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(-) Description

Title :  CRYSTALS OF PEPTIDE DEFORMYLASE FROM PLASMODIUM FALCIPARUM WITH TEN SUBUNITS PER ASYMMETRIC UNIT REVEAL CRITICAL CHARACTERISTICS OF THE ACTIVE SITE FOR DRUG DESIGN
 
Authors :  A. Kumar, K. T. Nguyen, S. Srivathsan, B. Ornstein, S. Turley, I. Hirsh, D. Pei, W. G. J. Hol
Date :  12 Sep 01  (Deposition) - 13 Mar 02  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H,I,J
Keywords :  Pdf, Malaria, Plasmodium, Deformylation, Metalloenzyme, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Kumar, K. T. Nguyen, S. Srivathsan, B. Ornstein, S. Turley, I. Hirsh, D. Pei, W. G. Hol
Crystals Of Peptide Deformylase From Plasmodium Falciparum Reveal Critical Characteristics Of The Active Site For Drug Design.
Structure V. 10 357 2002
PubMed-ID: 12005434  |  Reference-DOI: 10.1016/S0969-2126(02)00719-0
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B, C, D, E, F, G, H, I, J
    EC Number: 3.5.1.31
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET29B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PDF
    Organism Common: MALARIA PARASITE P. FALCIPARUM
    Organism Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 5833

 Structural Features

(-) Chains, Units

  12345678910
Asymmetric/Biological Unit : ABCDEFGHIJ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 40)

Asymmetric/Biological Unit (2, 40)
No.NameCountTypeFull Name
1CO10Ligand/IonCOBALT (II) ION
2MSE30Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLN A:111 , CYS A:155 , HIS A:196 , HIS A:200 , HOH A:9319BINDING SITE FOR RESIDUE CO A 300
02AC2SOFTWAREGLN B:111 , CYS B:155 , HIS B:196 , HIS B:200 , HOH B:9320BINDING SITE FOR RESIDUE CO B 1300
03AC3SOFTWAREGLN C:111 , CYS C:155 , HIS C:196 , HIS C:200 , HOH C:9321BINDING SITE FOR RESIDUE CO C 2300
04AC4SOFTWAREGLN D:111 , CYS D:155 , HIS D:196 , HIS D:200 , HOH D:9322BINDING SITE FOR RESIDUE CO D 3300
05AC5SOFTWAREGLN E:111 , CYS E:155 , HIS E:196 , HIS E:200 , HOH E:9323BINDING SITE FOR RESIDUE CO E 4300
06AC6SOFTWAREGLN F:111 , CYS F:155 , HIS F:196 , GLU F:197 , HIS F:200 , HOH F:9324BINDING SITE FOR RESIDUE CO F 5300
07AC7SOFTWAREGLN G:111 , CYS G:155 , HIS G:196 , HIS G:200 , HOH G:9325BINDING SITE FOR RESIDUE CO G 6300
08AC8SOFTWAREGLN H:111 , CYS H:155 , HIS H:196 , HIS H:200 , HOH H:9326BINDING SITE FOR RESIDUE CO H 7300
09AC9SOFTWAREGLN I:111 , CYS I:155 , HIS I:196 , HIS I:200 , HOH I:9327BINDING SITE FOR RESIDUE CO I 8300
10BC1SOFTWAREGLN J:111 , CYS J:155 , HIS J:196 , HIS J:200 , HOH J:9328BINDING SITE FOR RESIDUE CO J 9300

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1JYM)

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1JYM)

(-) Exons   (0, 0)

(no "Exon" information available for 1JYM)

(-) Sequences/Alignments

Asymmetric/Biological 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:179
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:181
                                                                                                                                                                                                            241  
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        |- 
         Q8I372_PLAF7    63 DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEEPAL--   -
               SCOP domains d1jyma_ A: Peptide  deformylase                                                                                                                                                       SCOP domains
               CATH domains 1jymA00 A:63-241 P eptide Deformylase                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeee....-..eeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jym A  63 DEIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHSEEPLEHH 241
                                    72       |81        91   |   101       111       121       131       141       151      |160       170       180       190       200       210       220       230       240 
                                            80 |            95-MSE                                                        158 |                                                210-MSE                           
                                              81                99-MSE                                                      159                                                                                  


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:181
                                                                                                                                                                                                            241  
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        |- 
         Q8I372_PLAF7    63 DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEEPAL--   -
               SCOP domains d1jymb_ B: Peptide  deformylase                                                                                                                                                       SCOP domains
               CATH domains 1jymB00 B:63-241 P eptide Deformylase                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhh.hhhhhhhhhhhhhhhhhhhhh....hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jym B  63 DEIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHSEEPLEHH 241
                                    72       |81        91   |   101       111       121       131       141       151      |160       170       180       190       200       210       220       230       240 
                                            80 |            95-MSE                                                        158 |                                                210-MSE                           
                                              81                99-MSE                                                      159                                                                                  


Chain C from PDB  Type:PROTEIN  Length:168
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:170
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233
         Q8I372_PLAF7    64 EIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKA 233
               SCOP domains d1jymc_ C: Peptid e deformylase                                                                                                                                            SCOP domains
               CATH domains 1jymC00 C:64-231  Peptide Deformylase                                                                                                                                      CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...-........hhhhhhhhhhhhh....eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jym C  64 EIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKA 231
                                    73      | 82        92  |   |102       112       122       132       142       152     | 161       171       181       191       201       211       221       231
                                           80 |            95-MSE                                                        158 |                                                210-MSE                 
                                             81                99-MSE                                                      159                                                                        


Chain D from PDB  Type:PROTEIN  Length:173
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:175
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     
         Q8I372_PLAF7    64 EIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEE 238
               SCOP domains d1jymd_ D: Peptid e deformylase                                                                                                                                                 SCOP domains
               CATH domains 1jymD00 D:64-236  Peptide Deformylase                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jym D  64 EIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHSEE 236
                                    73      | 82        92  |   |102       112       122       132       142       152     | 161       171       181       191       201       211       221       231     
                                           80 |            95-MSE                                                        158 |                                                210-MSE                      
                                             81                99-MSE                                                      159                                                                             


Chain E from PDB  Type:PROTEIN  Length:176
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:178
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232        
         Q8I372_PLAF7    63 DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEEPA 240
               SCOP domains d1jyme_ E: Peptide  deformylase                                                                                                                                                    SCOP domains
               CATH domains 1jymE00 E:63-238 P eptide Deformylase                                                                                                                                              CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhh.hhhhhhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jym E  63 DEIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHSEEPL 238
                                    72       |81        91   |   101       111       121       131       141       151      |160       170       180       190       200       210       220       230        
                                            80 |            95-MSE                                                        158 |                                                210-MSE                        
                                              81                99-MSE                                                      159                                                                               


Chain F from PDB  Type:PROTEIN  Length:172
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:174
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
         Q8I372_PLAF7    64 EIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSE 237
               SCOP domains d1jymf_ F: Peptid e deformylase                                                                                                                                                SCOP domains
               CATH domains 1jymF00 F:64-235  Peptide Deformylase                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ........hhhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee.......hhhhheeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jym F  64 EIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHSE 235
                                    73      | 82        92  |   |102       112       122       132       142       152     | 161       171       181       191       201       211       221       231    
                                           80 |            95-MSE                                                        158 |                                                210-MSE                     
                                             81                99-MSE                                                      159                                                                            


Chain G from PDB  Type:PROTEIN  Length:172
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:174
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
         Q8I372_PLAF7    63 DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHS 236
               SCOP domains d1jymg_ G: Peptide  deformylase                                                                                                                                                SCOP domains
               CATH domains 1jymG00 G:63-234 P eptide Deformylase                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeee.hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jym G  63 DEIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHS 234
                                    72       |81        91   |   101       111       121       131       141       151      |160       170       180       190       200       210       220       230    
                                            80 |            95-MSE                                                        158 |                                                210-MSE                    
                                              81                99-MSE                                                      159                                                                           


Chain H from PDB  Type:PROTEIN  Length:173
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:175
                                    73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233     
         Q8I372_PLAF7    64 EIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHSEE 238
               SCOP domains d1jymh_ H: Peptid e deformylase                                                                                                                                                 SCOP domains
               CATH domains 1jymH00 H:64-236  Peptide Deformylase                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhh...-........hhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeee.hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1jym H  64 EIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHSEE 236
                                    73      | 82        92  |   |102       112       122       132       142       152     | 161       171       181       191       201       211       221       231     
                                           80 |            95-MSE                                                        158 |                                                210-MSE                      
                                             81                99-MSE                                                      159                                                                             


Chain I from PDB  Type:PROTEIN  Length:172
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:174
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
         Q8I372_PLAF7    63 DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHS 236
               SCOP domains d1jymi_ I: Peptide  deformylase                                                                                                                                                SCOP domains
               CATH domains 1jymI00 I:63-234 P eptide Deformylase                                                                                                                                          CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........hhhhh....-........hhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeee..ee..e-eee..eeee..eeeeee.....eeeeeehhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jym I  63 DEIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHS 234
                                    72       |81        91   |   101       111       121       131       141       151      |160       170       180       190       200       210       220       230    
                                            80 |            95-MSE                                                        158 |                                                210-MSE                    
                                              81                99-MSE                                                      159                                                                           


Chain J from PDB  Type:PROTEIN  Length:172
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:174
                                    72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232    
         Q8I372_PLAF7    63 DEIKIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYKATHS 236
               SCOP domains d1jymj_ J: Peptide  deformylase                                                                                                                                                SCOP domains
               CATH domains 1jymJ00 J:63-234 P eptide Deformylase                                                                                                                                          CATH domains
           Pfam domains (1) -Pep_deformylase-1-jymJ01 J:64-216                                                               -                                                          ------------------ Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-1-jymJ02 J:64-216                                                               -                                                          ------------------ Pfam domains (2)
           Pfam domains (3) -Pep_deformylase-1-jymJ03 J:64-216                                                               -                                                          ------------------ Pfam domains (3)
           Pfam domains (4) -Pep_deformylase-1-jymJ04 J:64-216                                                               -                                                          ------------------ Pfam domains (4)
           Pfam domains (5) -Pep_deformylase-1-jymJ05 J:64-216                                                               -                                                          ------------------ Pfam domains (5)
           Pfam domains (6) -Pep_deformylase-1-jymJ06 J:64-216                                                               -                                                          ------------------ Pfam domains (6)
           Pfam domains (7) -Pep_deformylase-1-jymJ07 J:64-216                                                               -                                                          ------------------ Pfam domains (7)
           Pfam domains (8) -Pep_deformylase-1-jymJ08 J:64-216                                                               -                                                          ------------------ Pfam domains (8)
           Pfam domains (9) -Pep_deformylase-1-jymJ09 J:64-216                                                               -                                                          ------------------ Pfam domains (9)
          Pfam domains (10) -Pep_deformylase-1-jymJ10 J:64-216                                                               -                                                          ------------------ Pfam domains (10)
         Sec.struct. author .........hhhhhh...-.......hhhhhhhhhhhhhhh...eee.hhhh....eeee............eeeeeeeeeee...eeeeeeee..e-eeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1jym J  63 DEIKIVKYPDPILRRRSE-VTNFDDNLKRVVRKmFDImYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSF-GIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKmTQVDKKKVRPKLNELIRDYKATHS 234
                                    72       |81        91   |   101       111       121       131       141       151      |160       170       180       190       200       210       220       230    
                                            80 |            95-MSE                                                        158 |                                                210-MSE                    
                                              81                99-MSE                                                      159
   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, 10)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (1, 10)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)
(-)
Architecture: Alpha-Beta Complex (3881)
(-)
Topology: Peptide Deformylase (68)
(-)
Homologous Superfamily: Peptide Deformylase (68)
(-)
Malaria parasite p (Plasmodium falciparum) (2)
1a1jymE00E:63-238
1b1jymA00A:63-241
1c1jymB00B:63-241
1d1jymC00C:64-231
1e1jymD00D:64-236
1f1jymH00H:64-236
1g1jymF00F:64-235
1h1jymG00G:63-234
1i1jymI00I:63-234
1j1jymJ00J:63-234

(-) Pfam Domains  (1, 10)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: Pep_deformylase] (48)

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B,C,D,E,F,G,H,I,J   (Q8I372_PLAF7 | Q8I372)
molecular function
    GO:0008198    ferrous iron binding    Interacting selectively and non-covalently with ferrous iron, Fe(II).
    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:0005506    iron ion binding    Interacting selectively and non-covalently with iron (Fe) ions.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    GO:0042586    peptide deformylase activity    Catalysis of the reaction: formyl-L-methionyl peptide + H2O = formate + methionyl peptide.
biological process
    GO:0031365    N-terminal protein amino acid modification    The alteration of the N-terminal amino acid residue in a protein.
    GO:0043686    co-translational protein modification    The process of covalently altering one or more amino acids in a protein after translation has begun but before the protein has been released from the ribosome.
    GO:0006412    translation    The cellular metabolic process in which a protein is formed, using the sequence of a mature mRNA or circRNA molecule to specify the sequence of amino acids in a polypeptide chain. Translation is mediated by the ribosome, and begins with the formation of a ternary complex between aminoacylated initiator methionine tRNA, GTP, and initiation factor 2, which subsequently associates with the small subunit of the ribosome and an mRNA or circRNA. Translation ends with the release of a polypeptide chain from the ribosome.
cellular component
    GO:0020011    apicoplast    The plastid organelle found in apicomplexans.
    GO:0016021    integral component of membrane    The component of a membrane consisting of the gene products and protein complexes having at least some part of their peptide sequence embedded in the hydrophobic region of the membrane.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.

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  1jym
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  Q8I372_PLAF7 | Q8I372
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  3.5.1.31
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 Related Entries

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

UniProtKB/TrEMBL
        Q8I372_PLAF7 | Q8I372: 1rl4 1rqc

(-) Related Entries Specified in the PDB File

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