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
(-)Biological Unit 3
(-)Biological Unit 4
(-)Biological Unit 5
(-)Biological Unit 6
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)
Image Biological Unit 4
Biological Unit 4  (Jmol Viewer)
Image Biological Unit 5
Biological Unit 5  (Jmol Viewer)
Image Biological Unit 6
Biological Unit 6  (Jmol Viewer)

(-) Description

Title :  PROPLASMEPSIN II FROM PLASMODIUM FALCIPARUM
 
Authors :  N. K. Bernstein, M. M. Cherney, H. Loetscher, R. G. Ridley, M. N. G. James
Date :  07 Jul 98  (Deposition) - 13 Jan 99  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  D  (1x)
Biol. Unit 4:  C  (1x)
Biol. Unit 5:  B,D  (1x)
Biol. Unit 6:  A,C  (1x)
Keywords :  Aspartic Proteinase Zymogen, Hemoglobinase, Malaria, Hydrolase, Aspartyl Protease, Glycoprotein, Aspartic Protease Zymogen (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. K. Bernstein, M. M. Cherney, H. Loetscher, R. G. Ridley, M. N. James
Crystal Structure Of The Novel Aspartic Proteinase Zymogen Proplasmepsin Ii From Plasmodium Falciparum.
Nat. Struct. Biol. V. 6 32 1999
PubMed-ID: 9886289  |  Reference-DOI: 10.1038/4905
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROPLASMEPSIN II
    Cell Line: BL21
    Chains: A, B, C, D
    EC Number: 3.4.23.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBLUESCRIPT KS+
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 562
    Mutation: YES
    Organelle: DIGESTIVE VACUOLE
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):    D
Biological Unit 4 (1x):   C 
Biological Unit 5 (1x):  B D
Biological Unit 6 (1x): A C 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 4 (1, 2)
No.NameCountTypeFull Name
1GOL2Ligand/IonGLYCEROL
Biological Unit 5 (1, 1)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
Biological Unit 6 (1, 5)
No.NameCountTypeFull Name
1GOL5Ligand/IonGLYCEROL

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:192 , GLN A:194 , ILE A:212 , GOL A:331 , HOH A:391 , HOH A:493BINDING SITE FOR RESIDUE GOL A 330
2AC2SOFTWARELEU A:8 , ASP A:214 , PHE A:294 , ILE A:300 , GOL A:330 , HOH A:570BINDING SITE FOR RESIDUE GOL A 331
3AC3SOFTWARETHR A:81P , PHE A:167 , ARG A:176 , PHE A:177 , LEU A:329BINDING SITE FOR RESIDUE GOL A 332
4AC4SOFTWAREGLU C:78P , GLU C:150BINDING SITE FOR RESIDUE GOL C 330
5AC5SOFTWAREPHE C:167 , ARG C:176 , LEU C:329 , HOH C:468BINDING SITE FOR RESIDUE GOL C 331
6AC6SOFTWAREGLU D:207 , LYS D:208 , ALA D:209 , ASN D:210 , PRO D:297BINDING SITE FOR RESIDUE GOL D 330
7ASPUNKNOWNASP A:214CATALYTIC RESIDUES IN THE MATURE ENZYME.

(-) SS Bonds  (8, 8)

Asymmetric Unit
No.Residues
1A:47 -A:52
2A:249 -A:285
3B:47 -B:52
4B:249 -B:285
5C:47 -C:52
6C:249 -C:285
7D:47 -D:52
8D:249 -D:285

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1PFZ)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (2, 12)

Asymmetric Unit (2, 12)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
 
 		  4A:16-323
B:16-323
C:16-323
D:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
 
 
335-346
 
 
 		  8A:31-42
B:31-42
C:31-42
D:31-42
A:211-222
B:211-222
C:211-222
D: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
-
-
Biological Unit 3 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
 
 		  1-
-
-
D:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
 
 
335-346
 
 
 		  2-
-
-
D:31-42
-
-
-
D:211-222
Biological Unit 4 (2, 3)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
 
 		  1-
-
C:16-323
-
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
 
 
335-346
 
 
 		  2-
-
C:31-42
-
-
-
C:211-222
-
Biological Unit 5 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
 
 		  2-
B:16-323
-
D:16-323
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
 
 
335-346
 
 
 		  4-
B:31-42
-
D:31-42
-
B:211-222
-
D:211-222
Biological Unit 6 (2, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PEPTIDASE_A1PS51767 Peptidase family A1 domain profile.PLM2_PLAFA140-447
 
 
 		  2A:16-323
-
C:16-323
-
2ASP_PROTEASEPS00141 Eukaryotic and viral aspartyl proteases active site.PLM2_PLAFA155-166
 
 
 
335-346
 
 
 		  4A:31-42
-
C:31-42
-
A:211-222
-
C:211-222
-

(-) Exons   (0, 0)

(no "Exon" information available for 1PFZ)

(-) 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:370
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:375
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448     
          PLM2_PLAFA     79 HLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL  453
               SCOP domains d1pfza_ A: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains 1pfzA02 A:79P-14,A:176-328 Acid Proteases                   1pfzA01 A:15-175 Acid Proteases                                                                                                                                  1pfzA02 A:79P-14,A:176-328 Acid Proteases                                                                                                                - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee.hhhhhhhhhhh...hhhhhhhhhhh..................hhhh..eee..............eeee......eee........hhh.....hhh.............-----..eeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhh....eeee.............hhhhhhh.......eeeee.......eeeeee....hhh.....eeee.......eeeeeeee..eee..eeeee......eee.hhhhhhh.....eee......eeee........eeee....eeee.hhhheee.......eeee.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
                1pfz A  79P HLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEM-----TVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL  329
                            |||||||88P|||||||98P||||||108P||||||118P|||||||  4        14        24        34        44        54        64        74|     | 84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
                            ||||||87P||||||96P|||||105P|||||114P|||||123P||                                                                        75    81                                                                                                                                                                                                                                                        
                          79P||||||88P||||||97P|||||106P|||||115P|||||124P|                                                                                                                                                                                                                                                                                                                                        
                           80P||||||89P||||||98P|||||107P|||||116P||||||  1                                                                                                                                                                                                                                                                                                                                        
                            81P||||| 90P||||| 99P|||||108P|||||117P|||||                                                                                                                                                                                                                                                                                                                                           
                             82P||||  91P|||| 100P|||| 109P|||| 118P||||                                                                                                                                                                                                                                                                                                                                           
                              83P|||   92P|||  101P|||  110P|||  119P|||                                                                                                                                                                                                                                                                                                                                           
                               84P||    93P||   102P||   111P||   120P||                                                                                                                                                                                                                                                                                                                                           
                                85P|     94P|    103P|    112P|    121P|                                                                                                                                                                                                                                                                                                                                           
                                 86P      95P     104P     113P     122P                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:369
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:375
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447     
          PLM2_PLAFA     78 EHLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKN  452
               SCOP domains d1pfzb_ B: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -------------------------------------------------------------1pfzB01 B:15-175 Acid Proteases                                                                                                                                  1pfzB02 B:176-327 Acid Proteases                                                                                                                        - CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhh...hhhhhhhhhhh..................hhhh..eeee..eee....eee.eeee......eee........hhh.....hhh.............------.eeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhh....eeee.............hhhhhhh.......eeeee.......eeeeee....hhh.....eeee.......eeeeeeee..eee..eeeee......eee.hhhhhhhh....eee......eeee........eeee....eeee.hhhheee.......eeee.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
                1pfz B  78P EHLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEM------VSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKN  328
                            |||||||87P|||||||97P||||||107P||||||117P|||||||| 3        13        23        33        43        53        63        73 |      83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323     
                          78P||||||87P||||||96P|||||105P|||||114P|||||123P||                                                                        75     82                                                                                                                                                                                                                                                      
                           79P||||||88P||||||97P|||||106P|||||115P|||||124P|                                                                                                                                                                                                                                                                                                                                       
                            80P||||||89P||||||98P|||||107P|||||116P||||||  1                                                                                                                                                                                                                                                                                                                                       
                             81P||||| 90P||||| 99P|||||108P|||||117P|||||                                                                                                                                                                                                                                                                                                                                          
                              82P||||  91P|||| 100P|||| 109P|||| 118P||||                                                                                                                                                                                                                                                                                                                                          
                               83P|||   92P|||  101P|||  110P|||  119P|||                                                                                                                                                                                                                                                                                                                                          
                                84P||    93P||   102P||   111P||   120P||                                                                                                                                                                                                                                                                                                                                          
                                 85P|     94P|    103P|    112P|    121P|                                                                                                                                                                                                                                                                                                                                          
                                  86P      95P     104P     113P     122P                                                                                                                                                                                                                                                                                                                                          


Chain C from PDB  Type:PROTEIN  Length:356
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:376
                                    87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437       447      
          PLM2_PLAFA     78 EHLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL  453
               SCOP domains d1pfzc_ C: Plasmepsin (a hemoglobin-degra              ding enzyme)                                                                                                                                                                                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------1pfzC01 C:15-175 Acid Proteases                                                                                                                                  1pfzC02 C:176-327 Acid Proteases                                                                                                                        -- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee.hhhhhhhhhhh...hhhhhhhhhhhhh...--------------.....eeee.............eeee......eee........hhh.....hhh.............------.eeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhh....eeee.............hhhhhhh.......eeeee.......eeeeee....hhh.....eeee.......eeeeeeee..eee..eeeee......eee.hhhhhhhh....eee......eeee........eeee....eeee.hhhheee.......eeee.eee......eeee.hhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------------------------------------------------PEPTIDASE_A1  PDB: C:16-323 UniProt: 140-447                                                                                                                                                                                                                                                                        ------ PROSITE (1)
                PROSITE (2) -----------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pfz C  78P EHLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLT--------------VDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEM------VSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL  329
                            |||||||87P|||||||97P||||||107P||||||117P|        -     |  13        23        33        43        53        63        73 |      83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323      
                          78P||||||87P||||||96P|||||105P|||||114P||||              9                                                                75     82                                                                                                                                                                                                                                                       
                           79P||||||88P||||||97P|||||106P|||||115P|||                                                                                                                                                                                                                                                                                                                                               
                            80P||||||89P||||||98P|||||107P|||||116P||                                                                                                                                                                                                                                                                                                                                               
                             81P||||| 90P||||| 99P|||||108P|||||117P|                                                                                                                                                                                                                                                                                                                                               
                              82P||||  91P|||| 100P|||| 109P|||| 118P                                                                                                                                                                                                                                                                                                                                               
                               83P|||   92P|||  101P|||  110P|||                                                                                                                                                                                                                                                                                                                                                    
                                84P||    93P||   102P||   111P||                                                                                                                                                                                                                                                                                                                                                    
                                 85P|     94P|    103P|    112P|                                                                                                                                                                                                                                                                                                                                                    
                                  86P      95P     104P     113P                                                                                                                                                                                                                                                                                                                                                    


Chain D from PDB  Type:PROTEIN  Length:369
 aligned with PLM2_PLAFA | P46925 from UniProtKB/Swiss-Prot  Length:453

    Alignment length:375
                                    88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438       448     
          PLM2_PLAFA     79 HLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL  453
               SCOP domains d1pfzd_ D: Plasmepsin (a hemoglobin-degrading enzyme)                                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ------------------------------------------------------------1pfzD01 D:15-175 Acid Proteases                                                                                                                                  1pfzD02 D:176-328 Acid Proteases                                                                                                                         - CATH domains
           Pfam domains (1) ------------------------------------------------------------Asp-1pfzD01 D:15-325                                         ------                                                                                                                                                                                                                                                    ---- Pfam domains (1)
           Pfam domains (2) ------------------------------------------------------------Asp-1pfzD02 D:15-325                                         ------                                                                                                                                                                                                                                                    ---- Pfam domains (2)
           Pfam domains (3) ------------------------------------------------------------Asp-1pfzD03 D:15-325                                         ------                                                                                                                                                                                                                                                    ---- Pfam domains (3)
           Pfam domains (4) ------------------------------------------------------------Asp-1pfzD04 D:15-325                                         ------                                                                                                                                                                                                                                                    ---- Pfam domains (4)
         Sec.struct. author .eeeeeeee.hhhhhhhhhhh...hhhhhhhhhhhh.................hhhh..eee...eee....eee.eeee......eee........hhh.....hhh.............------.eeeeeeeeeee..eeeeeeeeeeee.hhhhhhhhh....eeee.............hhhhhhh.......eeeee.......eeeeee....hhh.....eeee.......eeeeeeee..eee..eeeee......eee.hhhhhhh.....eee......eeee........eeee....eeee.hhhheee.......eeee.eee......eeee.hhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------------------------------------------------PEPTIDASE_A1  PDB: D:16-323 UniProt: 140-447                                                                                                                                                                                                                                                                        ------ PROSITE (1)
                PROSITE (2) ----------------------------------------------------------------------------ASP_PROTEASE------------------------------------------------------------------------------------------------------------------------------------------------------------------------ASP_PROTEASE----------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                1pfz D  79P HLTIGFKVENAHDRILKTIKTHKLKNYIKESVNFLNSGLTKTNYLGSSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEM------VSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL  329
                            |||||||88P|||||||98P||||||108P||||||118P|||||||  4        14        24        34        44        54        64        74|      |84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324     
                          79P||||||88P||||||97P|||||106P|||||115P|||||124P|                                                                        75     82                                                                                                                                                                                                                                                       
                           80P||||||89P||||||98P|||||107P|||||116P||||||| 1                                                                                                                                                                                                                                                                                                                                        
                            81P||||||90P||||||99P|||||108P|||||117P||||||                                                                                                                                                                                                                                                                                                                                          
                             82P||||| 91P|||||100P|||||109P|||||118P|||||                                                                                                                                                                                                                                                                                                                                          
                              83P||||  92P|||| 101P|||| 110P|||| 119P||||                                                                                                                                                                                                                                                                                                                                          
                               84P|||   93P|||  102P|||  111P|||  120P|||                                                                                                                                                                                                                                                                                                                                          
                                85P||    94P||   103P||   112P||   121P||                                                                                                                                                                                                                                                                                                                                          
                                 86P|     95P|    104P|    113P|    122P|                                                                                                                                                                                                                                                                                                                                          
                                  87P      96P     105P     114P     123P
   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, 4)

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

(-) CATH Domains  (1, 8)

Asymmetric Unit
(-)
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)
1a1pfzB02B:176-327
1b1pfzB01B:15-175
1c1pfzC01C:15-175
1d1pfzD01D:15-175
1e1pfzA01A:15-175
1f1pfzA02A:79P-14,A:176-328
1g1pfzC02C:176-327
1h1pfzD02D:176-328

(-) Pfam Domains  (1, 4)

Asymmetric Unit
(-)
Clan: Peptidase_AA (368)
(-)
Family: Asp (155)
(-)
Plasmodium falciparum (15)
1aAsp-1pfzD01D:15-325
1bAsp-1pfzD02D:15-325
1cAsp-1pfzD03D:15-325
1dAsp-1pfzD04D:15-325

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (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
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    ASP  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1pfz)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]
    Biological Unit 4  [ Jena3D ]
    Biological Unit 5  [ Jena3D ]
    Biological Unit 6  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - sites PNG format | Biol. Unit 2 PNG format | Biol. Unit 3 PNG format | Biol. Unit 4 PNG format | Biol. Unit 5 PNG format | Biol. Unit 6 PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1pfz
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  PLM2_PLAFA | P46925
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  3.4.23.39
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  PLM2_PLAFA | P46925
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        PLM2_PLAFA | P46925: 1j8j 1lee 1lf2 1lf3 1lf4 1m43 1me6 1sme 1w6h 1w6i 1xdh 1xe5 1xe6 2bju 2bl3 2igx 2igy 2r9b 3f9q 4cku 4y6m 4ya8 4z22 5bwy

(-) Related Entries Specified in the PDB File

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