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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMEPSIN IV FROM P. FALCIPARUM IN COMPLEX WITH PEPSTATIN A
 
Authors :  O. A. Asojo, S. V. Gulnik, E. Afonina, B. Yu, J. A. Ellman, T. S. Haque, A. M
Date :  16 May 02  (Deposition) - 12 Jun 02  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Biol. Unit 3:  A,B,C,D  (2x)
Biol. Unit 4:  A,B,C,D  (1x)
Keywords :  Eukaryotic Aspartic Proteinase, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  O. A. Asojo, S. V. Gulnik, E. Afonina, B. Yu, J. A. Ellman, T. S. Haque, A. M. Silva
Novel Uncomplexed And Complexed Structures Of Plasmepsin Ii An Aspartic Protease From Plasmodium Falciparum.
J. Mol. Biol. V. 327 173 2003
PubMed-ID: 12614616  |  Reference-DOI: 10.1016/S0022-2836(03)00036-6

(-) Compounds

Molecule 1 - PLASMEPSIN IV
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
 
Molecule 2 - PEPSTATIN
    Chains: C, D
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A C 
Biological Unit 2 (1x):  B D
Biological Unit 3 (2x): ABCD
Biological Unit 4 (1x): ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1IVA2Mod. Amino AcidISOVALERIC ACID
2STA4Mod. Amino AcidSTATINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1IVA1Mod. Amino AcidISOVALERIC ACID
2STA2Mod. Amino AcidSTATINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1IVA1Mod. Amino AcidISOVALERIC ACID
2STA2Mod. Amino AcidSTATINE
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1IVA4Mod. Amino AcidISOVALERIC ACID
2STA8Mod. Amino AcidSTATINE
Biological Unit 4 (2, 6)
No.NameCountTypeFull Name
1IVA2Mod. Amino AcidISOVALERIC ACID
2STA4Mod. Amino AcidSTATINE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:14 , MET A:15 , ASP A:34 , GLY A:36 , SER A:37 , SER A:76 , TYR A:77 , GLY A:78 , SER A:79 , ILE A:114 , ILE A:123 , TYR A:192 , ASP A:214 , GLY A:216 , THR A:217 , SER A:218 , ILE A:294BINDING SITE FOR CHAIN C OF PEPSTATIN
2AC2SOFTWAREASP A:109 , MET B:15 , ASP B:34 , GLY B:36 , SER B:76 , TYR B:77 , GLY B:78 , SER B:79 , ILE B:123 , TYR B:192 , ASP B:214 , GLY B:216 , THR B:217 , SER B:218 , TYR B:288 , LEU B:290BINDING SITE FOR CHAIN D OF PEPSTATIN

(-) SS Bonds  (4, 4)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Glu A:112 -Pro A:113
2Leu A:242 -Pro A:243
3Asp A:275 -Pro A:276
4Glu B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1LS5)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1LS5)

(-) Exons   (0, 0)

(no "Exon" information available for 1LS5)

(-) Sequences/Alignments

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:328
 aligned with Q8IM16_PLAF7 | Q8IM16 from UniProtKB/TrEMBL  Length:449

    Alignment length:328
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441        
         Q8IM16_PLAF7   122 SENDSIELDDVANLMFYGEGQIGTNKQPFMFIFDTGSANLWVPSVNCDSIGCSTKHLYDASASKSYEKDGTKVEISYGSGTVRGYFSKDVISLGDLSLPYKFIEVTDADDLEPIYSGSEFDGILGLGWKDLSIGSIDPVVVELKKQNKIDNALFTFYLPVHDKHVGYLTIGGIESDFYEGPLTYEKLNHDLYWQIDLDIHFGKYVMQKANAVVDSGTSTITAPTSFLNKFFRDMNVIKVPFLPLYVTTCDNDDLPTLEFHSRNNKYTLEPEFYMDPLSDIDPALCMLYILPVDIDDNTFILGDPFMRKYFTVFDYEKESVGFAVAKNL 449
               SCOP domains d1ls5a_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1ls5A01 A:1-175 Acid Proteases                                                                                                                                                 1ls5A02 A:176-328 Acid Proteases                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeee.....ee..eee....eee..........eeee...............hhhhh........eeeeee..eeeeeee..eeeee..eeeee..eeeeehhhhhhhhhhh....ee...hhhhh.....hhhhhhhhh.......eeee........eeeee...hhhhh...............eeeeeee.....eeeeeeee......eeehhhhhhhhhh....ee......eeee........eeee....eeeehhhhhh.........eee..eee.......eeehhhhhh.eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ls5 A   1 SENDSIELDDVANLMFYGEGQIGTNKQPFMFIFDTGSANLWVPSVNCDSIGCSTKHLYDASASKSYEKDGTKVEISYGSGTVRGYFSKDVISLGDLSLPYKFIEVTDADDLEPIYSGSEFDGILGLGWKDLSIGSIDPVVVELKKQNKIDNALFTFYLPVHDKHVGYLTIGGIESDFYEGPLTYEKLNHDLYWQIDLDIHFGKYVMQKANAVVDSGTSTITAPTSFLNKFFRDMNVIKVPFLPLYVTTCDNDDLPTLEFHSRNNKYTLEPEFYMDPLSDIDPALCMLYILPVDIDDNTFILGDPFMRKYFTVFDYEKESVGFAVAKNL 328
                                    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 Q8IM16_PLAF7 | Q8IM16 from UniProtKB/TrEMBL  Length:449

    Alignment length:328
                                   131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441        
         Q8IM16_PLAF7   122 SENDSIELDDVANLMFYGEGQIGTNKQPFMFIFDTGSANLWVPSVNCDSIGCSTKHLYDASASKSYEKDGTKVEISYGSGTVRGYFSKDVISLGDLSLPYKFIEVTDADDLEPIYSGSEFDGILGLGWKDLSIGSIDPVVVELKKQNKIDNALFTFYLPVHDKHVGYLTIGGIESDFYEGPLTYEKLNHDLYWQIDLDIHFGKYVMQKANAVVDSGTSTITAPTSFLNKFFRDMNVIKVPFLPLYVTTCDNDDLPTLEFHSRNNKYTLEPEFYMDPLSDIDPALCMLYILPVDIDDNTFILGDPFMRKYFTVFDYEKESVGFAVAKNL 449
               SCOP domains d1ls5b_ B: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                    SCOP domains
               CATH domains 1ls5B01 B:1-175 Acid Proteases                                                                                                                                                 1ls5B02 B:176-328 Acid Proteases                                                                                                                          CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeee...eeeeeeee....eeeeeeee................................eeeeeee..........eeeeeeeeee..eeeeeeeeee..hhhhhhhhhhh...eeee............hhhhhhhhh......eeeee........eeeee...hhhhh.................eeeee....eeeeeeeee......eeehhhhhhhhhh....ee......eeee.........eee....eee.hhhhh.ee.......eee..eee......eeeehhhhhh.eeeeee....eeeeee.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1ls5 B   1 SENDSIELDDVANLMFYGEGQIGTNKQPFMFIFDTGSANLWVPSVNCDSIGCSTKHLYDASASKSYEKDGTKVEISYGSGTVRGYFSKDVISLGDLSLPYKFIEVTDADDLEPIYSGSEFDGILGLGWKDLSIGSIDPVVVELKKQNKIDNALFTFYLPVHDKHVGYLTIGGIESDFYEGPLTYEKLNHDLYWQIDLDIHFGKYVMQKANAVVDSGTSTITAPTSFLNKFFRDMNVIKVPFLPLYVTTCDNDDLPTLEFHSRNNKYTLEPEFYMDPLSDIDPALCMLYILPVDIDDNTFILGDPFMRKYFTVFDYEKESVGFAVAKNL 328
                                    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
                 1ls5 C   1 xVVxAx   6
                            |  | |
                            1-IVA|
                               4-STA
                                 6-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
                 1ls5 D 349 xVVxAx 354
                            |  | |
                            |  | |
                          349-IVA|
                             352-STA
                               354-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 '|'

 Classification and Annotation

(-) SCOP Domains  (1, 2)

Asymmetric Unit
(-)
Class: All beta proteins (24004)

(-) CATH Domains  (1, 4)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1LS5)

(-) Gene Ontology  (9, 9)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (Q8IM16_PLAF7 | Q8IM16)
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:0042540    hemoglobin catabolic process    The chemical reactions and pathways resulting in the breakdown of hemoglobin, an oxygen carrying, conjugated protein containing four heme groups and globin; especially, the proteolytic cleavage of hemoglobin to yield free heme, peptides, and amino acids.
    GO:0030163    protein catabolic process    The chemical reactions and pathways resulting in the breakdown of a protein by the destruction of the native, active configuration, with or without the hydrolysis of peptide bonds.
    GO:0006508    proteolysis    The hydrolysis of proteins into smaller polypeptides and/or amino acids by cleavage of their peptide bonds.
cellular component
    GO:0020020    food vacuole    Vacuole within a parasite used for digestion of the host cell cytoplasm. An example of this component is found in the Apicomplexa.
    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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  1ls5
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 Related Entries

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(-) Related Entries Specified in the PDB File

1sme PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A