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 TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIAE IN COMPLEX WITH TRIPEPTIDE MET-ALA-SER
 
Authors :  S. Fieulaine, C. Giglione, T. Meinnel
Date :  19 Apr 16  (Deposition) - 30 Nov 16  (Release) - 30 Nov 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym./Biol. Unit :  A,D
Keywords :  Pdf, Type 2, Nme, N-Terminal Methionine Excision, Streptococcus Agalactiae, Inhibitor, Tripeptide, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Fieulaine, R. Alves De Sousa, L. Maigre, K. Hamiche, M. Alimi, J. M. Bolla, A. Taleb, A. Denis, J. M. Pages, I. Artaud, T. Meinnel, C. Giglione
A Unique Peptide Deformylase Platform To Rationally Design And Challenge Novel Active Compounds.
Sci Rep V. 6 35429 2016
PubMed-ID: 27762275  |  Reference-DOI: 10.1038/SREP35429

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Taxid: 469008
    Expression System Variant: ROSETTA2 PLYSS
    Expression System Vector Type: PLASMID
    Gene: DEF, GBS1883
    Mutation: YES
    Organism Scientific: STREPTOCOCCUS AGALACTIAE
    Organism Taxid: 1311
    Synonym: PDF,POLYPEPTIDE DEFORMYLASE
 
Molecule 2 - MET-ALA-SER
    Chains: D
    Engineered: YES
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 10)

Asymmetric/Biological Unit (3, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
3ZN8Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:145 , GLU A:158 , ASP A:177 , ARG A:187 , ZN A:306 , HOH A:444 , HOH A:472 , HOH A:618binding site for residue ACT A 301
2AC2SOFTWAREGLN A:77 , OCS A:131 , HIS A:174 , HIS A:178 , HOH A:447 , HOH A:620binding site for residue ZN A 302
3AC3SOFTWAREHIS A:55 , GLU A:198 , HOH A:488 , HOH A:557 , HOH A:642binding site for residue ZN A 303
4AC4SOFTWAREHIS A:118 , ASP A:154 , HOH A:421 , HOH A:622 , HOH A:624 , HOH A:644 , HOH A:654binding site for residue ZN A 304
5AC5SOFTWAREASP A:94 , GLU A:190 , HOH A:484 , HOH A:527 , HOH A:556binding site for residue ZN A 305
6AC6SOFTWAREHIS A:145 , GLU A:158 , ACT A:301 , HOH A:627binding site for residue ZN A 306
7AC7SOFTWAREHIS A:12 , ASP A:18 , HOH A:418 , HOH A:424 , HOH A:436 , HOH A:626binding site for residue ZN A 307
8AC8SOFTWAREGLU A:43 , GLU A:47 , HOH A:525binding site for residue ZN A 308
9AC9SOFTWAREGLU A:102 , GLU A:151 , HOH A:582 , HOH A:617 , HOH A:636 , HOH A:641binding site for residue ZN A 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JEZ)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Phe A:36 -Pro A:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5JEZ)

(-) 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:203
                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhh.....hhhhh....hhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eee.hhhh....eeeeeee.............eeeeeeeeeeeeeee...eeee..................ee..eeeeee.....eeeeeehhhhhhhhhhhhhhhh..hhhhhh............eee. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5jez A   2 AAIDKLVKASHLIDMNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQFLKHSQDPIMAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPKEAYSLQEVMYNPKVVSHSVQDAALSDGEGcLSVDREVPGYVVRHARVTIEYFDKTGEKHRLKLKGYNSIVVQHEIDHIDGIMFYDRINEKNPFAVKEGLLILE 204
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
                                                                                                                                                           131-OCS                                                                     


Chain D from PDB  Type:PROTEIN  Length:3
                                   
               SCOP domains --- SCOP domains
               CATH domains --- CATH domains
               Pfam domains --- Pfam domains
         Sec.struct. author ... Sec.struct. author
                 SAPs(SNPs) --- SAPs(SNPs)
                    PROSITE --- PROSITE
                 Transcript --- Transcript
                 5jez D   1 MAS   3
   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 5JEZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OCS  [ 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 ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Phe A:36 - Pro A:37   [ 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
  5jez
    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
  DEF_STRA3 | Q8E378
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  DEF_STRA3 | Q8E378
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        DEF_STRA3 | Q8E378: 5jex 5jey 5jf0 5jf1 5jf2 5jf3 5jf4 5jf5 5jf6 5jf7 5jf8

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5JEZ)