668	chr7:81359095-81358921	175	HGF_HUMAN	289-347	59	0	-	-
1.11	ENST00000222390	11	ENSE00000698665	chr7:81355333-81355206	128	HGF_HUMAN	347-390	44	0	-	-
1.12	ENST00000222390	12	ENSE00000698663	chr7:81350163-81350061	103	HGF_HUMAN	390-424	35	0	-	-
1.13	ENST00000222390	13	ENSE00000698662	chr7:81346681-81346548	134	HGF_HUMAN	424-469	46	0	-	-
1.14	ENST00000222390	14	ENSE00000698661	chr7:81340835-81340797	39	HGF_HUMAN	469-482	14	0	-	-
1.15	ENST00000222390	15	ENSE00000698660	chr7:81339559-81339463	97	HGF_HUMAN	482-514	33	0	-	-
1.16	ENST00000222390	16	ENSE00000698659	chr7:81336680-81336606	75	HGF_HUMAN	514-539	26	0	-	-
1.17	ENST00000222390	17	ENSE00000698658	chr7:81335743-81335603	141	HGF_HUMAN	539-586	48	0	-	-
1.18	ENST00000222390	18	ENSE00000698657	chr7:81335069-81334963	107	HGF_HUMAN	586-622	37	0	-	-
1.19	ENST00000222390	19	ENSE00000698655	chr7:81334851-81334706	146	HGF_HUMAN	622-670	49	0	-	-
1.20b	ENST00000222390	20b	ENSE00001870741	chr7:81332073-81328322	3752	HGF_HUMAN	671-728	58	0	-	-

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
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Chain A from PDB  Type:PROTEIN  Length:171
 aligned with HGF_HUMAN | P14210 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:171
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207 
            HGF_HUMAN    38 TIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSE 208
               SCOP domains d1gmna1 A:38-125 Hepatocyte growth factor                                               d1gmna2 A:126-207 NK1 fragment of hepatocyte growth factor                        - SCOP domains
               CATH domains 1gmnA01 A:38-125 Hepatocyte Growth Factor                                               1gmnA02 A:126-207 Plasminogen Kringle 4                                           - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhh.eeeeeeeeee........eeee..hhhhhhhhhhh.........eeeee....eeeee.........eeeeeeeeeeeee.hhh.....................................hhhhh....................eee.......eee........ Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------I------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -----------------------------------------------------------------------------------------KRINGLE_2  PDB: A:127-206 UniProt: 127-206                                      -- PROSITE (1)
                PROSITE (2) ------------------------------------------------------------------------------------------------------------------------------------------KRINGLE_1     ------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: A:38-85 UniProt: 30-85          -------------------------------------Exon 1.5b  PDB: A:123-161              ----------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) -----------------------------------------------Exon 1.4b  PDB: A:85-123               -------------------------------------Exon 1.6a  PDB: A:161-208 UniProt: 161-209       Transcript 1 (2)
                 1gmn A  38 TIHEFKKSAKTTLIKIDPALKIKTKKVNTADQCADRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSE 208
                                    47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207

Chain B from PDB  Type:PROTEIN  Length:114
 aligned with HGF_HUMAN | P14210 from UniProtKB/Swiss-Prot  Length:728

    Alignment length:169
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201         
            HGF_HUMAN    42 FKKSAKTTLIKIDPALKIKTKKVNTADQCANRCTRNKGLPFTCKAFVFDKARKQCLWFPFNSMSSGVKKEFGHEFDLYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE 210
               SCOP domains d1gmnb1 B:                                42-1          25 Hepa             tocyte gd1gmnb2 B:126-209 NK1 fragment of hepatocyte growth factor                          - SCOP domains
               CATH domains 1gmnB01 B:                                42-1          25 Hepa             tocyte G1gmnB02 B:126-209 Plasminogen Kringle 4                                             - CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .ee.......--------------------------------..ee----------.......-------------.ee.hhhh.....................................hhhhhh...................eee.......eee.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------I--------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------------------------------KRINGLE_2  PDB: B:127-206 UniProt: 127-206                                      ---K PROSITE (1)
                PROSITE (2) --------------------------------------------------------------------------------------------------------------------------------------KRINGLE_1     --------------------- PROSITE (2)
           Transcript 1 (1) Exon 1.3b  PDB: B:42-85 (gaps) [INCOMPLETE] -------------------------------------Exon 1.5b  PDB: B:123-161              -----------------------------------------------1. Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.4b  PDB: B:85-123 (gaps)        -------------------------------------Exon 1.6a  PDB: B:161-209 UniProt: 161-209       - Transcript 1 (2)
                 1gmn B  42 FKKSAKTTLI--------------------------------CKAF----------WFPFNSM-------------LYENKDYIRNCIIGKGRSYKGTVSITKSGIKCQPWSSMIPHEHSFLPSSYRGKDLQENYCRNPRGEEGGPWCFTSNPEVRYEVCDIPQCSEVE 210
                                    51         -         -         -  |  |   -      |101  |      -      |121       131       141       151       161       171       181       191       201         
                                    51                               84 87         98   104           118

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/Biological Unit

Classes(

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Folds(

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Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

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Organisms( (-)

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Class: Small proteins (3458)

Fold: Hairpin loop containing domain-like (17)

Superfamily: Hairpin loop containing domain-like (17)

Family: Hairpin loop containing domain (15)

Protein domain: Hepatocyte growth factor (11)

Human (Homo sapiens) [TaxId: 9606] (11)

1a	d1gmna1	A:38-125
1b	d1gmnb1	B:42-125

Fold: Kringle-like (68)

Superfamily: Kringle-like (68)

Family: Kringle modules (54)

Protein domain: NK1 fragment of hepatocyte growth factor (8)

Human (Homo sapiens) [TaxId: 9606] (8)

2a	d1gmna2	A:126-207
2b	d1gmnb2	B:126-209

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(bba) Sandwich (528)

Topology: Hepatocyte Growth Factor (13)

Homologous Superfamily: Hepatocyte Growth Factor (13)

Human (Homo sapiens) (9)

1a	1gmnA01	A:38-125
1b	1gmnB01	B:42-125

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Plasminogen Kringle 4 (42)

Homologous Superfamily: Plasminogen Kringle 4 (42)

Human (Homo sapiens) (37)

2a	1gmnB02	B:126-209
2b	1gmnA02	A:126-207

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B (HGF_HUMAN | P14210)

molecular function
	GO:0042056	chemoattractant activity	Providing the environmental signal that initiates the directed movement of a motile cell or organism towards a higher concentration of that signal.
	GO:0008083	growth factor activity	The function that stimulates a cell to grow or proliferate. Most growth factors have other actions besides the induction of cell growth or proliferation.
	GO:0042802	identical protein binding	Interacting selectively and non-covalently with an identical protein or proteins.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0046982	protein heterodimerization activity	Interacting selectively and non-covalently with a nonidentical protein to form a heterodimer.
	GO:0004252	serine-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a catalytic mechanism that involves a catalytic triad consisting of a serine nucleophile that is activated by a proton relay involving an acidic residue (e.g. aspartate or glutamate) and a basic residue (usually histidine).
biological process
	GO:0000187	activation of MAPK activity	The initiation of the activity of the inactive enzyme MAP kinase (MAPK).
	GO:0031100	animal organ regeneration	The regrowth of a lost or destroyed animal organ.
	GO:0060326	cell chemotaxis	The directed movement of a motile cell guided by a specific chemical concentration gradient. Movement may be towards a higher concentration (positive chemotaxis) or towards a lower concentration (negative chemotaxis).
	GO:0000902	cell morphogenesis	The developmental process in which the size or shape of a cell is generated and organized.
	GO:0008283	cell proliferation	The multiplication or reproduction of cells, resulting in the expansion of a cell population.
	GO:0035729	cellular response to hepatocyte growth factor stimulus	Any process that results in a change in state or activity of a cell (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a hepatocyte growth factor stimulus.
	GO:0001837	epithelial to mesenchymal transition	A transition where an epithelial cell loses apical/basolateral polarity, severs intercellular adhesive junctions, degrades basement membrane components and becomes a migratory mesenchymal cell.
	GO:0048012	hepatocyte growth factor receptor signaling pathway	The series of molecular signals generated as a consequence of the hepatocyte growth factor receptor binding to one of its physiological ligands.
	GO:0030212	hyaluronan metabolic process	The chemical reactions and pathways involving hyaluronan, the naturally occurring anionic form of hyaluronic acid, any member of a group of glycosaminoglycans, the repeat units of which consist of beta-1,4 linked D-glucuronyl-beta-(1,3)-N-acetyl-D-glucosamine.
	GO:0001889	liver development	The process whose specific outcome is the progression of the liver over time, from its formation to the mature structure. The liver is an exocrine gland which secretes bile and functions in metabolism of protein and carbohydrate and fat, synthesizes substances involved in the clotting of the blood, synthesizes vitamin A, detoxifies poisonous substances, stores glycogen, and breaks down worn-out erythrocytes.
	GO:0051450	myoblast proliferation	The multiplication or reproduction of myoblasts, resulting in the expansion of a myoblast cell population. A myoblast is a mononucleate cell type that, by fusion with other myoblasts, gives rise to the myotubes that eventually develop into skeletal muscle fibers.
	GO:0043066	negative regulation of apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of cell death by apoptotic process.
	GO:0010507	negative regulation of autophagy	Any process that stops, prevents, or reduces the frequency, rate or extent of autophagy. Autophagy is the process in which cells digest parts of their own cytoplasm.
	GO:0043154	negative regulation of cysteine-type endopeptidase activity involved in apoptotic process	Any process that stops, prevents, or reduces the frequency, rate or extent of a cysteine-type endopeptidase activity involved in the apoptotic process.
	GO:1902042	negative regulation of extrinsic apoptotic signaling pathway via death domain receptors	Any process that stops, prevents or reduces the frequency, rate or extent of extrinsic apoptotic signaling pathway via death domain receptors.
	GO:1901299	negative regulation of hydrogen peroxide-mediated programmed cell death	Any process that stops, prevents or reduces the frequency, rate or extent of hydrogen peroxide-mediated programmed cell death.
	GO:0050728	negative regulation of inflammatory response	Any process that stops, prevents, or reduces the frequency, rate or extent of the inflammatory response.
	GO:0032715	negative regulation of interleukin-6 production	Any process that stops, prevents, or reduces the frequency, rate, or extent of interleukin-6 production.
	GO:0033137	negative regulation of peptidyl-serine phosphorylation	Any process that stops, prevents, or reduces the frequency, rate or extent of the phosphorylation of peptidyl-serine.
	GO:0090201	negative regulation of release of cytochrome c from mitochondria	Any process that decreases the rate, frequency or extent of release of cytochrome c from mitochondria, the process in which cytochrome c is enabled to move from the mitochondrial intermembrane space into the cytosol, which is an early step in apoptosis and leads to caspase activation.
	GO:0002576	platelet degranulation	The regulated exocytosis of secretory granules containing preformed mediators such as histamine and serotonin by a platelet.
	GO:0050918	positive chemotaxis	The directed movement of a motile cell or organism towards a higher concentration of a chemical.
	GO:2000573	positive regulation of DNA biosynthetic process	Any process that activates or increases the frequency, rate or extent of DNA biosynthetic process.
	GO:0045766	positive regulation of angiogenesis	Any process that activates or increases angiogenesis.
	GO:0030335	positive regulation of cell migration	Any process that activates or increases the frequency, rate or extent of cell migration.
	GO:0008284	positive regulation of cell proliferation	Any process that activates or increases the rate or extent of cell proliferation.
	GO:0032733	positive regulation of interleukin-10 production	Any process that activates or increases the frequency, rate, or extent of interleukin-10 production.
	GO:0031643	positive regulation of myelination	Any process that activates or increases the frequency, rate or extent of the formation of a myelin sheath around nerve axons.
	GO:0070572	positive regulation of neuron projection regeneration	Any process that activates or increases the frequency, rate or extent of neuron projection regeneration, the regrowth of neuronal processes such as axons or dendrites following their loss or damage.
	GO:0045669	positive regulation of osteoblast differentiation	Any process that activates or increases the frequency, rate or extent of osteoblast differentiation.
	GO:0050731	positive regulation of peptidyl-tyrosine phosphorylation	Any process that activates or increases the frequency, rate or extent of the phosphorylation of peptidyl-tyrosine.
	GO:0014068	positive regulation of phosphatidylinositol 3-kinase signaling	Any process that activates or increases the frequency, rate or extent of signal transduction mediated by the phosphatidylinositol 3-kinase cascade.
	GO:0045944	positive regulation of transcription from RNA polymerase II promoter	Any process that activates or increases the frequency, rate or extent of transcription from an RNA polymerase II promoter.
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
	GO:0060665	regulation of branching involved in salivary gland morphogenesis by mesenchymal-epithelial signaling	Any process that modulates the rate, frequency, or extent of branching involved in salivary gland morphogenesis as a result of signals being generated by the mesenchyme and received and interpreted by the salivary gland epithelium.
	GO:1900744	regulation of p38MAPK cascade	Any process that modulates the frequency, rate or extent of p38MAPK cascade.
	GO:1902947	regulation of tau-protein kinase activity	Any process that modulates the frequency, rate or extent of tau-protein kinase activity.
cellular component
	GO:0005576	extracellular region	The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.
	GO:0005615	extracellular space	That part of a multicellular organism outside the cells proper, usually taken to be outside the plasma membranes, and occupied by fluid.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
	GO:0031093	platelet alpha granule lumen	The volume enclosed by the membrane of the platelet alpha granule.

Asymmetric/Biological Unit
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	1gmn
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(no "Related Entries Specified in the PDB File" available for 1GMN)

Description

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Ligands, Modified Residues, Ions (3, 7)

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SS Bonds (7, 7)

Cis Peptide Bonds (2, 2)

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