1QS8 - JenaLib

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Title :   CRYSTAL STRUCTURE OF THE P. VIVAX ASPARTIC PROTEINASE PLASMEPSIN COMPLEXED WITH THE INHIBITOR PEPSTATIN A

Authors :   N. Khazanovich Bernstein, M. M. Cherney, C. A. Yowell, J. B. Dame, M. N.

Date :   25 Jun 99 (Deposition) - 07 Jul 99 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.50

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

Keywords :   Plasmepsin, Aspartic Proteinase, Haemoglobinase, Malaria, Pepstatin A, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. K. Bernstein, M. M. Cherney, C. A. Yowell, J. B. Dame, M. N. James
Structural Insights Into The Activation Of P. Vivax Plasmepsin.
J. Mol. Biol. V. 329 505 2003
PubMed-ID: 12767832 | Reference-DOI: 10.1016/S0022-2836(03)00444-3

Molecule 1 - PLASMEPSIN
	Chains	:	A, B
	Engineered	:	YES
	Expression System	:	BACTERIA
	Expression System Common	:	EUBACTERIA
	Expression System Taxid	:	2
	Organism Common	:	MALARIA PARASITE P. VIVAX
	Organism Scientific	:	PLASMODIUM VIVAX
	Organism Taxid	:	5855

Molecule 2 - PEPSTATIN A
	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
Biological Unit 3 (1x)	:	A (1x)	B (1x)	C (1x)	D (1x)
Biological Unit 4 (2x)	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 8)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	IVA	2	Mod. Amino Acid	ISOVALERIC ACID
3	STA	4	Mod. Amino Acid	STATINE

Biological Unit 1 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	STA	2	Mod. Amino Acid	STATINE

Biological Unit 2 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	STA	2	Mod. Amino Acid	STATINE

Biological Unit 3 (3, 4)

No.	Name	Count	Type	Full Name
1	ACT	1	Ligand/Ion	ACETATE ION
2	IVA	1	Mod. Amino Acid	ISOVALERIC ACID
3	STA	2	Mod. Amino Acid	STATINE

Biological Unit 4 (3, 16)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	IVA	4	Mod. Amino Acid	ISOVALERIC ACID
3	STA	8	Mod. Amino Acid	STATINE

Asymmetric Unit (4, 4)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	LYS A:46 , TYR A:66 , LYS A:68	BINDING SITE FOR RESIDUE ACT A 328
2	AC2	SOFTWARE	LYS B:46 , TYR B:66 , LYS B:68	BINDING SITE FOR RESIDUE ACT B 328
3	AC3	SOFTWARE	ASP A:34 , GLY A:36 , THR A:76 , TYR A:77 , GLY A:78 , SER A:79 , LEU A:131 , TYR A:192 , ASP A:214 , GLY A:216 , THR A:217 , THR A:218 , THR A:219 , PRO A:243 , PHE A:244 , LEU A:290 , ASP B:130 , HIS B:189 , HOH C:134 , HOH C:143	BINDING SITE FOR CHAIN C OF PEPSTATIN A
4	AC4	SOFTWARE	SER A:135 , ILE B:32 , ASP B:34 , GLY B:36 , SER B:37 , THR B:76 , TYR B:77 , GLY B:78 , SER B:79 , TYR B:192 , ASP B:214 , GLY B:216 , THR B:217 , THR B:218 , THR B:219 , PRO B:243 , LEU B:290 , HOH D:111	BINDING SITE FOR CHAIN D OF PEPSTATIN A

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 1QS8)

(no "PROSITE Motif" information available for 1QS8)

(no "Exon" information available for 1QS8)

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:327
 aligned with O60989_PLAVI | O60989 from UniProtKB/TrEMBL  Length:450

    Alignment length:327
                                   133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       
        O60989_PLAVI    124 SENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVTDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  450
               SCOP domains d1qs8a_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1qs8A01 A:1-175 Acid Proteases                                                                                                                                                 1qs8A02 A:176-327 Acid Proteases                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................................................hhhhhhh...hhhhh............................................hhhhhhhhhhh.........hhhhh.....hhhhhhhhh...........................hhhh................eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhh...ee......eeee........eeee....eeeehhhh.eee.......eeee.eee......eeeehhhhhh.................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qs8 A    1 SENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVIDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  327
                                    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:328
 aligned with O60989_PLAVI | O60989 from UniProtKB/TrEMBL  Length:450

    Alignment length:328
                                   132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392       402       412       422       432       442        
        O60989_PLAVI    123 GSENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVTDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  450
               SCOP domains d1qs8b_ B: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains -1qs8B01 B:1-175 Acid Proteases                                                                                                                                                 1qs8B02 B:176-327 Acid Proteases                                                                                                                         CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................................hhhhhhh...hhhhh............................................hhhhhhhhhhh.........hhhhh.....hhhhhhhhh...........................hhhh................eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhh..ee......eeee........eeee....eeeehhhh.eee.......eeee.eee.......eeehhhhhh.................... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1qs8 B 124P GSENDVIELDDVANIMFYGEGEVGDNHQKFMLIFDTGSANLWVPSKKCNSSGCSIKNLYDSSKSKSYEKDGTKVDITYGSGTVKGFFSKDLVTLGHLSMPYKFIEVIDTDDLEPIYSSVEFDGILGLGWKDLSIGSIDPIVVELKNQNKIDNALFTFYLPVHDVHAGYLTIGGIEEKFYEGNITYEKLNHDLYWQIDLDVHFGKQTMEKANVIVDSGTTTITAPSEFLNKFFANLNVIKVPFLPFYVTTCDNKEMPTLEFKSANNTYTLEPEYYMNPILEVDDTLCMITMLPVDIDSNTFILGDPFMRKYFTVFDYDKESVGFAIAKN  327
                            ||       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159       169       179       189       199       209       219       229       239       249       259       269       279       289       299       309       319        
                         124P|                                                                                                                                                                                                                                                                                                                                      
                             1

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
                1qs8 C  401 xVVxAx  406
                            |  | |
                          401-IVA|
                             404-STA
                               406-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
                1qs8 D  411 xVVxAx  416
                            |  | |
                            |  | |
                          411-IVA|
                             414-STA
                               416-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(

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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 vivax [TaxId: 5855] (2)

1a	d1qs8a_	A:
1b	d1qs8b_	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 vivax) (2)

1a	1qs8A02	A:176-327
1b	1qs8B02	B:176-327
1c	1qs8A01	A:1-175
1d	1qs8B01	B:1-175

(no "Pfam Domain" information available for 1QS8)

Asymmetric Unit(hide GO term definitions)

Chain A,B (O60989_PLAVI | O60989)

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:0016021	integral component of membrane	The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
	GO:0016020	membrane	A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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		Glu A:112 - Pro A:113	[ RasMol ]
		Glu B:112 - Pro B:113	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 1QS8)

Description

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Ligands, Modified Residues, Ions (3, 8)

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SS Bonds (4, 4)

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