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 :  CRYSTAL STRUCTURE OF DOMAIN-DUPLICATED SYNTHETIC CLASS II KETOL-ACID REDUCTOISOMERASE 2IA_KARI-DD
 
Authors :  J. K. B. Cahn, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold
Date :  07 Oct 15  (Deposition) - 23 Dec 15  (Release) - 06 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.94
Chains :  Asym./Biol. Unit :  A
Keywords :  Ketol-Acid Reductiosomerase, Protein Knot, Psuedodimer, Protein Engineering, Chimera Protein, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. K. Cahn, S. Brinkmann-Chen, A. R. Buller, F. H. Arnold
Artificial Domain Duplication Replicates Evolutionary History Of Ketol-Acid Reductoisomerases.
Protein Sci. V. 25 1241 2016
PubMed-ID: 26644020  |  Reference-DOI: 10.1002/PRO.2852

(-) Compounds

Molecule 1 - KETOL-ACID REDUCTOISOMERASE
    Chains: A
    EC Number: 1.1.1.86
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET22B(+)
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 1-335,189-335
    Gene: ILVC, IGAG_1561
    Organism Scientific: IGNISPHAERA AGGREGANS (STRAIN DSM 17230 / JCM 13409 / AQ1.S1)
    Organism Taxid: 583356
    Strain: DSM 17230 / JCM 13409 / AQ1.S1
    Synonym: ACETOHYDROXY-ACID ISOMEROREDUCTASE,ALPHA-KETO-BETA- HYDROXYLACYL REDUCTOISOMERASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 6)

Asymmetric/Biological Unit (5, 6)
No.NameCountTypeFull Name
140E1Ligand/IonOXO(PROPAN-2-YLAMINO)ACETIC ACID
2EDO1Ligand/Ion1,2-ETHANEDIOL
3GOL1Ligand/IonGLYCEROL
4MG2Ligand/IonMAGNESIUM ION
5NAP1Ligand/IonNADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLY A:24 , TYR A:25 , GLY A:26 , SER A:27 , GLN A:28 , LEU A:47 , SER A:53 , LEU A:80 , VAL A:81 , PRO A:82 , ASP A:83 , VAL A:85 , GLN A:86 , ALA A:107 , HIS A:108 , SER A:132 , PRO A:133 , GLY A:134 , ALA A:397 , VAL A:398 , SER A:399 , 40E A:504 , EDO A:505 , HOH A:613 , HOH A:641 , HOH A:670 , HOH A:672 , HOH A:686 , HOH A:704 , HOH A:709 , HOH A:712 , HOH A:728 , HOH A:751 , HOH A:775 , HOH A:802binding site for residue NAP A 501
2AC2SOFTWAREASP A:191 , GLU A:195 , MG A:503 , 40E A:504 , HOH A:683 , HOH A:775binding site for residue MG A 502
3AC3SOFTWAREASP A:191 , MG A:502 , 40E A:504 , HOH A:601 , HOH A:627 , HOH A:638 , HOH A:675binding site for residue MG A 503
4AC4SOFTWAREPRO A:133 , ASP A:191 , GLU A:195 , GLU A:378 , VAL A:398 , SER A:399 , ALA A:402 , NAP A:501 , MG A:502 , MG A:503 , HOH A:601 , HOH A:638 , HOH A:675 , HOH A:683 , HOH A:775binding site for residue 40E A 504
5AC5SOFTWARELEU A:23 , GLY A:46 , LEU A:47 , GLU A:48 , THR A:67 , VAL A:81 , LEU A:89 , NAP A:501 , HOH A:728binding site for residue EDO A 505
6AC6SOFTWAREASP A:7 , LEU A:12 , LYS A:170 , ARG A:176 , HOH A:676binding site for residue GOL A 506

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E4R)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E4R)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E4R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E4R)

(-) Exons   (0, 0)

(no "Exon" information available for 5E4R)

(-) 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:466
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eehhhhh.hhhhh..eeeee..hhhhhhhhhhhhhh..eeeeee...hhhhhhhhhh....eehhhhhhhh.eeee..hhhhhhhhhhhhh........eeee..hhhhhh..........eeeeee..hhhhhhhhhhh.....eeeeeee....hhhhhhhhhhhhhhhhhh.eee.hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5e4r A   2 AKIYKDEDISLEPIKNKTIAILGYGSQGRAWALNLRDSGLNVVVGLERQGDSWRRAIDDGFKPMYTKDAVAIADIIVFLVPDMVQKSLWLNSVKDFMKKGADLVFAHGFNIHFKIIEPPKDSDVYMIAPKSPGPIVRRSYEMGGGVPALVAVYQNVSGEALQKALAIAKGIGCARAGVIESTFKEETETDLFGEQVILVGGIMELIKASFETLVEEGYQPEVAYFETVNELKLIVDLIYEKGLTGMLRAVSDTAKYGGITVGKFIIDKSVRDKMKIVLERIRSGEFAREWIKEYERGMPTVFKELSELEGSTIETVGRKLREMMFRGMLFGEQVILVGGIMELIKASFETLVEEGYQPEVAYFETVNELKLIVDLIYEKGLTGMLRAVSDTAKYGGITVGKFIIDKSVRDKMKIVLERIRSGEFAREWIKEYERGMPTVFKELSELEGSTIETVGRKLREMMFRGM 476
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       340       350       360       370       380       390       400       410       420       430       440       450       460       470      
                                                                                                                                                                                                                                                                                                                                                                 329|                                                                                                                                         
                                                                                                                                                                                                                                                                                                                                                                  339
   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 5E4R)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E4R)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E4R)

(-) Gene Ontology  (9, 9)

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
    40E  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NAP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5e4r)
 

(-) 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
  5e4r
    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
  ILVC_IGNAA | E0SRA9
    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)
  1.1.1.86
    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
  ILVC_IGNAA | E0SRA9
    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
        ILVC_IGNAA | E0SRA9: 4xdz 4xeh

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5E4R)