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(-) Description

Title :  METHIONINE-ALANINE 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 :  2.20
Chains :  Asym./Biol. Unit :  A
Keywords :  Methionine-Alanine Complex, Peptide Deformylase, Xanthomonas, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. T. Ngo, L. W. Kang
Methionine-Alanine 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
    Expression System Taxid: 562
    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

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 10)

Asymmetric/Biological Unit (7, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ALA1Mod. Amino AcidALANINE
3CD3Ligand/IonCADMIUM ION
4CSD1Mod. Amino Acid3-SULFINOALANINE
5GOL1Ligand/IonGLYCEROL
6MET1Mod. Amino AcidMETHIONINE
7NA2Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , GLU A:132 , HOH A:301 , HOH A:374 , HOH A:376binding site for residue CD A 201
2AC2SOFTWAREGLN A:51 , CSD A:99 , HIS A:141 , HIS A:145 , HOH A:313 , HOH A:326binding site for residue CD A 202
3AC3SOFTWAREHIS A:43 , GLU A:128 , GLU A:130 , HOH A:303 , HOH A:312binding site for residue CD A 203
4AC4SOFTWAREARG A:149 , LEU A:150 , SER A:153 , ASP A:159 , HOH A:307 , HOH A:341 , HOH A:347binding site for residue ACT A 204
5AC5SOFTWARELEU A:14 , GLY A:148 , ASP A:159 , HOH A:308 , HOH A:362 , HOH A:386binding site for residue NA A 205
6AC6SOFTWARELEU A:105 , ASP A:164 , HOH A:366 , HOH A:381binding site for residue NA A 206
7AC7SOFTWAREASN A:22 , GLU A:27binding site for residue GOL A 207
8AC8SOFTWAREGLY A:44 , VAL A:45 , GLY A:46 , GLY A:98 , PHE A:134 , HIS A:141 , GLU A:142 , ALA A:209 , HOH A:313binding site for residue MET A 208
9AC9SOFTWAREARG A:68 , TYR A:69 , GLY A:98 , LEU A:100 , MET A:208binding site for residue ALA A 209

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5CPD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5CPD)

(-) 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    
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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:170
                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .........hhhhhh.........hhhhhhhhhhhhhhhhhh...eee.hhhh....eeeeee...........eeeeeeeeeeeee....eeeeeeee..eeeeeeeeeee.eeeeeee.....eeeeeeehhhhhhhhhhhhhhh..hhhhhh.hhhhhee....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5cpd A   1 MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTALANAQIEPLSDEMENGWEGcLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSMA 209
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       209
                                                                                                                             99-CSD                                                              168| 
                                                                                                                                                                                                  208
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  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 5CPD)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/TrEMBL
        Q5H3Z2_XANOR | Q5H3Z2: 4nt8 5cp0 5cvk 5cvp 5cvq 5cwx 5cwy 5cx0 5cxj 5cy7 5cy8 5e5d

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