Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  2.3 A RESOLUTION CRYSTAL STRUCTURE OF THE ORNITHINE AMINOTRANSFERASE FROM TOXOPLASMA GONDII ME49
 
Authors :  E. V. Filippova, G. Minasov, K. Flores, H. Van Le, R. B. Silverman, R. Mc W. F. Anderson, Center For Structural Genomics Of Infectious D (Csgid)
Date :  19 May 15  (Deposition) - 03 Jun 15  (Release) - 03 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.31
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Pyridoxal 5'-Phosphate (Plp)-Independent Aminotransferase, Center For Structural Genomics Of Infectious Diseases, Csgid, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. V. Filippova, G. Minasov, K. Flores, H. Van Le, R. B. Silverman, R. Mcleod, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
2. 3 A Resolution Crystal Structure Of The Ornithine Aminotransferase From Toxoplasma Gondii Me49
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ORNITHINE AMINOTRANSFERASE, MITOCHONDRIAL, PUTATIVE
    Chains: A, B
    EC Number: 2.6.1.13
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG28
    Expression System Strain: BL21(DE3)/PMAGIC
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: TGME49_269110
    Organism Scientific: TOXOPLASMA GONDII ME49
    Organism Taxid: 508771

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 14)

Asymmetric/Biological Unit (2, 14)
No.NameCountTypeFull Name
1PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE
2SO412Ligand/IonSULFATE ION

(-) Sites  (14, 14)

Asymmetric Unit (14, 14)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:136 , ALA A:137 , TYR A:171 , TRP A:172 , GLU A:224 , ASP A:257 , ILE A:259 , GLN A:260 , LYS A:286 , HOH A:635 , HOH A:653 , THR B:316 , HOH B:626binding site for residue PLP A 501
02AC2SOFTWARECYS A:264 , LYS A:335 , HOH A:603 , HOH A:642binding site for residue SO4 A 502
03AC3SOFTWAREVAL A:234 , ARG A:355 , ILE A:368 , ARG A:369 , GLY A:370binding site for residue SO4 A 503
04AC4SOFTWAREGLN A:349 , HIS A:421 , ARG A:422 , THR A:425binding site for residue SO4 A 504
05AC5SOFTWAREMET A:133 , GLU A:138 , GLU A:141 , SER A:142 , HIS A:313 , ARG B:174 , THR B:175binding site for residue SO4 A 505
06AC6SOFTWARELEU A:106 , ALA A:108 , TYR B:49 , GLU B:229 , ARG B:409binding site for residue SO4 A 506
07AC7SOFTWARETYR A:49 , LEU A:76 , GLU A:229 , LYS A:401 , ALA B:108binding site for residue SO4 A 507
08AC8SOFTWARETHR A:316 , GLY B:136 , ALA B:137 , TYR B:171 , TRP B:172 , GLU B:224 , ASP B:257 , ILE B:259 , GLN B:260 , LYS B:286 , HOH B:632binding site for residue PLP B 501
09AC9SOFTWAREARG A:90 , ALA A:93 , ALA A:94 , ARG A:97 , GLU A:329 , THR B:20 , ASN B:21binding site for residue SO4 B 502
10AD1SOFTWARELEU A:29 , LEU A:31 , CYS A:40 , TYR A:44 , ARG B:119 , HOH B:602binding site for residue SO4 B 503
11AD2SOFTWAREARG A:174 , THR A:175 , MET B:133 , GLU B:138 , GLU B:141 , SER B:142 , HIS B:313binding site for residue SO4 B 504
12AD3SOFTWAREVAL B:234 , ARG B:355 , ARG B:369 , GLY B:370 , HOH B:634binding site for residue SO4 B 505
13AD4SOFTWARELEU B:269 , LYS B:335 , HOH B:641binding site for residue SO4 B 506
14AD5SOFTWAREARG A:119 , LEU B:31 , CYS B:40 , TYR B:44binding site for residue SO4 B 507

(-) SS Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1A:96 -B:96

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Gly A:192 -Pro A:193
2Gly B:192 -Pro B:193

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZWM)

(-) 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:421
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhh...hhhhhhhhhhhhh........eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhhhh.......ee.hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh........eeeee.......hhhhhhh..hhhhhh........eeee...hhhhhhhhh....eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeee.....hhhhhhhhhhhh.ee.......eeee......hhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zwm A  18 RKTNIEAYRDGLKLKTEEDFFACDRQYVCQNYAVPVVISKGKGARVWDINGNEYYDFLAGVSSLSQGHCHPRVIAALCRQAERLTLTLRAFGNDVTGPACRFMAEMFGYDRVLLMNTGAEAGESALKIARKWAYEVKEIPPDSAKVILCNNNYWGRTITACSSSTTFDCYNNFGPFTPGFELIDYDDVGALEEALKDPNVAAFFVEPIQGEGGVNVPKPGYLKRAHELCRSKNVLLIVDEIQTGLCRTGRLLAADHDEVHPDILLLGKSLSAGVVPISAVMGRADVMDVLKPGTHGSTFGGNPLACAVAVEALTVLKDEKLADRAERLGAQFRDCLRRELYGKVPWIKEIRGRGLLNAVEVDSDAIDPNDVVMKLKENGILSKPTRGRVMRFIPPLVITDEEHRDATTRIIKSFLAVEEER 439
                                    27        37        47  ||    58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368       378       388       398       408       418       428       438 
                                                           50|                                                                                                                                                                                                                                                                                                                                                                                                   
                                                            52                                                                                                                                                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:423
                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhh...hhhhhhhhhhhhh........eeeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh.........ee.hhhhhhhhhhhhhh..eeeee.hhhhhhhhhhhhhhhhhhhh........eeeee.......hhhhhhh..hhhhhh........eeee...hhhhhhhhh....eeeeee..............hhhhhhhhhhhhh..eeeee............hhhhhhh....eeeehhhhhh.....eeeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeeeeee..eeeeee.....hhhhhhhhhhhh.ee.......eeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4zwm B  17 ARKTNIEAYRDGLKLKTEEDFFACDRQYVCQNYAVPVVISKGKGARVWDINGNEYYDFLAGVSSLSQGHCHPRVIAALCRQAERLTLTLRAFGNDVTGPACRFMAEMFGYDRVLLMNTGAEAGESALKIARKWAYEVKEIPPDSAKVILCNNNYWGRTITACSSSTTFDCYNNFGPFTPGFELIDYDDVGALEEALKDPNVAAFFVEPIQGEGGVNVPKPGYLKRAHELCRSKNVLLIVDEIQTGLCRTGRLLAADHDEVHPDILLLGKSLSAGVVPISAVMGRADVMDVLKPGTHGSTFGGNPLACAVAVEALTVLKDEKLADRAERLGAQFRDCLRRELYGKVPWIKEIRGRGLLNAVEVDSDAIDPNDVVMKLKENGILSKPTRGRVMRFIPPLVITDEEHRDATTRIIKSFLAVEEERK 440
                                    26        36        46   ||   57        67        77        87        97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377       387       397       407       417       427       437   
                                                            50|                                                                                                                                                                                                                                                                                                                                                                                                    
                                                             52
   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 4ZWM)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    PLP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
    AC4  [ RasMol ]  +environment [ RasMol ]
    AC5  [ RasMol ]  +environment [ RasMol ]
    AC6  [ RasMol ]  +environment [ RasMol ]
    AC7  [ RasMol ]  +environment [ RasMol ]
    AC8  [ RasMol ]  +environment [ RasMol ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Gly A:192 - Pro A:193   [ RasMol ]  
    Gly B:192 - Pro B:193   [ RasMol ]  
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4zwm
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  S8EY38_TOXGM | S8EY38
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  2.6.1.13
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  S8EY38_TOXGM | S8EY38
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        S8EY38_TOXGM | S8EY38: 4nog 4zlv 5dj9 5e3k 5e5i 5eav 5eqc

(-) Related Entries Specified in the PDB File

4nog
4zlv RELATED ID: CSGID-IDP92102 RELATED DB: TARGETTRACK