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(-) Description

Title :  FORMYL-METHIONINE-ALANINE COMPLEX STRUCTURE OF PEPTIDE DEFORMYLASE FROM XANTHOMOONAS ORYZAE PV. ORYZAE
 
Authors :  H. P. T. Ngo, J. K. Kim, L. W. Kang
Date :  02 Dec 13  (Deposition) - 03 Dec 14  (Release) - 03 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Metallopeptidase, Peptide Deformylase, Cadmium, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  H. P. T. Ngo, J. K. Kim, L. W. Kang
Substrate Complex Structure Of Xoo1075, A Peptide Deformylase, From Xanthomonas Oryzae Pv. Oryzae
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PEPTIDE DEFORMYLASE
    Chains: A
    EC Number: 3.5.1.88
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 42-212
    Gene: DEF, XOO1075
    Organism Scientific: XANTHOMONAS ORYZAE PV. ORYZAE
    Organism Taxid: 291331
    Strain: KACC10331 / KXO85
    Synonym: PDF, POLYPEPTIDE DEFORMYLASE

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (7, 10)
No.NameCountTypeFull Name
1ACT1Ligand/IonACETATE ION
2ALA1Mod. Amino AcidALANINE
3CD3Ligand/IonCADMIUM ION
4CSD1Mod. Amino Acid3-SULFINOALANINE
5FME1Mod. ResidueN-FORMYLMETHIONINE
6GOL1Ligand/IonGLYCEROL
7NA2Ligand/IonSODIUM ION
Biological Unit 1 (5, 10)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2ALA2Mod. Amino AcidALANINE
3CD-1Ligand/IonCADMIUM ION
4CSD2Mod. Amino Acid3-SULFINOALANINE
5FME2Mod. ResidueN-FORMYLMETHIONINE
6GOL2Ligand/IonGLYCEROL
7NA-1Ligand/IonSODIUM ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLU A:37 , GLU A:132 , HOH A:366 , HOH A:367 , HOH A:372BINDING SITE FOR RESIDUE CD A 201
2AC2SOFTWAREGLN A:51 , CSD A:99 , HIS A:141 , HIS A:145 , FME A:207 , HOH A:362BINDING SITE FOR RESIDUE CD A 202
3AC3SOFTWAREHIS A:43 , GLU A:128 , GLU A:130 , HOH A:368 , HOH A:373BINDING SITE FOR RESIDUE CD A 203
4AC4SOFTWARELEU A:14 , ARG A:149 , LEU A:150 , SER A:153 , ASP A:159 , HOH A:350 , HOH A:378 , HOH A:385BINDING SITE FOR RESIDUE ACT A 204
5AC5SOFTWARELEU A:14 , GLY A:148 , ASP A:159 , HOH A:370 , HOH A:371 , HOH A:374BINDING SITE FOR RESIDUE NA A 205
6AC6SOFTWARELEU A:105 , ASP A:164 , HOH A:337 , HOH A:359BINDING SITE FOR RESIDUE NA A 206
7AC7SOFTWAREGLY A:44 , VAL A:45 , GLY A:46 , GLN A:51 , GLY A:98 , PHE A:134 , HIS A:141 , GLU A:142 , HIS A:145 , CD A:202 , ALA A:208 , HOH A:362BINDING SITE FOR RESIDUE FME A 207
8AC8SOFTWAREARG A:68 , TYR A:69 , GLY A:98 , LEU A:100 , FME A:207BINDING SITE FOR RESIDUE ALA A 208
9AC9SOFTWAREASN A:22 , HOH A:394BINDING SITE FOR RESIDUE GOL A 209

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NT8)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NT8)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NT8)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NT8)

(-) Exons   (0, 0)

(no "Exon" information available for 4NT8)

(-) Sequences/Alignments

Asymmetric Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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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:169
                                                                                                                                                                                                         
               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
                 4nt8 A   1 MIRDIIRMGDKRLLRVAPQVTNLGSAELHALVSDMFETMGAAHGVGLAAPQIAVDLQLMVFGFEASERYPEAPAVPLTALANAQIEPLSDEMENGWEGcLSIPGLRAVIPRYRYIRYRGFAPDGSPIEREAEGFHARVVQHEYDHLVGRLYPSRIENFDTFGFDDVLSA 208
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       ||
                                                                                                                             99-CSD                                                              168|
                                                                                                                                                                                                  208
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 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4NT8)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NT8)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NT8)

(-) Gene Ontology  (5, 5)

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        Q5H3Z2_XANOR | Q5H3Z2: 5cp0 5cpd 5cvk 5cvp 5cvq 5cwx 5cwy 5cx0 5cxj 5cy7 5cy8 5e5d

(-) Related Entries Specified in the PDB File

3dld NATIVE STRUCTURE