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(-) Description

Title :  STRUCTURE OF PLASMEPSIN II FROM PLASMODIUM FALCIPARUM COMPLEXED WITH INHIBITOR PG394
 
Authors :  R. Recacha, J. Leitans, K. Tars, K. Jaudzems
Date :  17 Feb 15  (Deposition) - 09 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Plasmepsin Ii, Malaria, Inhibitor, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Recacha, J. Leitans, I. Akopjana, L. Aprupe, P. Trapencieris, K. Jaudzems, A. Jirgensons, K. Tars
Structures Of Plasmepsin Ii From Plasmodium Falciparum In Complex With Two Hydroxyethylamine-Based Inhibitors.
Acta Crystallogr. , Sect. F V. 71 1531 2015
PubMed-ID: 26625296  |  Reference-DOI: 10.1107/S2053230X15022049
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLASMEPSIN-2
    Chains: A, B, C, D
    EC Number: 3.4.23.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Synonym: ASPARTIC HEMOGLOBINASE II,PFAPD

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
149W4Ligand/IonN'-[(2S,3S)-3-HYDROXY-1-PHENYL-4-{[2-(PYRIDIN-2-YL)PROPAN-2-YL]AMINO}BUTAN-2-YL]-N,N-DIPROPYL-5-(PYRIDIN-1(2H)-YL)BENZENE-1,3-DICARBOXAMIDE
2GOL3Ligand/IonGLYCEROL
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
149W1Ligand/IonN'-[(2S,3S)-3-HYDROXY-1-PHENYL-4-{[2-(PYRIDIN-2-YL)PROPAN-2-YL]AMINO}BUTAN-2-YL]-N,N-DIPROPYL-5-(PYRIDIN-1(2H)-YL)BENZENE-1,3-DICARBOXAMIDE
2GOL-1Ligand/IonGLYCEROL
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
149W1Ligand/IonN'-[(2S,3S)-3-HYDROXY-1-PHENYL-4-{[2-(PYRIDIN-2-YL)PROPAN-2-YL]AMINO}BUTAN-2-YL]-N,N-DIPROPYL-5-(PYRIDIN-1(2H)-YL)BENZENE-1,3-DICARBOXAMIDE
2GOL1Ligand/IonGLYCEROL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
149W1Ligand/IonN'-[(2S,3S)-3-HYDROXY-1-PHENYL-4-{[2-(PYRIDIN-2-YL)PROPAN-2-YL]AMINO}BUTAN-2-YL]-N,N-DIPROPYL-5-(PYRIDIN-1(2H)-YL)BENZENE-1,3-DICARBOXAMIDE
2GOL2Ligand/IonGLYCEROL
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
149W1Ligand/IonN'-[(2S,3S)-3-HYDROXY-1-PHENYL-4-{[2-(PYRIDIN-2-YL)PROPAN-2-YL]AMINO}BUTAN-2-YL]-N,N-DIPROPYL-5-(PYRIDIN-1(2H)-YL)BENZENE-1,3-DICARBOXAMIDE
2GOL-1Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:32 , ASP A:34 , GLY A:36 , TYR A:77 , VAL A:78 , SER A:79 , PHE A:111 , THR A:114 , ILE A:123 , ASP A:214 , GLY A:216 , THR A:217 , SER A:218 , ILE A:290 , LEU A:292 , ILE A:300binding site for residue 49W A 400
2AC2SOFTWAREMET B:15 , ILE B:32 , ASP B:34 , VAL B:78 , SER B:79 , PHE B:111 , ILE B:123 , TYR B:192 , ASP B:214 , GLY B:216 , THR B:217 , SER B:218 , LEU B:292 , ILE B:300binding site for residue 49W B 401
3AC3SOFTWAREILE C:32 , ASP C:34 , GLY C:36 , VAL C:78 , SER C:79 , PHE C:111 , THR C:114 , ILE C:123 , TYR C:192 , ASP C:214 , GLY C:216 , THR C:217 , SER C:218 , LEU C:292 , ILE C:300 , GOL C:403binding site for residue 49W C 401
4AC4SOFTWAREASP C:279 , THR D:48binding site for residue GOL C 402
5AC5SOFTWAREMET C:75 , ASN C:76 , ILE C:133 , 49W C:401binding site for residue GOL C 403
6AC6SOFTWAREMET D:15 , ILE D:32 , ASP D:34 , GLY D:36 , VAL D:78 , SER D:79 , PHE D:111 , THR D:114 , SER D:118 , ILE D:123 , TYR D:192 , ASP D:214 , GLY D:216 , THR D:217 , SER D:218 , ILE D:300binding site for residue 49W D 400

(-) 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  (8, 8)

Asymmetric Unit
No.Residues
1Glu A:112 -Pro A:113
2Gln A:232 -Asn A:233
3Glu B:112 -Pro B:113
4Gln B:232 -Asn B:233
5Glu C:112 -Pro C:113
6Gln C:232 -Asn C:233
7Glu D:112 -Pro D:113
8Gln D:232 -Asn D:233

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YA8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YA8)

(-) Exons   (0, 0)

(no "Exon" information available for 4YA8)

(-) 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:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeee....eeeeeeee......eee......hhhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeee.....hhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh......eeee.......eeeeeeee..eee..eeeee......eeehhhhhhhhhh.............eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ya8 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         


Chain B from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeee....eeeeeeee......eee......hhhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh......eeee.......eeeeeeee..eee..eeeee......eeehhhhhhhhhh.............eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ya8 B   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         


Chain C from PDB  Type:PROTEIN  Length:329
                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee...eeeeeeee....eeeeeeee......eee......hhhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh......eeee.......eeeeeeee..eee..eeeee......eeehhhhhhhhhh.............eee........eeee....eeeehhhhheeee......eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ya8 C   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         


Chain D from PDB  Type:PROTEIN  Length:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeee....eeeeeeee......eee......hhhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhhhh...eeeee.......eeeeeeee..eee..eeeee......eeehhhhhhhhhh.............eee........eeee....eeeehhhhheee.......eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ya8 D   2 SNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNISLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321
   Legend:   → Mismatch (orange background)
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  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 4YA8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YA8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YA8)

(-) Gene Ontology  (5, 5)

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  4ya8
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 Related Entries

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

(-) Related Entries Specified in the PDB File

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