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 :  E198A MUTANT OF N-ACETYLORNITHINE AMINOTRANSFERASE FROM SALMONELLA TYPHIMURIUM
 
Authors :  S. Bisht, S. R. Bharath, M. R. N. Murthy
Date :  27 Feb 13  (Deposition) - 26 Mar 14  (Release) - 26 Mar 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.55
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Plp Dependent Fold Type I Sub Class Ii Family Aminotransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Bisht, S. R. Bharath, M. R. N. Murthy
Conformational Transitions, Ligand Specificity And Catalysi In N-Acetylornithine Aminotransferase: Implications On Drug Designing And Rational Enzyme Engineering In Omega Aminotransferases
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - ACETYLORNITHINE/SUCCINYLDIAMINOPIMELATE AMINOTRANSFERASE
    Chains: A, B
    EC Number: 2.6.1.11, 2.6.1.17
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PRSET C
    Expression System Strain: BL21 (DE3) ROSETTA
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: ARGD, DAPC, DTU, STM3468
    Mutation: YES
    Organism Scientific: SALMONELLA TYPHIMURIUM
    Organism Taxid: 99287
    Strain: LT2
    Synonym: ACOAT, DAPATASE, SUCCINYLDIAMINOPIMELATE TRANSFERASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 18)

Asymmetric/Biological Unit (4, 18)
No.NameCountTypeFull Name
1ACT5Ligand/IonACETATE ION
2EDO9Ligand/Ion1,2-ETHANEDIOL
3NA2Ligand/IonSODIUM ION
4PLP2Ligand/IonPYRIDOXAL-5'-PHOSPHATE

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:107 , GLY A:108 , THR A:109 , ASN A:112 , PHE A:141 , HIS A:142 , GLU A:193 , ASP A:226 , VAL A:228 , GLN A:229 , LYS A:255 , HOH A:707 , HOH A:747 , HOH A:748 , THR B:284 , HOH B:683 , HOH B:684BINDING SITE FOR RESIDUE PLP A 501
02AC2SOFTWAREGLY A:57 , HIS A:58 , CYS A:59 , HIS A:60 , LEU A:63 , GLY A:259 , HOH A:627 , TRP B:75BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREHIS A:76 , THR A:77 , SER A:78 , PHE A:81 , ACT A:504 , HOH A:626 , HOH A:662 , ASP B:46 , GLY B:50 , HIS B:58BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWARESER A:78 , VAL A:80 , PHE A:81 , EDO A:503 , HOH A:626 , HOH A:663 , ALA B:48 , GLY B:50 , LEU B:369BINDING SITE FOR RESIDUE ACT A 504
05AC5SOFTWAREMET A:105 , GLU A:110 , GLU A:113 , THR A:114 , HOH A:770 , HOH A:894 , HOH A:936 , THR B:109 , ARG B:144 , SER B:145 , HOH B:781BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWARELYS A:133 , ILE A:168 , ILE A:169 , HIS A:170 , HOH A:666 , HOH A:670 , HOH A:737 , HOH A:847BINDING SITE FOR RESIDUE ACT A 506
07AC7SOFTWAREPRO A:305 , HOH A:876 , HOH A:962BINDING SITE FOR RESIDUE EDO A 507
08AC8SOFTWAREILE A:94 , THR A:97 , PHE A:98 , ALA A:99 , HOH A:801 , HOH A:824BINDING SITE FOR RESIDUE NA A 508
09AC9SOFTWAREASN A:79 , MET A:105 , ASN A:106 , GLY A:286 , GLY A:287 , ASN A:288 , HOH A:647 , HOH A:877 , HOH A:920BINDING SITE FOR RESIDUE ACT A 509
10BC1SOFTWARESER A:128 , LYS A:131 , ASP A:185 , HIS A:186BINDING SITE FOR RESIDUE EDO A 510
11BC2SOFTWAREHOH A:733 , SER B:107 , GLY B:108 , THR B:109 , ASN B:112 , PHE B:141 , HIS B:142 , GLU B:193 , ASP B:226 , VAL B:228 , GLN B:229 , LYS B:255 , HOH B:783 , HOH B:933 , HOH B:948BINDING SITE FOR RESIDUE PLP B 501
12BC3SOFTWARETRP A:75 , GLY B:57 , CYS B:59 , HIS B:60 , LEU B:63 , GLY B:259 , HOH B:639BINDING SITE FOR RESIDUE EDO B 502
13BC4SOFTWAREPHE A:13 , ASN B:79 , THR B:82 , ALA B:86 , GLY B:287 , HOH B:702 , HOH B:805BINDING SITE FOR RESIDUE EDO B 503
14BC5SOFTWAREVAL A:80 , ASN B:370 , ARG B:377 , HOH B:777 , HOH B:939BINDING SITE FOR RESIDUE EDO B 504
15BC6SOFTWAREILE B:94 , THR B:97 , PHE B:98 , ALA B:99 , HOH B:745 , HOH B:847BINDING SITE FOR RESIDUE NA B 505
16BC7SOFTWARELYS B:133 , ILE B:168 , ILE B:169 , HIS B:170 , HOH B:653 , HOH B:712 , HOH B:726 , HOH B:756BINDING SITE FOR RESIDUE ACT B 506
17BC8SOFTWAREVAL A:80 , ALA B:22 , PRO B:23 , PHE B:26 , TYR B:359 , ALA B:362 , HOH B:646 , HOH B:852BINDING SITE FOR RESIDUE ACT B 507
18BC9SOFTWAREHIS B:60 , HOH B:799BINDING SITE FOR RESIDUE EDO B 508

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4JEY)

(-) 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:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4jeya_ A: automated matches                                                                                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhh..........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhh.hhhhhh........eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh....eeeeehhhhhh.....ee..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee.hhhh.hhhhhhhhhhhh.ee.ee....eeee......hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jey A   6 TAITRATFDEVILPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGAGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHGSTYGGNPLACAVAGATFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVAL 406
                                    15        25        35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275 ||    289       299       309       319       329       339       349       359       369       379       389       399       
                                                                                                                                                                                                                                                                                                         277|                                                                                                                            
                                                                                                                                                                                                                                                                                                          282                                                                                                                            


Chain B from PDB  Type:PROTEIN  Length:388
                                                                                                                                                                                                                                                                                                                                                                                                                                    
               SCOP domains d4jeyb_ B: automated matches                                                                                                                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeee..eeee....eeee.hhhhhh......hhhhhhhhhhhhh..........hhhhhhhhhhhhhhh...eeeee.hhhhhhhhhhhhhhhhhhhhh.....eeeee.......hhhhhhhh.hhhhhh........eeee...hhhhhhhhh...eeeeee..ee.....ee.hhhhhhhhhhhhhhhh.eeeee............hhhhhhh....eeeehhhhhh....eeeeehhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee..eeeeee.hhhh.hhhhhhhhhhhh.ee.ee....eeee......hhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4jey B  18 LPVYAPADFIPVKGKGSRVWDQQGKEYIDFAGGIAVTALGHCHPALVEALKSQGETLWHTSNVFTNEPALRLGRKLIDATFAERVLFMNSGTEANETAFKLARHYACVRHSPFKTKIIAFHNAFHGRSLFTVSVGGQPKYSDGFGPKPADIIHVPFNDLHAVKAVMDDHTCAVVVEPIQGAGGVQAATPEFLKGLRDLCDEHQALLVFDEVQCGMGRTGDLFAYMHYGVTPDILTSAKALGGGFPVSAMLTTQEIASAFHVGSHGSTYGGNPLACAVAGATFDIINTPEVLQGIHTKRQQFVQHLQAIDEQFDIFSDIRGMGLLIGAELKPKYKGRARDFLYAGAEAGVMVLNAGADVMRFAPSLVVEEADIHEGMQRFAQAVGKVVA 405
                                    27        37        47        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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (15, 15)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PLP  [ 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 ]
    BC1  [ RasMol ]  +environment [ RasMol ]
    BC2  [ RasMol ]  +environment [ RasMol ]
    BC3  [ RasMol ]  +environment [ RasMol ]
    BC4  [ RasMol ]  +environment [ RasMol ]
    BC5  [ RasMol ]  +environment [ RasMol ]
    BC6  [ RasMol ]  +environment [ RasMol ]
    BC7  [ RasMol ]  +environment [ RasMol ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4jey)
 

(-) 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
  4jey
    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
  ARGD_SALTY | P40732
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.6.1.11
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.6.1.17
    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
  ARGD_SALTY | P40732
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        ARGD_SALTY | P40732: 2pb0 2pb2 4jev 4jew 4jex 4jez 4jf0 4jf1

(-) Related Entries Specified in the PDB File

2pb0 2pb2 4jev 4jew 4jex 4jez 4jf0 4jf1