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 THE HIS281TYR/ALA460ILE DOUBLE MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
 
Authors :  H. R. Brodkin, M. J. Mcleish
Date :  20 Apr 13  (Deposition) - 15 May 13  (Release) - 15 May 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.24
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Thiamine Diphosphate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  H. R. Brodkin, F. H. Andrews, A. C. Milne, G. A. Petsko, D. Ringe, M. J. Mcleish
Crystal Structure Of The His281Tyr/Ala460Ile Double Mutant Of Benzoylformate Decarboxylase From Pseudomonas Putida
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BENZOYLFORMATE DECARBOXYLASE
    ChainsA, B, C, D
    EC Number4.1.1.7
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET24
    Expression System StrainBL21(DE3)PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneMDLC
    MutationYES
    Organism ScientificPSEUDOMONAS PUTIDA
    Organism Taxid303
    SynonymBFD, BFDC

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 16)

Asymmetric/Biological Unit (4, 16)
No.NameCountTypeFull Name
1CA4Ligand/IonCALCIUM ION
2GOL6Ligand/IonGLYCEROL
3MG2Ligand/IonMAGNESIUM ION
4TPP4Ligand/IonTHIAMINE DIPHOSPHATE

(-) Sites  (16, 16)

Asymmetric Unit (16, 16)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:428 , ASN A:455 , THR A:457 , TPP A:602 , HOH A:703BINDING SITE FOR RESIDUE CA A 601
02AC2SOFTWARETHR 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 , ILE A:460 , CA A:601 , HOH A:708 , ASN C:23 , PRO C:24 , GLY C:25 , GLU C:47 , HIS C:70 , ASN C:77BINDING SITE FOR RESIDUE TPP A 602
03AC3SOFTWAREASN A:117 , LEU A:118 , ARG A:120 , ASN C:117 , LEU C:118 , ARG C:120BINDING SITE FOR RESIDUE MG A 603
04AC4SOFTWAREASP A:18 , ASP A:38 , PHE A:39 , ARG A:40BINDING SITE FOR RESIDUE GOL A 604
05AC5SOFTWAREASP A:364 , ALA A:366 , GLU A:368 , ASP D:18BINDING SITE FOR RESIDUE GOL A 605
06AC6SOFTWAREASN A:363 , ASP A:364 , HOH A:788BINDING SITE FOR RESIDUE GOL A 606
07AC7SOFTWAREASP B:428 , ASN B:455 , THR B:457 , TPP B:602 , HOH B:703BINDING SITE FOR RESIDUE CA B 601
08AC8SOFTWAREGLU B:375 , THR B:377 , SER B:378 , GLY B:401 , LEU B:403 , GLY B:427 , ASP B:428 , GLY B:429 , SER B:430 , TYR B:433 , ASN B:455 , THR B:457 , TYR B:458 , GLY B:459 , ILE B:460 , CA B:601 , HOH B:733 , ASN D:23 , PRO D:24 , GLY D:25 , GLU D:47 , HIS D:70 , ASN D:77BINDING SITE FOR RESIDUE TPP B 602
09AC9SOFTWAREASN B:117 , LEU B:118 , ARG B:120 , ASN D:117 , LEU D:118 , ARG D:120BINDING SITE FOR RESIDUE MG B 603
10BC1SOFTWAREGLN B:421 , PRO B:447 , LEU B:511 , SER B:512 , ALA B:513BINDING SITE FOR RESIDUE GOL B 604
11BC2SOFTWAREASP C:428 , ASN C:455 , THR C:457 , TPP C:602 , HOH C:872BINDING SITE FOR RESIDUE CA C 601
12BC3SOFTWAREASN A:23 , PRO A:24 , GLY A:25 , GLU A:47 , HIS A:70 , ASN A:77 , THR C:377 , SER C:378 , GLY C:401 , LEU C:403 , GLY C:427 , ASP C:428 , GLY C:429 , SER C:430 , TYR C:433 , ASN C:455 , THR C:457 , TYR C:458 , GLY C:459 , ILE C:460 , LEU C:461 , CA C:601 , HOH C:709 , HOH C:872BINDING SITE FOR RESIDUE TPP C 602
13BC4SOFTWAREGLU B:128 , PRO B:129 , ALA B:130 , ARG C:101 , GLU C:128 , PRO C:129BINDING SITE FOR RESIDUE GOL C 603
14BC5SOFTWAREASP D:428 , ASN D:455 , THR D:457 , TPP D:602 , HOH D:706BINDING SITE FOR RESIDUE CA D 601
15BC6SOFTWAREASN B:23 , PRO B:24 , GLY B:25 , GLU B:47 , HIS B:70 , ASN B:77 , THR D:377 , SER D:378 , GLY D:401 , LEU D:403 , GLY D:427 , ASP D:428 , GLY D:429 , SER D:430 , TYR D:433 , ASN D:455 , THR D:457 , TYR D:458 , GLY D:459 , ILE D:460 , LEU D:461 , CA D:601 , HOH D:706 , HOH D:721BINDING SITE FOR RESIDUE TPP D 602
16BC7SOFTWAREARG A:101 , GLU A:128 , ALA A:130 , ARG D:101 , GLU D:128 , PRO D:129 , ALA D:130BINDING SITE FOR RESIDUE GOL D 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4K9P)

(-) Cis Peptide Bonds  (12, 12)

Asymmetric/Biological Unit
No.Residues
1Arg A:120 -Pro A:121
2Ala A:149 -Pro A:150
3Val A:277 -Phe A:278
4Arg B:120 -Pro B:121
5Ala B:149 -Pro B:150
6Val B:277 -Phe B:278
7Arg C:120 -Pro C:121
8Ala C:149 -Pro C:150
9Val C:277 -Phe C:278
10Arg D:120 -Pro D:121
11Ala D:149 -Pro D:150
12Val D:277 -Phe D:278

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4K9P)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4K9P)

(-) Exons   (0, 0)

(no "Exon" information available for 4K9P)

(-) 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:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4k9pa1 A:2-181 automated matches                                                                                                                                                   d4k9pa2 A:182-341 Benzoylformate decarboxylase                                                                                                                  d4k9pa3 A:342-526 automated matches                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhh....eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9p A   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYYQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGILRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSP 526
                                    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     

Chain B from PDB  Type:PROTEIN  Length:525
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains d4k9pb1 B:2-181 automated matches                                                                                                                                                   d4k9pb2 B:182-341 Benzoylformate decarboxylase                                                                                                                  d4k9pb3 B:342-526 automated matches                                                                                                                                                       SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhh....hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhh...eee...............eeee...hhhhhhhhh....eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhh..........................hhhhhhhhhhhhh....eeeee...hhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhh....eeeeee.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9p B   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYYQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGILRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVSP 526
                                    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     

Chain C from PDB  Type:PROTEIN  Length:524
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4k9pc1 C:2-181 automated matches                                                                                                                                                   d4k9pc2 C:182-341 Benzoylformate decarboxylase                                                                                                                  d4k9pc3 C:342-525 automated matches                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhh..eeeeeee.hhhhhh........hhhhh......eee...hhhhhhhhhhhhhhhhhh.....eeeeee........hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9p C   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYYQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGILRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVS 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    

Chain D from PDB  Type:PROTEIN  Length:524
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains d4k9pd1 D:2-181 automated matches                                                                                                                                                   d4k9pd2 D:182-341 Benzoylformate decarboxylase                                                                                                                  d4k9pd3 D:342-525 automated matches                                                                                                                                                      SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh...eeee..hhhhhhhhh......eeee..hhhhhhhhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhh...eeeeeee.hhhhhh........hhhhh.......ee...hhhhhhhhhhhhhhhhhh.....eeeeee.hhhhh..hhhhhhhh...ee..eeehhhhhhhhhhhhhhh...eeeehhhhhhh.hhhhhhhhhhhhh..eee...............eeee...hhhhhhhhhh...eeeee....................eeeeee.hhhhhhhh...eeee.hhhhhhhhhhhhh........................hhhhhhhhhhhhh....eeeeehhhhhhhhhhhh.......eee.......hhhhhhhhhhhhh....eeeeee.hhhhhhhhhhhhhhhh....eeeeee...hhhhhhhhhhh.............hhhhhhhhh..eeeee.hhhhhhhhhhhhhhh...eeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4k9p D   2 ASVHGTTYELLRRQGIDTVFGNPGSNELPFLKDFPEDFRYILALQEACVVGIADGYAQASRKPAFINLHSAAGTGNAMGALSNAWNSHSPLIVTAGQQTRAMIGVEALLTNVDAANLPRPLVKWSYEPASAAEVPHAMSRAIHMASMAPQGPVYLSVPYDDWDKDADPQSHHLFDRHVSSSVRLNDQDLDILVKALNSASNPAIVLGPDVDAANANADCVMLAERLKAPVWVAPSAPRCPFPTRHPCFRGLMPAGIAAISQLLEGHDVVLVIGAPVFRYYQYDPGQYLKPGTRLISVTCDPLEAARAPMGDAIVADIGAMASALANLVEESSRQLPTAAPEPAKVDQDAGRLHPETVFDTLNDMAPENAIYLNESTSTTAQMWQRLNMRNPGSYYFCAAGGLGFALPAAIGVQLAEPERQVIAVIGDGSANYSISALWTAAQYNIPTIFVIMNNGTYGILRWFAGVLEAENVPGLDVPGIDFRALAKGYGVQALKADNLEQLKGSLQEALSAKGPVLIEVSTVS 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  (2, 12)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4K9P)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4K9P)

(-) Gene Ontology  (10, 10)

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
    CA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TPP  [ 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 ]
 
  Cis Peptide Bonds
    Ala A:149 - Pro A:150   [ RasMol ]  
    Ala B:149 - Pro B:150   [ RasMol ]  
    Ala C:149 - Pro C:150   [ RasMol ]  
    Ala D:149 - Pro D:150   [ RasMol ]  
    Arg A:120 - Pro A:121   [ RasMol ]  
    Arg B:120 - Pro B:121   [ RasMol ]  
    Arg C:120 - Pro C:121   [ RasMol ]  
    Arg D:120 - Pro D:121   [ RasMol ]  
    Val A:277 - Phe A:278   [ RasMol ]  
    Val B:277 - Phe B:278   [ RasMol ]  
    Val C:277 - Phe C:278   [ RasMol ]  
    Val D:277 - Phe D:278   [ RasMol ]  
 

(-) 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
  4k9p
    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 4mpj 4mpp 4mpr 4mq5 4mzx 4qel 5dei 5dgd 5dgt

(-) Related Entries Specified in the PDB File

4k9k THE HIS281TYR MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9l THE HIS281THR MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9m THE HIS281ASN MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9n THE ALA460ILE MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA
4k9o THE PHE397ALA MUTANT OF BENZOYLFORMATE DECARBOXYLASE FROM PSEUDOMONAS PUTIDA