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
(-)Biological Unit 2
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)
Image Biological Unit 2
Biological Unit 2  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF THE NOVEL PHENAZINE PRENYLTRANSFERASE EPZP (METHYLATED)
 
Authors :  G. Zocher, T. Stehle
Date :  28 Mar 12  (Deposition) - 14 Nov 12  (Release) - 14 Nov 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.33
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Pt Fold, Dihydrophenazine Carboxylate Prenyltransferase, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Zocher, O. Saleh, J. B. Heim, D. A. Herbst, L. Heide, T. Stehle
Structure-Based Engineering Increased The Catalytic Turnove Rate Of A Novel Phenazine Prenyltransferase.
Plos One V. 7 48427 2012
PubMed-ID: 23119011  |  Reference-DOI: 10.1371/JOURNAL.PONE.0048427

(-) Compounds

Molecule 1 - PRENYLTRANSFERASE
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Gene: EPZP
    Organism Scientific: STREPTOMYCES CINNAMONENSIS
    Organism Taxid: 1900
 
Molecule 2 - PRENYLTRANSFERASE
    Chains: B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA 2
    Expression System Taxid: 562
    Gene: EPZP
    Organism Scientific: STREPTOMYCES CINNAMONENSIS
    Organism Taxid: 1900

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 35)

Asymmetric Unit (5, 35)
No.NameCountTypeFull Name
1CL12Ligand/IonCHLORIDE ION
2MG4Ligand/IonMAGNESIUM ION
3MLY16Mod. Amino AcidN-DIMETHYL-LYSINE
4MLZ1Mod. Amino AcidN-METHYL-LYSINE
5PG42Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 1 (3, 9)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MLY7Mod. Amino AcidN-DIMETHYL-LYSINE
4MLZ1Mod. Amino AcidN-METHYL-LYSINE
5PG41Ligand/IonTETRAETHYLENE GLYCOL
Biological Unit 2 (2, 10)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2MG-1Ligand/IonMAGNESIUM ION
3MLY9Mod. Amino AcidN-DIMETHYL-LYSINE
4MLZ-1Mod. Amino AcidN-METHYL-LYSINE
5PG41Ligand/IonTETRAETHYLENE GLYCOL

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREHOH A:638 , HOH A:644 , HOH A:885 , HOH A:886 , HOH B:729BINDING SITE FOR RESIDUE MG A 401
02AC2SOFTWARETHR A:276 , HOH A:607BINDING SITE FOR RESIDUE CL A 402
03AC3SOFTWAREPRO A:184 , ALA A:185 , HOH A:592 , ALA B:185 , HOH B:611BINDING SITE FOR RESIDUE CL A 403
04AC4SOFTWARETYR A:220 , SER A:236 , TYR A:271 , GLY A:272 , CL A:405 , HOH A:593BINDING SITE FOR RESIDUE CL A 404
05AC5SOFTWAREARG A:49 , TYR A:220 , MLY A:283 , CL A:404BINDING SITE FOR RESIDUE CL A 405
06AC6SOFTWAREARG A:49 , ASN A:172 , TYR A:220 , ARG A:232BINDING SITE FOR RESIDUE CL A 406
07AC7SOFTWAREARG A:267 , ASN A:268 , TYR A:287 , TRP A:290 , HOH A:734BINDING SITE FOR RESIDUE PG4 A 407
08AC8SOFTWAREHOH B:618 , HOH B:801 , HOH B:839BINDING SITE FOR RESIDUE MG B 401
09AC9SOFTWAREHOH B:843 , HOH B:850 , HOH B:893 , HOH B:894 , HOH B:897BINDING SITE FOR RESIDUE MG B 402
10BC1SOFTWAREHOH B:647 , HOH B:687 , HOH B:772 , HOH B:898 , HOH B:899BINDING SITE FOR RESIDUE MG B 403
11BC2SOFTWAREGLY B:80BINDING SITE FOR RESIDUE CL B 404
12BC3SOFTWAREASP B:141 , ALA B:142 , SER B:224 , TRP B:225 , SER B:227 , HOH B:512 , HOH B:579BINDING SITE FOR RESIDUE CL B 405
13BC4SOFTWAREARG B:49 , ASN B:172 , TYR B:220 , ARG B:232BINDING SITE FOR RESIDUE CL B 406
14BC5SOFTWARETYR B:220 , SER B:236 , TYR B:271 , GLY B:272 , CL B:410 , HOH B:529BINDING SITE FOR RESIDUE CL B 407
15BC6SOFTWARESER B:131 , ARG B:147BINDING SITE FOR RESIDUE CL B 408
16BC7SOFTWAREARG B:49 , ARG B:62 , HOH B:652 , HOH B:797BINDING SITE FOR RESIDUE CL B 409
17BC8SOFTWAREARG B:49 , TYR B:220 , MLY B:283 , CL B:407 , HOH B:529BINDING SITE FOR RESIDUE CL B 410
18BC9SOFTWAREGLY B:266 , ASN B:268 , TYR B:287 , TRP B:290 , HOH B:660BINDING SITE FOR RESIDUE PG4 B 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4EE6)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4EE6)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4EE6)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4EE6)

(-) Exons   (0, 0)

(no "Exon" information available for 4EE6)

(-) 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:288
                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ee6a_ A: automated matches                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhh..eeeeeee.hhhhhh.eeeeeee....hhhhhhhhh........hhhhhhhhhhhhh.eeeeeeeee...eeeeeeeee......hhhhhh......hhhhhhhhhhhhh.....eeeeeee....eeeeee........hhhhhhhhhhhhhhhhh.....hhhhhhhhh...eeeeeee.......eeeeeeee.hhhhh....hhhhhhhhhhh........eeeeeee....eeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ee6 A   3 ESADLTELYSIIEkTAQVVDVTASHDKVWPILNAFQDVIADSVISFRASTGSSADDLDCRFTMLPkGLDPYARALEHGLTPkTDHPVGSLLKEVHENLPITSCGVDFGVAGGFTkTWSFPSAEkLGKVSELVkLPSIPDAVAANRDFFEkWGIADMVSTVGIDYSKRTMNLYFGGGVGDRVPAGVFEEKGVRAILGELGLAAPSEELLKFCERSFVIYVTLSWDSPKINRFTYSVMTPEPLGLPVDLAPTFERLIKSAPYDTEGRNYVYGIASTPKGEYHkIASYYQW 290
                                    12   |    22        32        42        52        62     |  72        82 |      92       102       112    |  122   |   132  |    142       152       162       172       182       192       202       212       222       232       242       252       262       272       282|       
                                        16-MLY                                              68-MLY          84-MLY                          117-MLZ  126-MLY  135-MLY          152-MLY                                                                                                                            283-MLY   


Chain B from PDB  Type:PROTEIN  Length:291
                                                                                                                                                                                                                                                                                                                                   
               SCOP domains d4ee6b_ B: automated matches                                                                                                                                                                                                                                                                        SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhh.......eeeeeee.hhhhhh.eeeeeee....hhhhhhhhh........hhhhhhhhhhhhh.eeeeeeeee...eeeeeeeee......hhhhhh.....hhhhhhhhhhhhhh.....eeeeeee....eeeeee........hhhhhhhhhhhhhhhhh.....hhhhhhhhh...eeeeeee.......eeeeeeee.hhhhh....hhhhhhhhhhh........eeeeeee....eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ee6 B   1 MSESADLTELYSIIEkTAQVVDVTASHDKVWPILNAFQDVIADSVISFRASTGSSADDLDCRFTMLPkGLDPYARALEHGLTPkTDHPVGSLLKEVHENLPITSCGVDFGVAGGFTkTWSFPSAEkLGkVSELVkLPSIPDAVAANRDFFEKWGIADMVSTVGIDYSKRTMNLYFGGGVGDRVPAGVFEEKGVRAILGELGLAAPSEELLKFCERSFVIYVTLSWDSPkINRFTYSVMTPEPLGLPVDLAPTFERLIKSAPYDTEGRNYVYGIASTPKGEYHkIASYYQWQ 291
                                    10     |  20        30        40        50        60       |70        80   |    90       100       110      |120     | 130    |  140       150       160       170       180       190       200       210       220       230       240       250       260       270       280  |    290 
                                          16-MLY                                              68-MLY          84-MLY                          117-MLY  126-MLY    |                                                                                           229-MLY                                               283-MLY    
                                                                                                                                                          129-MLY |                                                                                                                                                            
                                                                                                                                                                135-MLY
   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  (1, 2)

Asymmetric Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4EE6)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4EE6)

(-) Gene Ontology  (1, 1)

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
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLY  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MLZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PG4  [ 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 ]
    BC8  [ RasMol ]  +environment [ RasMol ]
    BC9  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ee6)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 | Biol. Unit 2 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
  4ee6
    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
  E5KWG9_STRCM | E5KWG9
    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
  E5KWG9_STRCM | E5KWG9
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        E5KWG9_STRCM | E5KWG9: 4ee7 4ee8

(-) Related Entries Specified in the PDB File

4ee7 4ee8