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 :  BENZOYLFORMATE DECARBOXYLASE H70A MUTANT AT PH 8.5 FROM PSEUDOMONAS PUTIDA
 
Authors :  A. K. Bera, M. S. Hasson
Date :  28 Aug 15  (Deposition) - 23 Sep 15  (Release) - 23 Sep 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.08
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (4x)
Keywords :  Benzoylformate Decarboxylase Thiamin Thiazolone Diphosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  A. K. Bera, M. S. Hasson
Benzoylformate Decarboxylase H70A Mutant At Ph 8. 5 From Pseudomonas Putida
To Be Published
PubMed: search
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
    ChainsA
    EC Number4.1.1.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPREP7
    Expression System Taxid562
    GeneMDLC
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    SynonymBFDC

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit A
Biological Unit 1 (4x)A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric Unit (3, 5)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2MG1Ligand/IonMAGNESIUM ION
3TZD1Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2MG-1Ligand/IonMAGNESIUM ION
3TZD4Ligand/Ion2-{3-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-4-METHYL-2-OXO-2,3-DIHYDRO-1,3-THIAZOL-5-YL}ETHYL TRIHYDROGENDIPHOSPHATE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:117 , LEU A:118 , ARG A:120binding site for residue MG A 601
2AC2SOFTWAREASP A:428 , ASN A:455 , THR A:457 , TZD A:605 , HOH A:770binding site for residue CA A 602
3AC3SOFTWAREGLU A:37 , ASP A:364 , HOH A:884 , HOH A:1070 , HOH A:1212 , HOH A:1217 , HOH A:1245 , HOH A:1368binding site for residue CA A 603
4AC4SOFTWAREASP A:347 , ALA A:416 , HOH A:935 , HOH A:1019 , HOH A:1155 , HOH A:1204 , HOH A:1228 , HOH A:1244binding site for residue CA A 604
5AC5SOFTWAREASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , ALA A:70 , ASN A:77 , THR A:377 , SER A:378 , GLY A:401 , LEU A:403 , GLY A:427 , ASP A:428 , GLY A:429 , SER A:430 , TYR A:433 , ASN A:455 , THR A:457 , TYR A:458 , GLY A:459 , ALA A:460 , CA A:602 , HOH A:707 , HOH A:712 , HOH A:755binding site for residue TZD A 605

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (3, 3)

Asymmetric Unit
No.Residues
1Arg A:120 -Pro A:121
2Ala A:149 -Pro A:150
3Val A:277 -Phe A:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5DGT)

(-) 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:524
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeehhhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh..........hhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhhh...eeeeee...hhhhhhhhhhhh............hhhhhhhhhh.eeeee.hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5dgt A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLASAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYHQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGALRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVS 525
                                    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       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521    

   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 5DGT)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (10, 10)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TZD  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:149 - Pro A:150   [ RasMol ]  
    Arg A:120 - Pro A:121   [ RasMol ]  
    Val A:277 - Phe A:278   [ 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
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  5dgt
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  MDLC_PSEPU | P20906
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  4.1.1.7
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  MDLC_PSEPU | P20906
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        MDLC_PSEPU | P209061bfd 1mcz 1pi3 1po7 1q6z 1yno 2fn3 2fwn 2v3w 3f6b 3f6e 3fsj 3fzn 4gg1 4gm0 4gm1 4gm4 4gp9 4gpe 4jd5 4ju8 4ju9 4jua 4jub 4juc 4jud 4juf 4k9k 4k9l 4k9m 4k9n 4k9o 4k9p 4mpj 4mpp 4mpr 4mq5 4mzx 4qel 5dei 5dgd

(-) Related Entries Specified in the PDB File

5dei 5dgd