Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asymmetric Unit
(-)Asym. Unit - sites
(-)Biological Unit 1
(-)Biol. Unit 1 - sites
collapse expand < >
Image Asymmetric Unit
Asymmetric Unit  (Jmol Viewer)
Image Asym. Unit - sites
Asym. Unit - sites  (Jmol Viewer)
Image Biological Unit 1
Biological Unit 1  (Jmol Viewer)
Image Biol. Unit 1 - sites
Biol. Unit 1 - sites  (Jmol Viewer)

(-) Description

Title :  R66A MUTANT OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES
 
Authors :  M. Martinez-Julvez, B. Herguedas, M. Milagros
Date :  05 Sep 14  (Deposition) - 08 Apr 15  (Release) - 17 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.34
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (3x)
Keywords :  Transferase, Riboflavin Kinase, Nucleotide-Binding, Atp-Binding, Multifunctional Enzyme, Nucleotidyltransferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. Serrano, M. Sebastian, S. Arilla-Luna, S. Baquedano, M. C. Pallares, A. Lostao, B. Herguedas, A. Velazquez-Campoy, M. Martinez-Julvez, M. Medina
Quaternary Organization In A Bifunctional Prokaryotic Fad Synthetase: Involvement Of An Arginine At Its Adenylyltransferase Module On The Riboflavin Kinase Activity.
Biochim. Biophys. Acta V. 1854 897 2015
PubMed-ID: 25801930  |  Reference-DOI: 10.1016/J.BBAPAP.2015.03.005

(-) Compounds

Molecule 1 - RIBOFLAVIN BIOSYNTHESIS PROTEIN RIBF
    Chains: A, B
    EC Number: 2.7.1.26, 2.7.7.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Mutation: YES
    Organism Scientific: CORYNEBACTERIUM AMMONIAGENES
    Organism Taxid: 1697

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (3x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1PPV2Ligand/IonPYROPHOSPHATE
2SO42Ligand/IonSULFATE ION
Biological Unit 1 (2, 12)
No.NameCountTypeFull Name
1PPV6Ligand/IonPYROPHOSPHATE
2SO46Ligand/IonSULFATE ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:73 , LEU A:74 , TYR B:279BINDING SITE FOR RESIDUE SO4 A1339
2AC2SOFTWARETYR A:279 , HOH A:2061 , THR B:73 , LEU B:74BINDING SITE FOR RESIDUE SO4 B1339
3AC3SOFTWAREGLY A:22 , VAL A:23 , PHE A:24 , HIS A:28 , HIS A:31 , ASN A:125 , SER A:163 , SER A:164BINDING SITE FOR RESIDUE PPV A1340
4AC4SOFTWAREGLY B:22 , VAL B:23 , PHE B:24 , HIS B:28 , HIS B:31 , ASN B:125 , SER B:163 , SER B:164 , HOH B:2005BINDING SITE FOR RESIDUE PPV B1340

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Asp A:55 -Pro A:56
2Gly A:198 -Arg A:199
3Gly A:261 -Asp A:262
4Asp B:55 -Pro B:56
5Pro B:258 -Thr B:259
6Glu B:263 -Gln B:264

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4UZE)

(-) Sequences/Alignments

Asymmetric 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:338
                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhh......eeeee......hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.........hhhhhhhhhhhh...eeeee.........hhhhhhhhhh.....eeeeeee...eehhhhheehhhhhhhh....eeeee...ee..ee.hhhhhhhhhhhhhhhhhhhhhh..eeeeee................eeeee.........eeeeeeeee.......ee......eeeeeeeeee........eeeeeee....ee....eeeeeeeeeee......hhhhhhhhhhhhhhhhhhhhhhhhhh.......ee..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uze A   1 MDIWYGTAAVPKDLDNSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRAAPLGITTLAERFALAESFGIDGVLVIDFTRELSGTSPEKYVEFLLEDTLHASHVVVGANFTFGENAAGTADSLRQICQSRLTVDVIDLLDDEGVRISSTTVREFLSEGDVARANWALGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTFGDEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES 338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330        


Chain B from PDB  Type:PROTEIN  Length:335
                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee.hhhh......eeeee......hhhhhhhhhhhhhhhhhh..eeeeeee..hhhhhhh.........hhhhhhhhhhhh...eeeee.........hhhhhhhhhh.....eeeeeee...eehhhhheehhhhhhhh.......ee..eee..eeehhhhhhhhhhh.hhhhhhhhhh..eeeeee................eeeee.........eeeeeeeee.......ee......eeeeeeeeee.....eeeeeee....ee....eeeeeeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhh........ee..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4uze B   1 MDIWYGTAAVPKDLDNSAVTIGVFDGVHRGHQKLINATVEKAREVGAKAIMVTFDPHPVSVFLPRAAPLGITTLAERFALAESFGIDGVLVIDFTRELSGTSPEKYVEFLLEDTLHASHVVVGANFTFGENAAGTADSLRQICQSRLTVDVIDLLDDEGVRISSTTVREFLSEGDVARANWALGRHFYVTGPVVRGAGRGGKELGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNMEPEVAYAAAISVGTNPTEQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDSVEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQAES 338
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       263       273       283       293       303       313       323       333     
                                                                                                                                                                                                                                                                                            259|                                                                           
                                                                                                                                                                                                                                                                                             263
   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 4UZE)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric 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
    PPV  [ 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 ]
 
  Cis Peptide Bonds
    Asp A:55 - Pro A:56   [ RasMol ]  
    Asp B:55 - Pro B:56   [ RasMol ]  
    Glu B:263 - Gln B:264   [ RasMol ]  
    Gly A:198 - Arg A:199   [ RasMol ]  
    Gly A:261 - Asp A:262   [ RasMol ]  
    Pro B:258 - Thr B:259   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym. Unit PNG format | Asym. Unit - sites PNG format | Biol. Unit 1 PNG format | Biol. Unit 1 - 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
  4uze
    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
  RIBF_CORAM | Q59263
    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)
  2.7.1.26
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
  2.7.7.2
    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
  RIBF_CORAM | Q59263
    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
        RIBF_CORAM | Q59263: 2x0k 3zug 4uzf 5a88 5a89 5a8a 5fnz 5fo0 5fo1

(-) Related Entries Specified in the PDB File

4uzf R66E MUTANT OF FAD SYNTHETASE FROM CORYNEBACTERIUM AMMONIAGENES