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(-) Description

Title :  THEORETICAL INTERACTION MODEL OF PLASMEPSIN II FROM PLASMODIUM FALCIPARUM WITH A LIGAND FROM AN ECODED STATIN COMBINATORIAL LIBRARY
 
Authors :  S. Mahanta, S. Hazarika
Date :  22 Feb 05  (Deposition) - 03 Mar 05  (Release) - 03 Mar 05  (Revision)
Method :  THEORETICAL MODEL
Resolution :  NOT APPLICABLE
Chains :  Theor. Model :  A
Keywords :  Aspartyl Protease, Direct Protein Sequencing, Glycoprotein, Hydrolase, Signal, Zymogen, Statin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Mahanta, S. Hazarika
Interaction Model Of Plasmepsin Ii With A Molecule From Statin Combinatorial Library
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMEPSIN II
    Chains: A
    EC Number: 3.4.23.39
    Engineered: YES
    Other Details: THE SUBMITTED FILE IS A COMPLEX OF PLASMEPSIN II FROM PLASMODIUM FALCIPARUM WITH A LIGAND FROM AN ENCODED COMBINATORIAL LIBRARY OF STATIN
    Synonym: ASPARTIC HEMOGLOBINASE II, PFAPD
    Synthetic: YES

 Structural Features

(-) Chains, Units

  
Theoretical Model : 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Theoretical Model (1, 1)
No.NameCountTypeFull Name
1OPQ1Ligand/Ion((3S,4S)-4-((2S,3S)-2-(2-(NAPTHALEN-6-YL)ACETAMIDO)-3-METHYLPENTANAMIDO)-N-BUTYL-3-HYDROXY-6-METHYLHEPTANAMIDE)

(-) Sites  (0, 0)

(no "Site" information available for 2BL3)

(-) SS Bonds  (2, 2)

Theoretical Model
No.Residues
1A:47 -A:52
2A:249 -A:285

(-) Cis Peptide Bonds  (1, 1)

Theoretical Model
No.Residues
1Glu A:112 -Pro A:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2BL3)

(-) PROSITE Motifs  (2, 3)

Theoretical Model (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447  1A:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
335-346		  2A:31-42
A:211-222

(-) Exons   (0, 0)

(no "Exon" information available for 2BL3)

(-) Sequences/Alignments

Theoretical Model
   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 ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee....eeeeeeee.....eeee......hhhhhh...hhhhh...eeeeeeeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhh.hhhhh...eeee..hhhhh.....hhhhhhhhh...........................hhh.................eeeeeeee..eeeeeeeeee......eeehhhhhhhhhh...eee......eeee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhh..................... 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
                 2bl3 A   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNISLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 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
   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  (0, 0)

(no "SCOP Domain" information available for 2BL3)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2BL3)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2BL3)

(-) Gene Ontology  (5, 5)

Theoretical Model(hide GO term definitions)
Chain A   (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.

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  Cis Peptide Bonds
    Glu A:112 - Pro A:113   [ RasMol ]  
 

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  PLM2_PLAFA | P46925
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 Related Entries

(-) Entries Sharing at Least One Protein Chain (UniProt ID)

UniProtKB/Swiss-Prot
        PLM2_PLAFA | P46925: 1j8j 1lee 1lf2 1lf3 1lf4 1m43 1me6 1pfz 1sme 1w6h 1w6i 1xdh 1xe5 1xe6 2bju 2igx 2igy 2r9b 3f9q 4cku 4y6m 4ya8 4z22 5bwy

(-) Related Entries Specified in the PDB File

1j8j A NEW CLASS OF SMALL NON-PEPTIDYL COMPOUNDS BLOCKSPLASMODIUM FALCIPARUM DEVELOPMENT IN VITRO BY INHIBITINGPLASMEPSINS
1lee CRYSTAL STRUCTURE OF PLASMEPSIN FROM P. FALCIPARUM INCOMPLEX WITH INHIBITOR RS367
1lf2 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM INCOMPLEX WITH INHIBITOR RS370
1lf3 CRYSTAL STRUCTURE OF PLASMEPSIN II FROM P FALCIPARUM INCOMPLEX WITH INHIBITOR EH58
1lf4 STRUCTURE OF PLASMEPSIN II
1m43 CRYSTAL STRUCTURE OF PMII IN COMPLEX WITH PEPSTATIN A TO2.4 A
1me6 CRYSTAL STRUCTURE OF PLASMEPSIN II, AN ASPARTYL PROTEASEFROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH A STATINE-BASED INHIBITOR
1pfz PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM
1sme PLASMEPSIN II, A HEMOGLOBIN-DEGRADING ENZYME FROM PLASMODIUM FALCIPARUM, IN COMPLEX WITH PEPSTATIN A
1w6h NOVEL PLASMEPSIN II-INHIBITOR COMPLEX
1w6i PLASMEPSIN II-PEPSTATIN A COMPLEX
2bju PLASMEPSIN II COMPLEXED WITH A HIGHLY ACTIVE ACHIRAL INHIBITOR