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(-) Description

Title :  CRYSTAL STRUCTURE OF TYPE 2 PDF FROM STREPTOCOCCUS AGALACTIAE IN COMPLEX WITH TRIPEPTIDE MET-ALA-ARG
 
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 :  1.60
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
    Other Details: METHIONINE 16 IS OXIDIZED.
    Synonym: PDF,POLYPEPTIDE DEFORMYLASE
 
Molecule 2 - MET-ALA-ARG
    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  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2NI8Ligand/IonNICKEL (II) ION
3OCS1Mod. Amino AcidCYSTEINESULFONIC ACID
4SME1Mod. Amino AcidMETHIONINE SULFOXIDE

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:145 , GLU A:158 , ASP A:177 , ARG A:187 , NI A:306 , HOH A:452 , HOH A:516 , HOH A:648binding site for residue ACT A 301
2AC2SOFTWAREGLN A:77 , OCS A:131 , HIS A:174 , HIS A:178 , HOH A:418 , HOH A:637binding site for residue NI A 302
3AC3SOFTWAREHIS A:55 , GLU A:198 , HOH A:582 , HOH A:640 , HOH A:651binding site for residue NI A 303
4AC4SOFTWAREHIS A:118 , HOH A:415 , HOH A:623 , HOH A:629 , HOH A:645binding site for residue NI A 304
5AC5SOFTWAREASP A:94 , GLU A:190 , HOH A:447 , HOH A:526 , HOH A:553binding site for residue NI A 305
6AC6SOFTWAREHIS A:145 , GLU A:158 , ACT A:301 , HOH A:634binding site for residue NI A 306
7AC7SOFTWAREHIS A:12 , ASP A:18 , HOH A:426 , HOH A:429 , HOH A:481 , HOH A:647binding site for residue NI A 307
8AC8SOFTWAREGLU A:43 , GLU A:47 , HOH A:565binding site for residue NI A 308
9AC9SOFTWAREGLU A:102 , GLU A:151 , HOH A:541 , HOH A:614 , HOH A:619binding site for residue NI A 309

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5JF0)

(-) 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 5JF0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5JF0)

(-) Exons   (0, 0)

(no "Exon" information available for 5JF0)

(-) 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
                 5jf0 A   2 AAIDKLVKASHLIDmNDIIREGNPTLRKVAEEVTFPLSEKEEILGEKMMQFLKHSQDPIMAEKLGLRGGVGLAAPQLDISKRIIAVLVPNVEDAQGNPPKEAYSLQEVMYNPKVVSHSVQDAALSDGEGcLSVDREVPGYVVRHARVTIEYFDKTGEKHRLKLKGYNSIVVQHEIDHIDGIMFYDRINEKNPFAVKEGLLILE 204
                                    11    |   21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201   
                                         16-SME                                                                                                            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
                 5jf0 D   1 MAR   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 5JF0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5JF0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5JF0)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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    Phe A:36 - Pro A:37   [ RasMol ]  
 

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 Related Entries

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

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