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(-) Description

Title :  STRUCTURE OF PLASMEPSIN II FROM PLASMODIUM FALCIPARUM COMPLEXED WITH INHIBITOR PG418
 
Authors :  R. Recacha, I. Akopjana, K. Tars, K. Jaudzems
Date :  13 Feb 15  (Deposition) - 09 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.27
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Plasmepsin Ii Hydroxyethylamine-Basd 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
    EC Number: 3.4.23.39
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 125-453
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833
    Synonym: ASPARTIC HEMOGLOBINASE II,PFAPD

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (1x): A  
Biological Unit 2 (1x):  B 
Biological Unit 3 (1x):   C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 9)

Asymmetric Unit (2, 9)
No.NameCountTypeFull Name
148Q3Ligand/Ion~{N}1-[(~{Z},3~{R})-4-[2-(3-METHOXYPHENYL)PROPAN-2-YLAMINO]-3-OXIDANYL-1-PHENYL-BUT-1-EN-2-YL]-5-PIPERIDIN-1-YL-~{N}3,~{N}3-DIPROPYL-BENZENE-1,3-DICARBOXAMIDE
2GOL6Ligand/IonGLYCEROL
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
148Q1Ligand/Ion~{N}1-[(~{Z},3~{R})-4-[2-(3-METHOXYPHENYL)PROPAN-2-YLAMINO]-3-OXIDANYL-1-PHENYL-BUT-1-EN-2-YL]-5-PIPERIDIN-1-YL-~{N}3,~{N}3-DIPROPYL-BENZENE-1,3-DICARBOXAMIDE
2GOL2Ligand/IonGLYCEROL
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
148Q1Ligand/Ion~{N}1-[(~{Z},3~{R})-4-[2-(3-METHOXYPHENYL)PROPAN-2-YLAMINO]-3-OXIDANYL-1-PHENYL-BUT-1-EN-2-YL]-5-PIPERIDIN-1-YL-~{N}3,~{N}3-DIPROPYL-BENZENE-1,3-DICARBOXAMIDE
2GOL2Ligand/IonGLYCEROL
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
148Q1Ligand/Ion~{N}1-[(~{Z},3~{R})-4-[2-(3-METHOXYPHENYL)PROPAN-2-YLAMINO]-3-OXIDANYL-1-PHENYL-BUT-1-EN-2-YL]-5-PIPERIDIN-1-YL-~{N}3,~{N}3-DIPROPYL-BENZENE-1,3-DICARBOXAMIDE
2GOL2Ligand/IonGLYCEROL

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:32 , ASP A:34 , GLY A:36 , SER A:37 , VAL A:78 , PHE A:111 , THR A:114 , SER A:118 , ILE A:123 , TYR A:192 , ASP A:214 , GLY A:216 , THR A:217 , SER A:218 , THR A:221 , ILE A:290 , LEU A:292 , ILE A:300 , HOH A:656 , HOH A:675 , ASP C:279 , GLY C:281binding site for residue 48Q A 501
2AC2SOFTWAREGOL C:502binding site for residue GOL A 502
3AC3SOFTWAREASN A:95 , LEU A:96 , SER A:97 , HOH A:644 , HOH A:695binding site for residue GOL A 503
4AC4SOFTWAREGLY A:281 , PRO A:282 , ILE B:32 , ASP B:34 , GLY B:36 , VAL B:78 , SER B:79 , PHE B:111 , ILE B:123 , ASP B:214 , GLY B:216 , THR B:217 , SER B:218 , LEU B:292 , ILE B:300 , VAL C:78binding site for residue 48Q B 501
5AC5SOFTWARETYR B:192 , ILE B:212 , PHE B:294 , VAL B:296 , THR B:298 , HOH B:650binding site for residue GOL B 502
6AC6SOFTWAREPRO B:295 , MET C:15 , ILE C:32 , ASP C:34 , GLY C:36 , SER C:37 , THR C:114 , TYR C:192 , ASP C:214 , GLY C:216 , THR C:217 , SER C:218 , ILE C:300binding site for residue 48Q C 501
7AC7SOFTWAREVAL A:239 , GOL A:502binding site for residue GOL C 502
8AC8SOFTWAREPRO C:243 , TYR C:245 , ILE C:289 , GLY C:291binding site for residue GOL C 503

(-) SS Bonds  (6, 6)

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

(-) Cis Peptide Bonds  (4, 5)

Asymmetric Unit
No.Residues
1Glu A:112 -Pro A:113
2Glu B:112 -Pro B:113
3Gly B:202 -Asn B:203
4Glu C:112 -Pro C:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4Y6M)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4Y6M)

(-) Exons   (0, 0)

(no "Exon" information available for 4Y6M)

(-) 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.......hhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh......eeee.......eeeeeeee..eee..eeeee......eeehhhhhhhhh....eee......eeee........eeee....eeeehhhhheeeee.....eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6m A   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 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:328
                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeee...eeeeeeee....eeeeeeee......eee.......hhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh......eeee.......eeeeeee........eeeee......eeehhhhhhhhhh...eee......eeee........eeee....eeeehhhhheeeee.....eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6m B   2 SNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 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        


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.......hhhhh...hhhhh........eeeee....eeeeeeeeeeeee..eeeeeeeeeeeehhhhhhhhhhh...eeee..hhhhh.....hhhhhhhhh......eeeee........eeeee...hhh......eeee.......eeeeeeee..eee..eeeee......eeehhhhhhhhh..............eee........eeee....eeeehhhhheeeee.....eeee.eee......eeeehhhhhhheeeeee....eeeeee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4y6m C   1 SSNDNIELVDFQNIMFYGDAEVGDNQQPFTFILDTGSANLWVPSVKCTTAGCLTKHLYDSSKSRTYEKDGTKVEMNYVSGTVSGFFSKDLVTVGNLSLPYKFIEVIDTNGFEPTYTASTFDGILGLGWKDLSIGSVDPIVVELKNQNKIENALFTFYLPVHDKHTGFLTIGGIEERFYEGPLTYEKLNHDLYWQITLDAHVGNIMLEKANCIVDSGTSAITVPTDFLNKMLQNLDVIKVPFLPFYVTLCNNSKLPTFEFTSENGKYTLEPEYYLQHIEDVGPGLCMLNIIGLDFPVPTFILGDPFMRKYFTVFDYDNHSVGIALAKKNL 329
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  x → Chemical Group (purple background, 'x', labelled with number + name, e.g. ACE or NH2)
  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4Y6M)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4Y6M)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4Y6M)

(-) Gene Ontology  (5, 5)

Asymmetric Unit(hide GO term definitions)

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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 4ya8 4z22 5bwy

(-) Related Entries Specified in the PDB File

4cku