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 :  THE CRYSTAL STRUCTURE OF AN EPOXIDE HYDROLASE FROM STREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS.
 
Authors :  K. Tan, L. Bigelow, S. Clancy, G. Babnigg, C. A. Bingman, R. Yennamalli, M. Ma, B. Shen, G. N. Phillips Jr. , A. Joachimiak, Midwest Center Fo Structural Genomics (Mcsg), Enzyme Discovery For Natural Pro Biosynthesis (Natpro)
Date :  20 Nov 12  (Deposition) - 05 Dec 12  (Release) - 30 Jan 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym. Unit :  A
Biol. Unit 1:  A  (2x)
Keywords :  Structural Genomics, Psi-Biology, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Enzyme Discovery For Natural Product Biosynthesi, Natpro, Enzyme Discovery For Natural Product Biosynthesis, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  K. Tan, L. Bigelow, S. Clancy, G. Babnigg, C. A. Bingman, R. Yennamalli J. Lohman, M. Ma, B. Shen, G. N. Phillips Jr. , A. Joachimiak
The Crystal Structure Of An Epoxide Hydrolase From Streptomyces Carzinostaticus Subsp. Neocarzinostaticus.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - EPOXIDE HYDROLASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)MAGIC
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Organism Scientific: STREPTOMYCES CARZINOSTATICUS SUBSP. NEOCARZINOSTATICUS
    Organism Taxid: 167636
    Strain: SUBSP. NEOCARZINOSTATICUS

 Structural Features

(-) Chains, Units

  1
Asymmetric Unit : A
Biological Unit 1 (2x): A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 23)

Asymmetric Unit (3, 23)
No.NameCountTypeFull Name
1ACT2Ligand/IonACETATE ION
2FMT10Ligand/IonFORMIC ACID
3MSE11Mod. Amino AcidSELENOMETHIONINE
Biological Unit 1 (3, 46)
No.NameCountTypeFull Name
1ACT4Ligand/IonACETATE ION
2FMT20Ligand/IonFORMIC ACID
3MSE22Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:174 , ILE A:175 , PHE A:178 , MSE A:235 , HIS A:303 , PRO A:311BINDING SITE FOR RESIDUE ACT A 401
02AC2SOFTWAREALA A:177 , PHE A:178 , LEU A:198 , GLN A:200 , FMT A:405 , HOH A:667BINDING SITE FOR RESIDUE ACT A 402
03AC3SOFTWAREPRO A:85 , ASP A:114BINDING SITE FOR RESIDUE FMT A 403
04AC4SOFTWARESER A:319 , FMT A:405 , HOH A:600BINDING SITE FOR RESIDUE FMT A 404
05AC5SOFTWAREGLN A:200 , SER A:319 , ACT A:402 , FMT A:404 , FMT A:406BINDING SITE FOR RESIDUE FMT A 405
06AC6SOFTWAREASN A:202 , ARG A:345 , ASP A:346 , FMT A:405 , HOH A:590BINDING SITE FOR RESIDUE FMT A 406
07AC7SOFTWAREASP A:174 , MSE A:235 , HIS A:361 , HOH A:620BINDING SITE FOR RESIDUE FMT A 407
08AC8SOFTWAREARG A:60 , SER A:214 , ASP A:215 , HOH A:618BINDING SITE FOR RESIDUE FMT A 408
09AC9SOFTWAREASP A:276 , ALA A:277 , FMT A:410BINDING SITE FOR RESIDUE FMT A 409
10BC1SOFTWAREASP A:276 , ALA A:277 , GLU A:366 , GLU A:367 , FMT A:409 , HOH A:506 , HOH A:572BINDING SITE FOR RESIDUE FMT A 410
11BC2SOFTWARELYS A:17 , TRP A:49 , ARG A:50BINDING SITE FOR RESIDUE FMT A 411
12BC3SOFTWAREPRO A:311 , THR A:313BINDING SITE FOR RESIDUE FMT A 412

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4I19)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Trp A:98 -Pro A:99

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4I19)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4I19)

(-) Exons   (0, 0)

(no "Exon" information available for 4I19)

(-) 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:386
                                                                                                                                                                                                                                                                                                                                                                                                                                  
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee....hhhhhhhhhhhhhh...............hhhhhhhhhhhhhhh.hhhhhhhhhhh..eeeeee..eeeeeeee.......eeeeee.....hhhhhhhhhhhhhhhhhhh.hhhh.eeeeee....hhhhh.......hhhhhhhhhhhhhhhh....eeeee.hhhhhhhhhhhhhh...eeeeee.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...............eeeee........hhhhhhhhh..eeeeee......hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4i19 A   0 AmRPFQVQIPQADIDDLKRRLSETRWPELVDVGWSRGAPLSYIKELAEYWRDGFDWRAAERRINQYPQFTTEIDGATIHFLHVRSPEPDATPmVITHGWPGTPVEFLDIIGPLTDPRAHGGDPADAFHLVIPSLPGFGLSGPLKSAGWELGRIAmAWSKLmASLGYERYIAQGGDIGAFTSLLLGAIDPSHLAGIHVNLLQTNLSGEPGELETLSDADKARLAVSERFLDDLSGPmKmQSTRPHTIGYmLNDSPVAQLAYLLEmFKHWAQTENVPEDAVDRDLmLTHISLFWFTATGGSAAQAHYELKPFLPITSLIGRSPTLDVPmGVAVYPGALFQPVRSLAERDFKQIVHWAELDRGGHFSAmEEPDLFVDDLRTFNRTLKKL 385
                             |       9        19        29        39        49        59        69        79        89  |     99       109       119       129       139       149    |  159|      169       179       189       199       209       219       229     | 239       249       259   |   269       279   |   289       299       309       319      |329       339       349       359     | 369       379      
                             |                                                                                         92-MSE                                                       154-MSE |                                                                        235-MSE      248-MSE        263-MSE             283-MSE                                    326-MSE                                365-MSE                
                             1-MSE                                                                                                                                                        160-MSE                                                                      237-MSE
   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 4I19)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4I19)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4I19)

(-) Gene Ontology  (3, 3)

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
    ACT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    FMT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ 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 ]
 
  Cis Peptide Bonds
    Trp A:98 - Pro A:99   [ 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
  4i19
    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
  Q84HB8_STRCZ | Q84HB8
    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
  Q84HB8_STRCZ | Q84HB8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q84HB8_STRCZ | Q84HB8: 4qa9

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4I19)