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(-) Description

Title :  STRUCTURE OF PROPLASMEPSIN IV FROM PLASMODIUM FALCIPARUM
 
Authors :  R. Recacha, I. Akopjana, K. Tars, K. Jaudzems
Date :  02 May 16  (Deposition) - 17 Aug 16  (Release) - 28 Sep 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.53
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A (1x),B (1x)
Biol. Unit 2:  A (1x),B (1x)
Keywords :  Malaria, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. Recacha, K. Jaudzems, I. Akopjana, A. Jirgensons, K. Tars
Crystal Structure Of Plasmodium Falciparum Proplasmepsin Iv The Plasticity Of Proplasmepsins.
Acta Crystallogr. , Sect. F V. 72 659 2016
PubMed-ID: 27599854  |  Reference-DOI: 10.1107/S2053230X16011663
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PROPLASMEPSIN IV
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 75-449
    Gene: PFBG_05102
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 9)

Asymmetric Unit (1, 9)
No.NameCountTypeFull Name
1GOL9Ligand/IonGLYCEROL
Biological Unit 1 (1, 3)
No.NameCountTypeFull Name
1GOL3Ligand/IonGLYCEROL
Biological Unit 2 (1, 6)
No.NameCountTypeFull Name
1GOL6Ligand/IonGLYCEROL

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:264 , LYS A:265 , HOH A:538 , HOH A:587 , HOH A:599 , HOH A:718binding site for residue GOL A 401
2AC2SOFTWARELYS A:85P , ASP A:162 , HIS A:164 , VAL A:165 , HOH A:501 , HOH A:638 , SER B:95P , LEU B:98Pbinding site for residue GOL A 402
3AC3SOFTWAREPHE A:16 , ASP A:87P , GLU A:119 , HOH A:503 , HOH A:583 , LEU B:98P , LYS B:101P , HOH B:656binding site for residue GOL A 403
4AC4SOFTWARETHR A:81P , TYR A:167 , HOH A:512binding site for residue GOL A 404
5AC5SOFTWAREGLU A:179 , ALA A:325 , ASN A:327 , HOH A:732binding site for residue GOL A 405
6AC6SOFTWAREHIS A:79P , THR A:80P , ASP A:95 , LEU A:96 , LYS A:148 , ILE A:149 , ILE A:170 , HOH A:669binding site for residue GOL A 406
7AC7SOFTWAREGLU B:179 , ALA B:325 , LYS B:326 , ASN B:327 , HOH B:694 , HOH B:744binding site for residue GOL B 401
8AC8SOFTWAREVAL B:11 , HIS B:90P , SER B:218 , PRO B:243 , MET B:286 , LEU B:290 , HOH B:553binding site for residue GOL B 402
9AC9SOFTWAREPHE B:177binding site for residue GOL B 403

(-) 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  (3, 3)

Asymmetric Unit
No.Residues
1Glu A:112 -Pro A:113
2Gly B:121P-Tyr B:122P
3Glu B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5JOD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JOD)

(-) Exons   (0, 0)

(no "Exon" information available for 5JOD)

(-) 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:375
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhh...............hhhhhh.eeee...ee....ee..eeee.....eeee.....hhhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhh.........eeee............hhhhhhhhh......eeeee.......eeeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhh..ee......eeee........eeee....eeeehhhhheeee...eeeeeee.eee......eeeehhhhhhheeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jod A  78P KHTTIGFKIDRPHDKVLSSVLKNKLSTYVKESFKFFKSGYAQKGYLGSENDSIELDDVANLMFYGEGQIGTNKQPFMFIFDTGSANLWVPSVNCDSIGCSTKHLYDASASKSYEKDGTKVEISYGSGTVRGYFSKDVISLGDLSLPYKFIEVTDADDLEPIYSGSEFDGILGLGWKDLSIGSIDPVVVELKKQNKIDNALFTFYLPVHDKHVGYLTIGGIESDFYEGPLTYEKLNHDLYWQIDLDIHFGKYVMQKANAVVDSGTSTITAPTSFLNKFFRDMNVIKVPFLPLYVTTCDNDDLPTLEFHSRNNKYTLEPEFYMDPLSDIDPALCMLYILPVDIDDNTFILGDPFMRKYFTVFDYEKESVGFAVAKNL  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     
                            ||||||86P||||||95P|||||104P|||||113P|||||122P|||                                                                                                                                                                                                                                                                                                                                       
                          78P||||||87P||||||96P|||||105P|||||114P|||||123P||                                                                                                                                                                                                                                                                                                                                       
                           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                                                                                                                                                                                                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:375
                                                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeeeeehhhhhhhhhhhhh.hhhhhhhhhhhhhh...............hhhhhh..eeeeeeee....eeeeeeee.....eeee.....hhhhhhh...hhhhh...eeeeeeeeeee..eeeeeeeeeeeeee..eeeeeeeeeeeehhhhh.........eeee............hhhhhhhhh......eeeee.......eeeeee...hhh.eeeeeeeee.......eeeeeeee..eeeeeeeeee......eeehhhhhhhhhhhh..ee......eeee........eeee....eeeehhhhheeee...eeeeeee.eee......eeeehhhhhhheeeeee....eeeeeee... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5jod B  78P KHTTIGFKIDRPHDKVLSSVLKNKLSTYVKESFKFFKSGYAQKGYLGSENDSIELDDVANLMFYGEGQIGTNKQPFMFIFDTGSANLWVPSVNCDSIGCSTKHLYDASASKSYEKDGTKVEISYGSGTVRGYFSKDVISLGDLSLPYKFIEVTDADDLEPIYSGSEFDGILGLGWKDLSIGSIDPVVVELKKQNKIDNALFTFYLPVHDKHVGYLTIGGIESDFYEGPLTYEKLNHDLYWQIDLDIHFGKYVMQKANAVVDSGTSTITAPTSFLNKFFRDMNVIKVPFLPLYVTTCDNDDLPTLEFHSRNNKYTLEPEFYMDPLSDIDPALCMLYILPVDIDDNTFILGDPFMRKYFTVFDYEKESVGFAVAKNL  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||                                                                                                                                                                                                                                                                                                                                       
                           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
   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 5JOD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JOD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JOD)

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)

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  Cis Peptide Bonds
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4y7h OTHER EXPERIMENTAL DATA WAS ANALYZED AND USED FOR STRUCTURE SOLUTION AND REFINEMENT