Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  NOVEL PLASMEPSIN II-INHIBITOR COMPLEX
 
Authors :  J. Lindberg, P. -O. Johansson, A. Rosenquist, I. Kvarnstroem, L. Vrang, B. Samuelsson, T. Unge
Date :  18 Aug 04  (Deposition) - 05 Jul 06  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Malaria, Drug, Aspartic Protease, Plasmepsin, Hydrolase, Glycoprotein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lindberg, P. -O. Johansson, A. Rosenquist, I. Kvarnstroem, L. Vrang, B. Samuelsson, T. Unge
Structural Study Of A Novel Inhibitor With Bulky P1 Side Chain In Complex With Plasmepsin Ii - Implications For Drug Design
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PLASMEPSIN 2
    ChainsA, B
    EC Number3.4.23.39
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    Organism ScientificPLASMODIUM FALCIPARUM
    Organism Taxid5833
    SynonymASPARTIC PROTEASE, ASPARTIC HEMOGLOBINASE II, PFAPD

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1TIT2Ligand/IonN-((3S,4S)-5-[(4-BROMOBENZYL)OXY]-3-HYDROXY-4-{[N-(PYRIDIN-2-YLCARBONYL)-L-VALYL]AMINO}PENTANOYL)-L-ALANYL-L-LEUCINAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1TIT1Ligand/IonN-((3S,4S)-5-[(4-BROMOBENZYL)OXY]-3-HYDROXY-4-{[N-(PYRIDIN-2-YLCARBONYL)-L-VALYL]AMINO}PENTANOYL)-L-ALANYL-L-LEUCINAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1TIT1Ligand/IonN-((3S,4S)-5-[(4-BROMOBENZYL)OXY]-3-HYDROXY-4-{[N-(PYRIDIN-2-YLCARBONYL)-L-VALYL]AMINO}PENTANOYL)-L-ALANYL-L-LEUCINAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:32 , ASP A:34 , GLY A:36 , SER A:37 , ASN A:76 , TYR A:77 , VAL A:78 , SER A:79 , PHE A:111 , THR A:114 , PHE A:120 , TYR A:192 , ASP A:214 , GLY A:216 , THR A:217 , SER A:218BINDING SITE FOR RESIDUE TIT A1330
2AC2SOFTWAREASP B:34 , GLY B:36 , SER B:37 , ASN B:76 , TYR B:77 , VAL B:78 , SER B:79 , PHE B:111 , THR B:114 , TYR B:192 , ASP B:214 , GLY B:216 , THR B:217 , SER B:218BINDING SITE FOR RESIDUE TIT B1330

(-) 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  (2, 2)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1W6H)

(-) PROSITE Motifs  (2, 6)

Asymmetric Unit (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
  2A:16-323
B:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
335-346
 
  4A:31-42
B:31-42
A:211-222
B:211-222
Biological Unit 1 (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
-
Biological Unit 2 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
  1-
B:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
335-346
 
  2-
B:31-42
-
B:211-222

(-) Exons   (0, 0)

(no "Exon" information available for 1W6H)

(-) 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:325
 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 d1w6ha_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1w6hA01 A:1-175 Acid Proteases                                                                                                                                                 1w6hA02 A:176-329 Acid Proteases                                                                                                                           CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...hhhhh........eeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh...........................hhh..............................................hhhhhhhhhh....ee.----.eeee....................hhhhheee.......eeee..............hhhhhhh..................... 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
                 1w6h A   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKV----FYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        |-   |   250       260       270       280       290       300       310       320         
                                                                                                                                                                                                                                                                        239  244                                                                                     

Chain B from PDB  Type:PROTEIN  Length:325
 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 d1w6hb_ B: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains 1w6hB01 B:1-175 Acid Proteases                                                                                                                                                 1w6hB02 B:176-329 Acid Proteases                                                                                                                           CATH domains
           Pfam domains (1) --------------Asp-1w6hB01 B:15-325                                                                                                                                                                                                                                                                                                   ---- Pfam domains (1)
           Pfam domains (2) --------------Asp-1w6hB02 B:15-325                                                                                                                                                                                                                                                                                                   ---- Pfam domains (2)
         Sec.struct. author ..............eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...hhhhh........eeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh...........................hhh.................eeeeeee....eeeeeeeee......eeehhhhhhhhhh...ee..----..eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhh..................... 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
                 1w6h B   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKV----FYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230        |-   |   250       260       270       280       290       300       310       320         
                                                                                                                                                                                                                                                                        239  244                                                                                     

   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

(-) CATH Domains  (1, 4)

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

(-) Pfam Domains  (1, 2)

Asymmetric Unit
(-)
Family: Asp (155)
1aAsp-1w6hB01B:15-325
1bAsp-1w6hB02B:15-325

(-) Gene Ontology  (5, 5)

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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    TIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Glu A:112 - Pro A:113   [ RasMol ]  
    Glu B:112 - Pro B:113   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1w6h
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLM2_PLAFA | P46925
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.23.39
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  PLM2_PLAFA | P46925
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLM2_PLAFA | P469251j8j 1lee 1lf2 1lf3 1lf4 1m43 1me6 1pfz 1sme 1w6i 1xdh 1xe5 1xe6 2bju 2bl3 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
1w6i PLASMEPSIN II-PEPSTATIN A COMPLEX
1xdh STRUCTURE OF PLASMEPSIN II IN COMPLEX WITH PEPSTATIN A
1xe5 STRUCTURE OF PLASMEPSIN II IN COMPLEX OF AN PEPSTATINANALOGUE
1xe6 STRUCTURE OF PLASMEPSIN II IN COMPLEX OF AN PEPSTATINANALOGUE
2bju PLASMEPSIN II COMPLEXED WITH A HIGHLY ACTIVE ACHIRAL INHIBITOR
2bl3 THEORITICAL INTERACTION MODEL OF PLASMEPSIN II FROM PLASMODIUM FALCIPARUM WITH A LIGAND FROM AN ECODED STATIN COMBINATORIAL LIBRARY