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 :  PREDICTED DNA ALKYLATION REPAIR ENZYME FROM ENTEROCOCCUS FAECALIS.
 
Authors :  J. Osipiuk, C. Hatzos, S. Moy, F. Collart, A. Joachimiak, Midwest Cent Structural Genomics (Mcsg)
Date :  30 Sep 05  (Deposition) - 15 Nov 05  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomis, Dna Repair Enzyme, Structural Genomics, Psi, Protein Structure Initiative, Midwest Center For Structural Genomics, Mcsg, Unknown Function (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. Osipiuk, C. Hatzos, S. Moy, F. Collart, A. Joachimiak
Xray Structure Of Predicted Dna Alkylation Repair Enzyme From Enterococcus Faecalis.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HYPOTHETICAL PROTEIN EF3068
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PMCSG7
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: EF3068
    Organism Scientific: ENTEROCOCCUS FAECALIS
    Organism Taxid: 1351

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 20)

Asymmetric/Biological Unit (5, 20)
No.NameCountTypeFull Name
1BME2Ligand/IonBETA-MERCAPTOETHANOL
2CL1Ligand/IonCHLORIDE ION
3GOL4Ligand/IonGLYCEROL
4MSE8Mod. Amino AcidSELENOMETHIONINE
5SO45Ligand/IonSULFATE ION

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARELYS A:92 , ALA A:132 , GLU A:133 , ASN A:134 , ASN A:137BINDING SITE FOR RESIDUE SO4 A 401
02AC2SOFTWARELYS B:92 , ALA B:132 , GLU B:133 , ASN B:134 , ASN B:137BINDING SITE FOR RESIDUE SO4 B 402
03AC3SOFTWAREARG B:181 , LYS B:185 , TYR B:211 , LYS B:214 , SER B:216 , HOH B:542BINDING SITE FOR RESIDUE SO4 B 403
04AC4SOFTWAREPRO A:49 , LYS A:50 , HOH A:435 , HOH A:508 , HOH A:551 , PRO B:49 , LYS B:50BINDING SITE FOR RESIDUE SO4 A 404
05AC5SOFTWAREGLN A:62 , LYS A:63 , THR A:64 , GLU A:65BINDING SITE FOR RESIDUE SO4 A 405
06AC6SOFTWAREARG A:34 , ALA A:215BINDING SITE FOR RESIDUE CL A 412
07AC7SOFTWARECYS A:54 , GLU A:87 , PHE A:91BINDING SITE FOR RESIDUE BME A 406
08AC8SOFTWARECYS B:54 , GLU B:87 , ALA B:90 , PHE B:91 , HOH B:458BINDING SITE FOR RESIDUE BME B 407
09AC9SOFTWAREGLU A:169 , PHE A:171 , LYS B:8 , THR B:64 , GLU B:65 , HOH B:527BINDING SITE FOR RESIDUE GOL B 408
10BC1SOFTWARELYS A:21 , SER B:17 , HIS B:22 , HOH B:465 , HOH B:511BINDING SITE FOR RESIDUE GOL B 409
11BC2SOFTWAREHIS A:46 , ARG A:82 , HIS B:46 , GLN B:78 , ASN B:79 , VAL B:80 , GLN B:81 , ARG B:82BINDING SITE FOR RESIDUE GOL B 410
12BC3SOFTWAREMSE A:16 , SER A:184 , PRO A:188 , TYR A:211BINDING SITE FOR RESIDUE GOL A 411

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2B6C)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2B6C)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2B6C)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2B6C)

(-) Exons   (0, 0)

(no "Exon" information available for 2B6C)

(-) 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:213
 aligned with Q82ZI8_ENTFA | Q82ZI8 from UniProtKB/TrEMBL  Length:217

    Alignment length:213
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212   
         Q82ZI8_ENTFA     3 TLQFQKNPETAAKMSAYMKHQFVFAGIPAPERQALSKQLLKESHTWPKEKLCQEIEAYYQKTEREYQYVAIDLALQNVQRFSLEEVVAFKAYVPQKAWWDSVDAWRKFFGSWVALHLTELPTIFALFYGAENFWNRRVALNLQLMLKEKTNQDLLKKAIIYDRTTEEFFIQKAIGWSLRQYSKTNPQWVEELMKELVLSPLAQREGSKYLAKA 215
               SCOP domains d2b6ca1 A:3-215 Hypothetical protein EF3068                                                                                                                                                                           SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2b6cA02 A:119-215 ARM repeat domains                                                              CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b6c A   3 TLQFQKNPETAAKmSAYmKHQFVFAGIPAPERQALSKQLLKESHTWPKEKLCQEIEAYYQKTEREYQYVAIDLALQNVQRFSLEEVVAFKAYVPQKAWWDSVDAWRKFFGSWVALHLTELPTIFALFYGAENFWNRRVALNLQLmLKEKTNQDLLKKAIIYDRTTEEFFIQKAIGWSLRQYSKTNPQWVEELmKELVLSPLAQREGSKYLAKA 215
                                    12   |   |22        32        42        52        62        72        82        92       102       112       122       132       142    |  152       162       172       182       192  |    202       212   
                                        16-MSE                                                                                                                            147-MSE                                         195-MSE                
                                            20-MSE                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:215
 aligned with Q82ZI8_ENTFA | Q82ZI8 from UniProtKB/TrEMBL  Length:217

    Alignment length:215
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212     
         Q82ZI8_ENTFA     3 TLQFQKNPETAAKMSAYMKHQFVFAGIPAPERQALSKQLLKESHTWPKEKLCQEIEAYYQKTEREYQYVAIDLALQNVQRFSLEEVVAFKAYVPQKAWWDSVDAWRKFFGSWVALHLTELPTIFALFYGAENFWNRRVALNLQLMLKEKTNQDLLKKAIIYDRTTEEFFIQKAIGWSLRQYSKTNPQWVEELMKELVLSPLAQREGSKYLAKASE 217
               SCOP domains d2b6cb_ B: Hypothetical protein EF3068                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------2b6cB02 B:119-217 ARM repeat domains                                                                CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh.........hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhh..hhhhhhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhh..hhhhhhhhhhhh..hhhhhhhhh........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2b6c B   3 TLQFQKNPETAAKmSAYmKHQFVFAGIPAPERQALSKQLLKESHTWPKEKLCQEIEAYYQKTEREYQYVAIDLALQNVQRFSLEEVVAFKAYVPQKAWWDSVDAWRKFFGSWVALHLTELPTIFALFYGAENFWNRRVALNLQLmLKEKTNQDLLKKAIIYDRTTEEFFIQKAIGWSLRQYSKTNPQWVEELmKELVLSPLAQREGSKYLAKASE 217
                                    12   |   |22        32        42        52        62        72        82        92       102       112       122       132       142    |  152       162       172       182       192  |    202       212     
                                        16-MSE                                                                                                                            147-MSE                                         195-MSE                  
                                            20-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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Mainly Alpha (13335)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2B6C)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 2B6C)

 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
    BME  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MSE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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
(no "Cis Peptide Bonds" information available for 2b6c)
 

(-) 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
  2b6c
    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
  Q82ZI8_ENTFA | Q82ZI8
    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
  Q82ZI8_ENTFA | Q82ZI8
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

(no "Entries Sharing at Least One Protein Chain" available for 2B6C)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2B6C)