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 NITRILE HYDRATASE MUTANT BR56K COMPLEXED WITH TRIMETHYLACETONITRILE, PHOTO-ACTIVATED FOR 50 MIN
 
Authors :  Y. Yamanaka, K. Hashimoto, K. Noguchi, M. Yohda, M. Odaka
Date :  17 May 14  (Deposition) - 17 Jun 15  (Release) - 04 Nov 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.18
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Cysteine Sulfinic Acid, Cys-So2H, Cys-Soh, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Y. Yamanaka, Y. Kato, K. Hashimoto, K. Iida, K. Nagasawa, H. Nakayama, N. Dohmae, K. Noguchi, T. Noguchi, M. Yohda, M. Odaka
Time-Resolved Crystallography Of The Reaction Intermediate Of Nitrile Hydratase: Revealing A Role For The Cysteinesulfenic Acid Ligand As A Catalytic Nucleophile.
Angew. Chem. Int. Ed. Engl. V. 54 10763 2015
PubMed-ID: 26333053  |  Reference-DOI: 10.1002/ANIE.201502731

(-) Compounds

Molecule 1 - NITRILE HYDRATASE SUBUNIT ALPHA
    Chains: A
    EC Number: 4.2.1.84
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NTHA
    Organism Scientific: RHODOCOCCUS ERYTHROPOLIS
    Organism Taxid: 1833
    Synonym: NHASE, NITRILASE
 
Molecule 2 - NITRILE HYDRATASE SUBUNIT BETA
    Chains: B
    EC Number: 4.2.1.84
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NTHB, NHA2
    Mutation: YES
    Organism Scientific: RHODOCOCCUS ERYTHROPOLIS
    Organism Taxid: 1833
    Synonym: NHASE, NITRILASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 7)

Asymmetric/Biological Unit (5, 7)
No.NameCountTypeFull Name
1CSD1Mod. Amino Acid3-SULFINOALANINE
2CSO1Mod. Amino AcidS-HYDROXYCYSTEINE
3FE1Ligand/IonFE (III) ION
4MG3Ligand/IonMAGNESIUM ION
5TAN1Ligand/Ion2,2-DIMETHYLPROPANENITRILE

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:109 , CSD A:112 , SER A:113 , CSO A:114 , TAN A:303BINDING SITE FOR RESIDUE FE A 301
2AC2SOFTWAREHOH A:481 , HOH A:489 , HOH A:490 , HOH A:491 , HOH A:492 , HOH A:538BINDING SITE FOR RESIDUE MG A 302
3AC3SOFTWAREGLN A:90 , CSD A:112 , SER A:113 , CSO A:114 , TRP A:117 , FE A:301BINDING SITE FOR RESIDUE TAN A 303
4AC4SOFTWAREMG B:302 , HOH B:413 , HOH B:447 , HOH B:455 , HOH B:473 , HOH B:475 , HOH B:511BINDING SITE FOR RESIDUE MG B 301
5AC5SOFTWAREVAL B:10 , MG B:301 , HOH B:444 , HOH B:447 , HOH B:455 , HOH B:475 , HOH B:511BINDING SITE FOR RESIDUE MG B 302

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3WVD)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3WVD)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3WVD)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3WVD)

(-) Exons   (0, 0)

(no "Exon" information available for 3WVD)

(-) 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:196
                                                                                                                                                                                                                                    
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .......hhhhhhhhhhhhhhh......hhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........eeeee....eeeeee.......hhhhhh..hhhhhhhhhhhhh..hhhhhhhhhh.......eeeeee.....eeeee..........hhhhhhhhhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvd A  10 NAAPAQAPVSDRAWALFRALDGKGLVPDGYVEGWKKTFEEDFSPRRGAELVARAWTDPEFRQLLLTDGTAAVAQYGYLGPQGEYIVAVEDTPTLKNVIVCSLcScTAWPILGLPPTWYKSFEYRARVVREPRKVLSEMGTEIASDIEIRVYDTTAETRYMVLPQRPAGTEGWSQEQLQEIVTKDCLIGVAIPQVPT 205
                                    19        29        39        49        59        69        79        89        99       109  | |  119       129       139       149       159       169       179       189       199      
                                                                                                                                112-CSD                                                                                         
                                                                                                                                  114-CSO                                                                                       


Chain B from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .................................hhhhhhhhhhhhh....hhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh...........................eeee...........hhhhh..eeeeeee......hhhhhh..........eeeeeeehhhhhh......eeeeeee...eee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3wvd B   1 MDGVHDLAGVQGFGKVPHTVNADIGPTFHAEWEHLPYSLMFAGVAELGAFSVDEVKYVVERMEPRHYMMTPYYERYVIGVATLMVEKGILTQDELESLAGGPFPLSRPSESEGRPAPVETTTFEVGQRVRVRDEYVPGHIRMPAYCRGRVGTISHRTTEKWPFPDAIGHGRNDAGEEPTYHVKFAAEELFGSDTDGGSVVVDLFEGYLEPAA 212
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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 3WVD)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3WVD)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3WVD)

(-) Gene Ontology  (7, 12)

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
    CSD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CSO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    TAN  [ 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
(no "Cis Peptide Bonds" information available for 3wvd)
 

(-) 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
  3wvd
    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
  NHAA_RHOER | P13448
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
  NHAB_RHOER | P13449
    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)
  4.2.1.84
    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
  NHAA_RHOER | P13448
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)
  NHAB_RHOER | P13449
    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
        NHAA_RHOER | P13448: 1ahj 2ahj 2cyz 2cz0 2cz1 2cz6 2cz7 2d0q 2qdy 2zcf 2zpb 2zpe 2zpf 2zpg 2zph 2zpi 3a8g 3a8h 3a8l 3a8m 3a8o 3wve 3x20 3x24 3x25 3x26 3x28
        NHAB_RHOER | P13449: 1ahj 2ahj 2cyz 2cz0 2cz1 2cz6 2cz7 2d0q 2qdy 2zcf 2zpb 2zpe 2zpf 2zpg 2zph 2zpi 3a8g 3a8h 3a8l 3a8m 3a8o 3wve 3x20 3x24 3x25 3x26 3x28

(-) Related Entries Specified in the PDB File

3wve