1SME - JenaLib

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Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A

Authors :   A. M. Silva, A. Y. Lee, S. V. Gulnik, D. E. Goldberg, J. W. Erickson

Date :   11 Jun 96 (Deposition) - 11 Jan 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.70

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

Keywords :   Aspartyl Proteinase, Aspartic Proteinase, Aspartyl Protease, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. M. Silva, A. Y. Lee, S. V. Gulnik, P. Maier, J. Collins, T. N. Bhat, P. J. Collins, R. E. Cachau, K. E. Luker, I. Y. Gluzman, S. E. Francis, A. Oksman, D. E. Goldberg, J. W. Erickson
Structure And Inhibition Of Plasmepsin Ii, A Hemoglobin-Degrading Enzyme From Plasmodium Falciparum.
Proc. Natl. Acad. Sci. Usa V. 93 10034 1996
PubMed-ID: 8816746 | Reference-DOI: 10.1073/PNAS.93.19.10034

Molecule 1 - PLASMEPSIN II
	Chains	:	A, B
	EC Number	:	3.4.23.39
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET VECTOR 22B (NOVAGEN)
	Expression System Strain	:	PET
	Expression System Taxid	:	562
	Expression System Vector Type	:	PET
	Organism Common	:	MALARIA PARASITE P. FALCIPARUM
	Organism Scientific	:	PLASMODIUM FALCIPARUM
	Organism Taxid	:	5833

Molecule 2 - PEPSTATIN
	Chains	:	C, D
	Engineered	:	YES
	Synthetic	:	YES

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (2, 6)

No.	Name	Count	Type	Full Name
1	IVA	2	Mod. Amino Acid	ISOVALERIC ACID
2	STA	4	Mod. Amino Acid	STATINE

Biological Unit 1 (2, 3)

No.	Name	Count	Type	Full Name
1	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
2	STA	2	Mod. Amino Acid	STATINE

Biological Unit 2 (2, 3)

No.	Name	Count	Type	Full Name
1	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
2	STA	2	Mod. Amino Acid	STATINE

Asymmetric Unit (2, 2)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ASP A:34 , GLY A:36 , ASN A:76 , TYR A:77 , VAL A:78 , SER A:79 , ILE A:123 , TYR A:192 , ASP A:214 , GLY A:216 , THR A:217 , SER A:218 , ILE A:290 , LEU B:242	BINDING SITE FOR CHAIN C OF PEPSTATIN
2	AC2	SOFTWARE	PHE A:241 , LEU A:242 , ASP B:34 , GLY B:36 , SER B:37 , ASN B:76 , TYR B:77 , VAL B:78 , SER B:79 , ILE B:123 , TYR B:192 , ASP B:214 , GLY B:216 , THR B:217 , SER B:218 , ILE B:290 , LEU B:292	BINDING SITE FOR CHAIN D OF PEPSTATIN

Asymmetric Unit

No.	Residues
1	A:47	-	A:52
2	A:249	-	A:285
3	B:47	-	B:52
4	B:249	-	B:285

Asymmetric Unit

No.	Residues
1	Glu A:112	-	Pro A:113
2	Glu B:112	-	Pro B:113

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

Asymmetric Unit (2, 6)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PLM2_PLAFA	140-447	2	A:16-323 B:16-323
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PLM2_PLAFA	155-166 335-346	4	A:31-42 B:31-42 A:211-222 B:211-222

Biological Unit 1 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PLM2_PLAFA	140-447	1	A:16-323 -
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PLM2_PLAFA	155-166 335-346	2	A:31-42 - A:211-222 -

Biological Unit 2 (2, 3)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	PEPTIDASE_A1	PS51767	Peptidase family A1 domain profile.	PLM2_PLAFA	140-447	1	- B:16-323
2	ASP_PROTEASE	PS00141	Eukaryotic and viral aspartyl proteases active site.	PLM2_PLAFA	155-166 335-346	2	- B:31-42 - B:211-222

(no "Exon" information available for 1SME)

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:329
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:329
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
           PLM2_PLAFA   125 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 453
               SCOP domains d1smea_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1smeA01 A:1-175 Acid Proteases                                                                                                                                                 1smeA02 A:176-329 Acid Proteases                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeee...eeeeeee......eeeeeee......eee......hhhhh.................eeeee....eeeeeeeeeeeee..eeeeeeeeeeee......hhhh....eeee...hhh.......hhhhhhh.......eeee.........eee......hhh.....eeee.......eeee...........eeeee......eee.hhhhhhh...............eee........eeee....eeee.hhhh..........eee..eee......eeee.hhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: A:16-323 UniProt: 140-447                                                                                                                                                                                                                                                                        ------ PROSITE (1)
                PROSITE (2) ------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sme A   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain B from PDB  Type:PROTEIN  Length:329
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:329
                                   134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444         
           PLM2_PLAFA   125 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 453
               SCOP domains d1smeb_ B: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1smeB01 B:1-175 Acid Proteases                                                                                                                                                 1smeB02 B:176-329 Acid Proteases                                                                                                                           CATH domains
           Pfam domains (1) --------------Asp-1smeB01 B:15-325                                                                                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) --------------Asp-1smeB02 B:15-325                                                                                                                                                                                                                                                                                                   ---- Pfam domains (2)
         Sec.struct. author .......eeee...eeeeeee......eeee.........eee........hhh.....hhh.........eeeeee..eeeeeeeeeeeeee..eeeeeeeeeeee......hhhh...........hhh.hhh...hhhhhhh.......eeee..................hhh.....eeee.......eeeeeee........eeeee......eee.hhhhhhhhhh............eee........eeee....eeee.hhhh..........eee..eee......eeee.hhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) ---------------PEPTIDASE_A1  PDB: B:16-323 UniProt: 140-447                                                                                                                                                                                                                                                                        ------ PROSITE (1)
                PROSITE (2) ------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1sme B   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320

Chain C from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1sme C 347 xVVxAx 352
                            |  | |
                          347-IVA|
                             350-STA
                               352-STA

Chain D from PDB  Type:PROTEIN  Length:6
                                      
               SCOP domains ------ SCOP domains
               CATH domains ------ CATH domains
               Pfam domains ------ Pfam domains
         Sec.struct. author ...... Sec.struct. author
                 SAPs(SNPs) ------ SAPs(SNPs)
                    PROSITE ------ PROSITE
                 Transcript ------ Transcript
                 1sme D 347 xVVxAx 352
                            |  | |
                            |  | |
                          347-IVA|
                             350-STA
                               352-STA

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Acid proteases (1120)

Superfamily: Acid proteases (1120)

Family: Pepsin-like (505)

Protein domain: Plasmepsin (a hemoglobin-degrading enzyme) (21)

Plasmodium falciparum, plasmepsin II [TaxId: 5833] (18)

1a	d1smea_	A:
1b	d1smeb_	B:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Beta Barrel (4804)

Topology: Cathepsin D, subunit A; domain 1 (745)

Homologous Superfamily: Acid Proteases (745)

Malaria parasite p (Plasmodium falciparum) (14)

1a	1smeA02	A:176-329
1b	1smeB02	B:176-329
1c	1smeA01	A:1-175
1d	1smeB01	B:1-175

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: Peptidase_AA (368)

Family: Asp (155)

Plasmodium falciparum (15)

1a	Asp-1smeB01	B:15-325
1b	Asp-1smeB02	B:15-325

Asymmetric Unit(hide GO term definitions)

Chain A,B (PLM2_PLAFA | P46925)

molecular function
	GO:0004190	aspartic-type endopeptidase activity	Catalysis of the hydrolysis of internal, alpha-peptide bonds in a polypeptide chain by a mechanism in which a water molecule bound by the side chains of aspartic residues at the active center acts as a nucleophile.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0008233	peptidase activity	Catalysis of the hydrolysis of a peptide bond. A peptide bond is a covalent bond formed when the carbon atom from the carboxyl group of one amino acid shares electrons with the nitrogen atom from the amino group of a second amino acid.
biological process
	GO:0006508	proteolysis	The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
	GO:0005773	vacuole	A closed structure, found only in eukaryotic cells, that is completely surrounded by unit membrane and contains liquid material. Cells contain one or several vacuoles, that may have different functions from each other. Vacuoles have a diverse array of functions. They can act as a storage organelle for nutrients or waste products, as a degradative compartment, as a cost-effective way of increasing cell size, and as a homeostatic regulator controlling both turgor pressure and pH of the cytosol.

Asymmetric Unit
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	Cis Peptide Bonds
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		Glu B:112 - Pro B:113	[ RasMol ]

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	1sme
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(no "Related Entries Specified in the PDB File" available for 1SME)

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SS Bonds (4, 4)

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