3S8J - JenaLib

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Biological Unit 1 (Jmol Viewer)

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Biological Unit 2 (Jmol Viewer)

Title :   CRYSTAL STRUCTURE OF A PAPAYA LATEX SERINE PROTEASE INHIBITOR (PPI) AT 2.6A RESOLUTION

Authors :   A. Garcia-Pino

Date :   29 May 11 (Deposition) - 02 Nov 11 (Release) - 19 Jun 13 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

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

Keywords :   Kunitz-Sti Fold, Serine Protease Inhibitor, Hydrolase Inhibitor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. Azarkan, S. Martinez-Rodriguez, L. Buts, D. Baeyens-Volant, A. Garcia-Pino
The Plasticity Of The Beta-Trefoil Fold Constitutes An Evolutionary Platform For Protease Inhibition
J. Biol. Chem. V. 286 43726 2011
PubMed-ID: 22027836 | Reference-DOI: 10.1074/JBC.M111.291310

Molecule 1 - LATEX SERINE PROTEINASE INHIBITOR
	Chains	:	A, B
	Organism Common	:	MAMON
	Organism Scientific	:	CARICA PAPAYA
	Organism Taxid	:	3649
	Other Details	:	PPI WAS EXTRACTED FROM C. PAPAYA LATEX

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 10)

No.	Name	Count	Type	Full Name
1	ACT	5	Ligand/Ion	ACETATE ION
2	FMT	2	Ligand/Ion	FORMIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	NAG	2	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 1 (4, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	GOL	1	Ligand/Ion	GLYCEROL
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Biological Unit 2 (3, 6)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	FMT	1	Ligand/Ion	FORMIC ACID
3	GOL	-1	Ligand/Ion	GLYCEROL
4	NAG	1	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE

Asymmetric Unit (10, 10)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GLY A:17 , ASP A:19 , ILE A:61 , ASN A:84 , HOH A:220	BINDING SITE FOR RESIDUE NAG A 185
02	AC2	SOFTWARE	ASP B:19 , ASN B:84	BINDING SITE FOR RESIDUE NAG B 185
03	AC3	SOFTWARE	ALA B:29 , GLN B:51 , ARG B:166	BINDING SITE FOR RESIDUE ACT B 186
04	AC4	SOFTWARE	PHE B:119 , GLU B:120 , HIS B:123 , THR B:148 , HOH B:209	BINDING SITE FOR RESIDUE ACT B 187
05	AC5	SOFTWARE	LYS A:175 , GLU A:176	BINDING SITE FOR RESIDUE ACT A 186
06	AC6	SOFTWARE	PHE B:159 , PHE B:160	BINDING SITE FOR RESIDUE ACT B 188
07	AC7	SOFTWARE	PHE A:54 , HOH B:217	BINDING SITE FOR RESIDUE ACT B 189
08	AC8	SOFTWARE	TYR A:16 , ASN A:71	BINDING SITE FOR RESIDUE GOL A 187
09	AC9	SOFTWARE	SER A:24 , ILE A:26 , ALA A:29 , GLY A:31	BINDING SITE FOR RESIDUE FMT A 188
10	BC1	SOFTWARE	ARG B:99 , HOH B:216	BINDING SITE FOR RESIDUE FMT B 190

Asymmetric Unit

No.	Residues
1	A:45	-	A:89
2	A:142	-	A:153
3	B:45	-	B:89
4	B:142	-	B:153

Asymmetric Unit

No.	Residues
1	Cys A:45	-	Pro A:46
2	Cys B:45	-	Pro B:46

(no "SAP(SNP)/Variant" information available for 3S8J)

Asymmetric Unit (1, 2)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	LSPI_CARPA	6-22	2	A:6-22 B:6-22

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	LSPI_CARPA	6-22	1	A:6-22 -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	SOYBEAN_KUNITZ	PS00283	Soybean trypsin inhibitor (Kunitz) protease inhibitors family signature.	LSPI_CARPA	6-22	1	- B:6-22

(no "Exon" information available for 3S8J)

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:182
 aligned with LSPI_CARPA | P80691 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:182
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181  
           LSPI_CARPA     2 APKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVFESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTN 183
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..................eeeee.........eeee..........eeee........eeeee..............eeeee............eeeee..eeeeeee.........hhhhhhh.eeee......eeeee............eeeeeee.....eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----SOYBEAN_KUNITZ   ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8j A   2 APKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVRESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTN 183
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181

Chain B from PDB  Type:PROTEIN  Length:181
 aligned with LSPI_CARPA | P80691 from UniProtKB/Swiss-Prot  Length:184

    Alignment length:181
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182 
           LSPI_CARPA     3 PKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVFESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTN 183
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................eeeeee..hhhhh..eeee..........eeee........eeee................eeee...................................hhhhhhh.eeee......eeeee............eeeeeee.....eeeeee.....eeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---SOYBEAN_KUNITZ   ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3s8j B   3 PKPIVDIDGKPVLYGVDYFVVSAIWGAGGGGLTVYGPGNKKKCPLSVVQDPFDNGEPIIFSAIKNVKDNIVRESVDLNVKFNITINCNETTAWKVDRFPGVIGWTVTLGGEKGYHGFESTHSMFKIKKAGLPFSYKFHFCPSYPRTRLIPCNNVDIFFDKYRIRRLILTNDAKEFVFIKTN 183
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

(no "SCOP Domain" information available for 3S8J)

(no "CATH Domain" information available for 3S8J)

(no "Pfam Domain" information available for 3S8J)

Asymmetric Unit(hide GO term definitions)

Chain A,B (LSPI_CARPA | P80691)

molecular function
	GO:0004866	endopeptidase inhibitor activity	Stops, prevents or reduces the activity of an endopeptidase, any enzyme that hydrolyzes nonterminal peptide bonds in polypeptides.
	GO:0030414	peptidase inhibitor activity	Stops, prevents or reduces the activity of a peptidase, any enzyme that catalyzes the hydrolysis peptide bonds.
	GO:0004867	serine-type endopeptidase inhibitor activity	Stops, prevents or reduces the activity of serine-type endopeptidases, enzymes that catalyze the hydrolysis of nonterminal peptide bonds in a polypeptide chain; a serine residue (and a histidine residue) are at the active center of the enzyme.
biological process
	GO:0010951	negative regulation of endopeptidase activity	Any process that decreases the frequency, rate or extent of endopeptidase activity, the endohydrolysis of peptide bonds within proteins.
	GO:0010466	negative regulation of peptidase activity	Any process that stops or reduces the rate of peptidase activity, the hydrolysis of peptide bonds within proteins.
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.

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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
		Cys A:45 - Pro A:46	[ RasMol ]
		Cys B:45 - Pro B:46	[ RasMol ]

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]

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Description

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Ligands, Modified Residues, Ions (4, 10)

Sites (10, 10)

SS Bonds (4, 4)

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