Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
(-)Biological Unit 2
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  PLASMODIUM FALCIPARUM PEPTIDE DEFORMYLASE COMPLEX WITH INHIBITOR
 
Authors :  M. A. Robien, K. T. Nguyen, A. Kumar, I. Hirsh, S. Turley, D. Pei, W. G. J. H
Date :  24 Nov 03  (Deposition) - 09 Dec 03  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Crystal Engineering, Drug Design, Malaria, Pdf, Peptide Deformylase, Plasmodium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. A. Robien, K. T. Nguyen, A. Kumar, I. Hirsh, S. Turley, D. Pei, W. G. J. Hol
An Improved Crystal Form Of Plasmodium Falciparum Peptide Deformylase.
Protein Sci. V. 13 1155 2004
PubMed-ID: 15010544  |  Reference-DOI: 10.1110/PS.03456404
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - FORMYLMETHIONINE DEFORMYLASE
    Chains: A, B
    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 Scientific: PLASMODIUM FALCIPARUM
    Organism Taxid: 36329
    Strain: 3D7

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric Unit (3, 6)
No.NameCountTypeFull Name
1BL52Ligand/Ion2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE
2BRR2Ligand/Ion(2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID
3CO2Ligand/IonCOBALT (II) ION
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1BL51Ligand/Ion2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE
2BRR1Ligand/Ion(2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID
3CO-1Ligand/IonCOBALT (II) ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1BL51Ligand/Ion2-{N'-[2-(5-AMINO-1-PHENYLCARBAMOYL-PENTYLCARBAMOYL)-HEXYL]-HYDRAZINOMETHYL}-HEXANOIC ACID(5-AMINO-1-PHENYLCARBAMOYL-PENTYL)-AMIDE
2BRR1Ligand/Ion(2R)-2-{[FORMYL(HYDROXY)AMINO]METHYL}HEXANOIC ACID
3CO-1Ligand/IonCOBALT (II) ION

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:112 , CYS A:156 , HIS A:198 , HIS A:202 , BRR A:401BINDING SITE FOR RESIDUE CO A 301
2AC2SOFTWAREGLN B:112 , CYS B:156 , HIS B:198 , HIS B:202 , BRR B:1401BINDING SITE FOR RESIDUE CO B 1301
3AC3SOFTWAREGLY A:105 , ILE A:106 , GLY A:107 , GLN A:112 , CYS A:156 , LEU A:157 , HIS A:198 , GLU A:199 , HIS A:202 , CO A:301BINDING SITE FOR RESIDUE BRR A 401
4AC4SOFTWARELEU A:152 , ILE A:153 , TYR A:177 , ASN A:180 , GLY A:181 , TYR A:182 , GLY A:190 , ILE A:191 , HOH A:705 , HOH A:814 , LEU B:147BINDING SITE FOR RESIDUE BL5 A 501
5AC5SOFTWAREGLY B:105 , ILE B:106 , GLY B:107 , GLN B:112 , CYS B:156 , LEU B:157 , HIS B:198 , GLU B:199 , HIS B:202 , CO B:1301BINDING SITE FOR RESIDUE BRR B 1401
6AC6SOFTWARELEU A:147 , VAL A:148 , LEU B:152 , ILE B:153 , TYR B:177 , ASN B:180 , GLY B:181 , TYR B:182 , GLY B:190 , HOH B:1705BINDING SITE FOR RESIDUE BL5 B 1501

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1RL4)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Tyr A:70 -Pro A:71
2Tyr B:70 -Pro B:71

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1RL4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1RL4)

(-) Exons   (0, 0)

(no "Exon" information available for 1RL4)

(-) 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:154
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:165
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225     
         Q8I372_PLAF7    66 KIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRD 230
               SCOP domains d1rl4a_ A: Peptide deformylase                                                                                                                                        SCOP domains
               CATH domains 1rl4A00 A:66-230 Peptide Deformylase                                                                                                                                  CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.-----------.eeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rl4 A  66 KIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWN-----------RIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRD 230
                                    75        85        95       105       115       | -       135       145       155       165       175       185       195       205       215       225     
                                                                                   123         135                                                                                               


Chain B from PDB  Type:PROTEIN  Length:156
 aligned with Q8I372_PLAF7 | Q8I372 from UniProtKB/TrEMBL  Length:241

    Alignment length:167
                                    75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       
         Q8I372_PLAF7    66 KIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWNALYEKRKEENERIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYK 232
               SCOP domains d1rl4b_ B: Peptide deformylase                                                                                                                                          SCOP domains
               CATH domains 1rl4B00 B:66-232 Peptide Deformylase                                                                                                                                    CATH domains
           Pfam domains (1) Pep_deformylase-1rl4B01 B:66-218                                                                                                                         -------------- Pfam domains (1)
           Pfam domains (2) Pep_deformylase-1rl4B02 B:66-218                                                                                                                         -------------- Pfam domains (2)
         Sec.struct. author ......hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.-----------.eeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1rl4 B  66 KIVKYPDPILRRRSEEVTNFDDNLKRVVRKMFDIMYESKGIGLSAPQVNISKRIIVWN-----------RIFINPSIVEQSLVKLKLIEGCLSFPGIEGKVERPSIVSISYYDINGYKHLKILKGIHSRIFQHEFDHLNGTLFIDKMTQVDKKKVRPKLNELIRDYK 232
                                    75        85        95       105       115       | -       135       145       155       165       175       185       195       205       215       225       
                                                                                   123         135
   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, 2)

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

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (11, 11)

Asymmetric Unit(hide GO term definitions)
Chain A,B   (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.

 Visualization

(-) Interactive Views

Asymmetric Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    BL5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    BRR  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Tyr A:70 - Pro A:71   [ RasMol ]  
    Tyr B:70 - Pro B:71   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]

(-) Still Images

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

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  1rl4
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  Q8I372_PLAF7 | Q8I372
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  3.5.1.31
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  Q8I372_PLAF7 | Q8I372
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q8I372_PLAF7 | Q8I372: 1jym 1rqc

(-) Related Entries Specified in the PDB File

1jym