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

(-) Description

Title :  CRYSTAL STRUCTURE OF PEPTIDE DEFORMYLASE FROM EHRLICHIA CHAFFEENSIS
 
Authors :  Seattle Structural Genomics Center For Infectious Disease (S
Date :  09 Aug 10  (Deposition) - 08 Sep 10  (Release) - 15 Sep 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ssgcid, Ehrlichia Chaffeensis, Peptide Deformylase, Structural Genomics, Seattle Structural Genomics Center For Infectious Disease, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Seattle Structural Genomics Center For Infectious Disease (Ssgcid), J. Abendroth, B. Sankaran, T. E. Edwards, B. Staker
Crystal Structure Of Peptide Deformylase From Ehrlichia Chaffeensis
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A, B
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: AVA0421
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: EHRLICHIA CHAFFEENSIS
    Organism Taxid: 205920
    Strain: ARKANSAS

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1CL2Ligand/IonCHLORIDE ION
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:51 , CYS A:111 , HIS A:153 , HIS A:157 , HOH A:189BINDING SITE FOR RESIDUE ZN A 300
2AC2SOFTWAREGLU A:138BINDING SITE FOR RESIDUE CL A 301
3AC3SOFTWAREGLU B:138BINDING SITE FOR RESIDUE CL B 301
4AC4SOFTWARECYS B:111 , HIS B:153 , HIS B:157 , HOH B:238BINDING SITE FOR RESIDUE ZN B 300

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:17 -B:17

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Val A:9 -Pro A:10
2Gly A:88 -Pro A:89
3Val B:9 -Pro B:10
4Gly B:88 -Pro B:89

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3OCA)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3OCA)

(-) Exons   (0, 0)

(no "Exon" information available for 3OCA)

(-) 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 Q2GI30_EHRCR | Q2GI30 from UniProtKB/TrEMBL  Length:188

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
         Q2GI30_EHRCR     2 SVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVKKKERTDLI 188
               SCOP domains d3ocaa_ A: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhhh..eee.hhhh....eeeeee..--------.............eeeeeeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oca A   2 SVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPE--------ENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVKKKERTDLI 188
                                    11        21        31        41        51        61   |     -  |     81        91       101       111       121       131       141       151       161       171       181       
                                                                                          65       74                                                                                                                  


Chain B from PDB  Type:PROTEIN  Length:179
 aligned with Q2GI30_EHRCR | Q2GI30 from UniProtKB/TrEMBL  Length:188

    Alignment length:187
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       
         Q2GI30_EHRCR     2 SVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPEEFEDSEDIENVEDKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVKKKERTDLI 188
               SCOP domains d3ocab_ B: automated matches                                                                                                                                                                SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -Pep_deformylase-3ocaB01 B:3-173                                                                                                                                            --------------- Pfam domains (1)
           Pfam domains (2) -Pep_deformylase-3ocaB02 B:3-173                                                                                                                                            --------------- Pfam domains (2)
         Sec.struct. author .........hhhhhh........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee......--------.........eeeeeeeeeeeeee...eeeeee.........eeeeee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3oca B   2 SVLSIVTVPDKRLSLCSEEVEKVDQSIRKLVDDMFETMHANQGLGLAAVQVGVHKRILVMNVPEEFED--------DKIEGYELYGGPYCIINPKIVDISQEKVKLKEGCLSVPGYFDYIVRPQRIAVQYLDYNGNECIIKAQGWLARCLQHEIDHLNGTVFLKYLSKFKRDFAIEKVKKKERTDLI 188
                                    11        21        31        41        51        61       | -      | 81        91       101       111       121       131       141       151       161       171       181       
                                                                                              69       78
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OCA)

(-) Pfam Domains  (1, 2)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q2GI30_EHRCR | Q2GI30)
molecular function
    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: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.

 Visualization

(-) Interactive Views

Asymmetric/Biological 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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    ZN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:88 - Pro A:89   [ RasMol ]  
    Gly B:88 - Pro B:89   [ RasMol ]  
    Val A:9 - Pro A:10   [ RasMol ]  
    Val B:9 - Pro B:10   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites 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
  3oca
    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
  Q2GI30_EHRCR | Q2GI30
    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)
  3.5.1.88
    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
  Q2GI30_EHRCR | Q2GI30
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q2GI30_EHRCR | Q2GI30: 3u04

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3OCA)