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 :  AEROCOCCUS VIRIDANS L-LACTATE OXIDASE Y191F MUTANT
 
Authors :  D. Rainer, B. Nidetzky, D. K. Wilson
Date :  04 Mar 15  (Deposition) - 26 Aug 15  (Release) - 11 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Flavin, Oxidase, Tim Barrel, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Stoisser, M. Klimacek, D. K. Wilson, B. Nidetzky
Speeding Up The Product Release: A Second-Sphere Contribution From Tyr191 To The Reactivity Of L-Lactate Oxidase Revealed In Crystallographic And Kinetic Studies Of Site-Directed Variants.
Febs J. V. 282 4130 2015
PubMed-ID: 26260739  |  Reference-DOI: 10.1111/FEBS.13409

(-) Compounds

Molecule 1 - LACTATE OXIDASE
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21
    Expression System Taxid: 511693
    Organism Scientific: AEROCOCCUS VIRIDANS
    Organism Taxid: 1377

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric/Biological Unit (2, 8)
No.NameCountTypeFull Name
1FMN4Ligand/IonFLAVIN MONONUCLEOTIDE
2PYR4Ligand/IonPYRUVIC ACID

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREILE A:41 , ALA A:92 , PRO A:93 , ILE A:94 , ALA A:95 , SER A:122 , GLN A:144 , TYR A:146 , THR A:172 , LYS A:241 , SER A:263 , HIS A:265 , GLY A:266 , ARG A:268 , ASP A:296 , SER A:297 , GLY A:298 , VAL A:299 , ARG A:300 , GLY A:319 , ARG A:320 , PYR A:402 , HOH A:517 , HOH A:519 , HOH A:579binding site for residue FMN A 401
2AC2SOFTWARETYR A:40 , ALA A:95 , TYR A:124 , TYR A:146 , ARG A:181 , TYR A:215 , HIS A:265 , ARG A:268 , FMN A:401binding site for residue PYR A 402
3AC3SOFTWAREILE B:41 , PRO B:93 , ILE B:94 , ALA B:95 , SER B:122 , GLN B:144 , TYR B:146 , THR B:172 , LYS B:241 , SER B:263 , HIS B:265 , GLY B:266 , ARG B:268 , ASP B:296 , SER B:297 , GLY B:298 , VAL B:299 , ARG B:300 , GLY B:319 , ARG B:320 , PYR B:402 , HOH B:529 , HOH B:538 , HOH B:549binding site for residue FMN B 401
4AC4SOFTWARETYR B:40 , ALA B:95 , TYR B:124 , TYR B:146 , ARG B:181 , LEU B:211 , TYR B:215 , HIS B:265 , ARG B:268 , FMN B:401binding site for residue PYR B 402
5AC5SOFTWARETYR C:40 , ILE C:41 , ALA C:92 , PRO C:93 , ILE C:94 , ALA C:95 , SER C:122 , GLN C:144 , TYR C:146 , THR C:172 , LYS C:241 , SER C:263 , HIS C:265 , GLY C:266 , ARG C:268 , ASP C:296 , SER C:297 , GLY C:298 , ARG C:300 , GLY C:319 , ARG C:320 , PYR C:402 , HOH C:555 , HOH C:585 , HOH C:625binding site for residue FMN C 401
6AC6SOFTWARETYR C:40 , ALA C:95 , TYR C:124 , TYR C:146 , ARG C:181 , LEU C:211 , TYR C:215 , HIS C:265 , ARG C:268 , FMN C:401binding site for residue PYR C 402
7AC7SOFTWARETYR D:40 , ILE D:41 , ALA D:92 , PRO D:93 , ILE D:94 , ALA D:95 , SER D:122 , GLN D:144 , TYR D:146 , THR D:172 , LYS D:241 , SER D:263 , HIS D:265 , GLY D:266 , ARG D:268 , ASP D:296 , SER D:297 , GLY D:298 , ARG D:300 , GLY D:319 , ARG D:320 , PYR D:402 , HOH D:519 , HOH D:526 , HOH D:532binding site for residue FMN D 401
8AC8SOFTWARETYR D:40 , TYR D:124 , TYR D:146 , ARG D:181 , LEU D:211 , TYR D:215 , HIS D:265 , ARG D:268 , FMN D:401binding site for residue PYR D 402

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4YL2)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YL2)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4YL2)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4YL2)

(-) Exons   (0, 0)

(no "Exon" information available for 4YL2)

(-) 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:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...ee...............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhhh.........hhhhh.......hhhhhhhhh....hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....ee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yl2 A   8 YNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHATKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKGDGATAIILTADSTVSGNRDRDVKNKFVFPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAAHSGLPVFVKGIQHPEDADMAIKAGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    17        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       


Chain B from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhh..........hhhhh.......hhhhhhhhh....hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh...eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yl2 B   8 YNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHATKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKGDGATAIILTADSTVSGNRDRDVKNKFVFPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAAHSGLPVFVKGIQHPEDADMAIKAGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    17        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       


Chain C from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ................hhhhhhhh..hhhhhhhhhh....hhhhhhhhhh...eee..............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhh.......hhhhhhhhh......hhhhhhhhh....hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhh..eee....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yl2 C   8 YNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHATKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKGDGATAIILTADSTVSGNRDRDVKNKFVFPFGMPIVQRYLRGTAEGMSLNNIYGASKQKISPRDIEEIAAHSGLPVFVKGIQHPEDADMAIKAGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    17        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       


Chain D from PDB  Type:PROTEIN  Length:365
                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............hhhhhhhhh...hhhhhhhhhh....hhhhhhhhhh...ee...............eee..eee...eee....hhhhh..hhhhhhhhhhhhhh..eeee.....hhhhhhhhhh...eeeee....hhhhhhhhhhhhhhhh...eeee........hhhhhhh.......hhhhhhhh.....hhhhhhhhh....hhhhhhhhhhhhh..eeeeee.hhhhhhhhhhh...eeee.hhhhh......hhhhhhhhhhhhhh....eee.....hhhhhhhhhhh...eeeehhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhh....ee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4yl2 D   8 YNAPSEIKYIDVVNTYDLEEEASKVVPHGGFNYIAGASGDEWTKRANDRAWKHKLLYPRLAQDVEAPDTSTEILGHKIKAPFIMAPIAAHGLAHATKEAGTARAVSEFGTIMSISAYSGATFEEISEGLNGGPRWFQIYMAKDDQQNRDILDEAKGDGATAIILTADSTVSGNRDRDVKNKFVFPFGMPIVQRYLTAEGMSLNNIYGASKQKISPRDIEEIAAHSGLPVFVKGIQHPEDADMAIKAGASGIWVSNHGARQLYEAPGSFDTLPAIAERVNKRVPIVFDSGVRRGEHVAKALASGADVVALGRPVLFGLALGGWQGAYSVLDYFQKDLTRVMQLTGSQNVEDLKGLDLFDNPYGYEY 374
                                    17        27        37        47        57        67        77        87        97       107       117       127       137       147       157       167       177       187       197    || 209       219       229       239       249       259       269       279       289       299       309       319       329       339       349       359       369     
                                                                                                                                                                                                                            202|                                                                                                                                                                         
                                                                                                                                                                                                                             205
   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 4YL2)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4YL2)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4YL2)

(-) Gene Ontology  (6, 6)

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
    FMN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PYR  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4yl2)
 

(-) 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
  4yl2
    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
  Q44467_9LACT | Q44467
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/TrEMBL
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    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
  Q44467_9LACT | Q44467
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q44467_9LACT | Q44467: 2du2 2e77 2j6x 2nli 2zfa 4rje 5ebu

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4YL2)