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(-) Description

Title :  CRYSTAL STRUCTURE OF ODC-PLP-AZ1 TERNARY COMPLEX
 
Authors :  D. H. Wu
Date :  07 Jun 15  (Deposition) - 09 Dec 15  (Release) - 09 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.20
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Ornithine Decarboxylase, Antizyme1, Ornithine Decarboxylase-Antizyme1 Complex, Polyamine Biosynthesis, Polyamine Homeostasis, Lyase-Lyase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  D. H. Wu, H. Y. Kaan, X. Zheng, X. Tang, Y. He, Q. Vanessa Tan, N. Zhang, H. Song
Structural Basis Of Ornithine Decarboxylase Inactivation An Accelerated Degradation By Polyamine Sensor Antizyme1
Sci Rep V. 5 14738 2015
PubMed-ID: 26443277  |  Reference-DOI: 10.1038/SREP14738

(-) Compounds

Molecule 1 - ORNITHINE DECARBOXYLASE
    Chains: A
    EC Number: 4.1.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: ODC1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ODC
 
Molecule 2 - ORNITHINE DECARBOXYLASE ANTIZYME 1
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 69-228
    Gene: OAZ1, OAZ
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ODC-AZ

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 1)

Asymmetric/Biological Unit (1, 1)
No.NameCountTypeFull Name
1PLP1Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:69 , ASP A:88 , ALA A:111 , HIS A:197 , GLY A:237 , GLU A:274 , GLY A:276 , ARG A:277 , TYR A:389binding site for residue PLP A 600

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (7, 7)

Asymmetric/Biological Unit
No.Residues
1Asn A:398 -Gly A:399
2Lys B:112 -Thr B:113
3Gly B:146 -Ala B:147
4Ser B:152 -Lys B:153
5Phe B:162 -Ala B:163
6Lys B:178 -Asn B:179
7Asn B:179 -Arg B:180

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5BWA)

(-) 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:350
                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhh...eeeeehhhhhhhhhhhhhhh...eeeee.hhh.hhhhhhhhhhhh.eeee.hhhhhhhhhhh......eee.....hhhhhhhhhh....eeee.hhhhhhhhhhhh...eeeee............hhhhhhhhhhhhhh....eeeee........hhhhhhhhhhhhhhhhhhhhhhh....eee...........hhhhhhhhhhhhhhhh...eee..hhhhhh..eeeeeeeeeeeee........eeeeee........hhhhhh..........eeee........eeeeee.........eeeee................eeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bwa A  19 TAKDILDQKINDAFYVADLGDILKKHLRWLKALPRVTPFYAVKCNDSKAIVKTLAATGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAANNGVQMMTFDSEVELMKVARAHPKAKLVLRIATDRLSVKFGATLRTSRLLLERAKELNIDVVGVSFHVGSGCTDPETFVQAISDARCVFDMGAEVGFSMYLLDIGGGFPGSEDKFEEITGVINPALDKYFPSRIIAEPGRYYVASAFTLAVNIIAKKIVLKEQTSEQTFMYYVNDGVYGSFNCILYDHAHVKPLLQSSSIWGPTCDGLDRIVERCDLPEMHVGDWMLFENMGAYTVATFNGFQRPTIYYVMS 410
                                    28||      46        56        66        76        86        96       106       116       126       136       146       156 ||    172       182       192       202       212       222       232       242||     255       265|      279       289       299 ||    317       327       337   ||  357       367       377       387    || 400       410
                                     29|                                                                                                                     158|                                                                           243|               265|                            301|                            341|                                     392|              
                                      38                                                                                                                      165                                                                            247                270                             310                             352                                      396              


Chain B from PDB  Type:PROTEIN  Length:121
                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...ee....eeee.....eeeeee.......eeeeeeee..eeeee..........hhhhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhh.eee...........eeeeeee.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bwa B  93 NLFYSDDRLNVTEEDKTRILNVQSRLTDAKRINWRTVLSGGSLYIEIPGGALPEGSKDSFAVLLEFAEEQLRADHVFICFHKNREDRAALLRTFSFLGFEIVRPGHPLVRPDACFMAYTFE 219
                                   102   ||  116       126       136       146       156       166       176       186       196       208       218 
                                       106|                                                                                           205|           
                                        111                                                                                            208
   Legend:   → Mismatch (orange background)
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  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 5BWA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (25, 30)

Asymmetric/Biological Unit(hide GO term definitions)

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  Cis Peptide Bonds
    Asn A:398 - Gly A:399   [ RasMol ]  
    Asn B:179 - Arg B:180   [ RasMol ]  
    Gly B:146 - Ala B:147   [ RasMol ]  
    Lys B:112 - Thr B:113   [ RasMol ]  
    Lys B:178 - Asn B:179   [ RasMol ]  
    Phe B:162 - Ala B:163   [ RasMol ]  
    Ser B:152 - Lys B:153   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        DCOR_HUMAN | P11926: 1d7k 2on3 2oo0 4zgy
        OAZ1_HUMAN | P54368: 4zgy 4zgz

(-) Related Entries Specified in the PDB File

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