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(-) Description

Title :  MAS COMPLEX STRUCTURE OF PEPTIDE DEFORMYLASE FROM XANTHOMONAS ORYZAE PV ORYZAE
 
Authors :  H. P. T. Ngo, L. W. Kang
Date :  21 Jul 15  (Deposition) - 03 Aug 16  (Release) - 03 Aug 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,C
Keywords :  Substrate, Hydrolase-Substrate Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. T. Ngo, L. W. Kang
Mas Complex Structure Of Peptide Deformylase From Xanthomonas Oryzae Pv Oryzae
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI K-12
    Expression System Plasmid: PET11A
    Expression System Strain: K-12
    Expression System Taxid: 83333
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 42-212
    Gene: DEF, XOO1075
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE KACC10331
    Organism Taxid: 291331
    Strain: KACC10331
    Synonym: PDF,POLYPEPTIDE DEFORMYLASE
 
Molecule 2 - MET-ALA-SER
    Chains: C
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 9)

Asymmetric/Biological Unit (3, 9)
No.NameCountTypeFull Name
1ACT3Ligand/IonACETATE ION
2CD5Ligand/IonCADMIUM ION
3NA1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHIS A:43 , GLU A:128 , GLU A:130 , HOH A:347 , HOH A:382 , HOH A:402binding site for residue CD A 201
2AC2SOFTWAREGLU A:37 , GLU A:132 , HOH A:319 , HOH A:449binding site for residue CD A 202
3AC3SOFTWAREGLN A:51 , CYS A:99 , HIS A:141 , HIS A:145 , HOH A:306 , HOH C:101binding site for residue CD A 203
4AC4SOFTWARELEU A:14 , ARG A:149 , LEU A:150 , SER A:153 , ASP A:159 , HOH A:312 , HOH A:323 , HOH A:411binding site for residue ACT A 204
5AC5SOFTWAREASP A:170 , HOH A:371binding site for residue ACT A 205
6AC6SOFTWAREARG A:3 , HOH A:327 , HOH A:337binding site for residue ACT A 206
7AC7SOFTWAREGLU A:91 , HOH A:414binding site for residue CD A 207
8AC8SOFTWARELEU A:105 , ASP A:164 , HOH A:466binding site for residue CD A 208
9AC9SOFTWARELEU A:14 , HOH A:350 , HOH A:407 , HOH A:428 , HOH A:448 , HOH A:470binding site for residue NA A 209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CP0)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Ala A:72 -Pro A:73

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CP0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CP0)

(-) Exons   (0, 0)

(no "Exon" information available for 5CP0)

(-) 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:167
                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeee.............eeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.hhhhhee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cp0 A   1 MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASPEAPAVPLTALANAQIEPLSDEMENGWEGCLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSYD 170
                                    10        20        30        40        50        60     || 73        83        93       103       113       123       133       143       153       163       
                                                                                            66|                                                                                                    
                                                                                             70                                                                                                    


Chain C 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
                 5cp0 C   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 5CP0)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CP0)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CP0)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Ala A:72 - Pro A:73   [ RasMol ]  
 

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        Q5H3Z2_XANOR | Q5H3Z2: 4nt8 5cpd 5cvk 5cvp 5cvq 5cwx 5cwy 5cx0 5cxj 5cy7 5cy8 5e5d

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