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 :  THE STRUCTURE OF A PROTEIN IN GLYCOSYL TRANSFERASE FAMILY 8 FROM ANAEROCOCCUS PREVOTII.
 
Authors :  M. E. Cuff, C. Tesar, J. Bearden, A. Joachimiak, Midwest Center For S Genomics (Mcsg)
Date :  27 Sep 11  (Deposition) - 07 Dec 11  (Release) - 09 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Structural Genomics, Psi-Biology, Midwest Center For Structural Genomics, Mcsg, Putative Glycosyl Transferase, General Stress Protein, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. E. Cuff, C. Tesar, J. Bearden, A. Joachimiak
The Structure Of A Protein In Glycosyl Transferase Family 8 From Anaerococcus Prevotii.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLYCOSYL TRANSFERASE FAMILY 8
    Chains: A, B
    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
    Gene: APRE_0416
    Organism Common: PEPTOSTREPTOCOCCUS PREVOTII
    Organism Scientific: ANAEROCOCCUS PREVOTII
    Organism Taxid: 525919
    Strain: DSM 20548

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (3, 23)
No.NameCountTypeFull Name
1CIT1Ligand/IonCITRIC ACID
2EDO7Ligand/Ion1,2-ETHANEDIOL
3MSE15Mod. Amino AcidSELENOMETHIONINE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:116 , THR A:120 , TYR A:210 , HOH A:430 , HOH A:473BINDING SITE FOR RESIDUE EDO A 301
2AC2SOFTWAREASP A:3 , ALA A:4 , ILE A:101 , LEU A:118 , HOH A:538BINDING SITE FOR RESIDUE EDO A 302
3AC3SOFTWAREARG A:165 , ARG A:254 , ASN A:255 , LYS A:256 , HOH A:426 , ARG B:254 , LYS B:256BINDING SITE FOR RESIDUE CIT A 303
4AC4SOFTWAREASP A:34 , THR A:60 , TYR A:62 , TYR B:36 , TYR B:62BINDING SITE FOR RESIDUE EDO A 304
5AC5SOFTWARELYS A:262 , MSE A:265 , SER A:266 , LYS A:269 , ALA B:231 , ASP B:235BINDING SITE FOR RESIDUE EDO B 301
6AC6SOFTWAREASP B:3 , ALA B:4 , LEU B:118BINDING SITE FOR RESIDUE EDO B 302
7AC7SOFTWAREASP B:105 , ASP B:107 , HIS B:241 , GLY B:244 , ARG B:245 , LYS B:247BINDING SITE FOR RESIDUE EDO B 303
8AC8SOFTWAREHIS B:132 , ASP B:207 , ASN B:211BINDING SITE FOR RESIDUE EDO B 304

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3TZT)

(-) 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:234
 aligned with C7RG54_ANAPD | C7RG54 from UniProtKB/TrEMBL  Length:273

    Alignment length:274
                             1                                                                                                                                                                                                                                                                                
                             |       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    
         C7RG54_ANAPD     - -MADALLLTLDENYIPQMKVLMTSIYINNPGRIFDVYLIHSRISEDKLKDLGEDLKKFSYTLYPIRATDDLFSFAKVTDRYPKEMYYRLLAGEFLPENLGEILYLDPDMLVINPLDDLLRTDISDYILAAASHTGKTDMANNVNRIRLGTDTDYYNSGLLLINLKRAREEIDPDEIFSFVEDNHMNLLLPDQDILNAMYGDRIYPLDDLIYNYDARNYSSYLIRSKKQADLAWLMDHTVVLHFCGRDKPWKKNHRNKFTSLYKHYMSLTKRYLA 273
               SCOP domains d3tzta_ A: automated matches                                                                                                                                                                                                                                                       SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh...eeeeee...------------.hhhhhhhhhhhhh.....eeeee...eee...hhhhhh.......eeeee.--------------------.....eeeeehhhhhhhhhhhhhhhhhhhh--------.hhhhhhhh..eeeeehhhhhee..hhhhhhhhh....hhhhhhhhh.eee...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzt A   0 AmADALLLTLDENYIPQmKVLmTSIYINNPGRIFDVYLIHSRISEDKLKDLGEDLKKFSYTLYPIRATD------------PKEmYYRLLAGEFLPENLGEILYLDPDmLVINPLDDLLRTDISDYILAAASH--------------------YYNSGLLLINLKRAREEIDPDEIFSFVEDN--------QDILNAmYGDRIYPLDDLIYNYDARNYSSYLIRSKKQADLAWLmDHTVVLHFCGRDKPWKKNHRNKFTSLYKHYmSLTKRYLA 273
                             |       9       |19 |      29        39        49        59        |-         - |  |   89        99       109       119       129  |      -         -   |   159       169       179  |      - |     199       209       219       229    |  239       249       259     | 269    
                             |              17-MSE                                             68           81  |                     108-MSE                 132                  153                          182      191     |                                  234-MSE                        265-MSE    
                             1-MSE              21-MSE                                                         84-MSE                                                                                                          197-MSE                                                                        


Chain B from PDB  Type:PROTEIN  Length:231
 aligned with C7RG54_ANAPD | C7RG54 from UniProtKB/TrEMBL  Length:273

    Alignment length:272
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271  
         C7RG54_ANAPD     2 ADALLLTLDENYIPQMKVLMTSIYINNPGRIFDVYLIHSRISEDKLKDLGEDLKKFSYTLYPIRATDDLFSFAKVTDRYPKEMYYRLLAGEFLPENLGEILYLDPDMLVINPLDDLLRTDISDYILAAASHTGKTDMANNVNRIRLGTDTDYYNSGLLLINLKRAREEIDPDEIFSFVEDNHMNLLLPDQDILNAMYGDRIYPLDDLIYNYDARNYSSYLIRSKKQADLAWLMDHTVVLHFCGRDKPWKKNHRNKFTSLYKHYMSLTKRYLA 273
               SCOP domains d3tztb_ B: automated matches                                                                                                                                                                                                                                                     SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee.hhhhhhhhhhhhhhhhhhh....eeeeeee...hhhhhhhhhhhhhh...eeeeee..--------------.hhhhhhhhhhhh.....eeeee...eee...hhhhhhh......eeeee.-------------------......eeeeehhhhhhhhhhhhhhhhh--------..hhhhhhhhhh..eeeeehhhhhee..hhhhhhhhh....hhhhhhhhh.eee...............hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tzt B   2 ADALLLTLDENYIPQmKVLmTSIYINNPGRIFDVYLIHSRISEDKLKDLGEDLKKFSYTLYPIRAT--------------KEmYYRLLAGEFLPENLGEILYLDPDmLVINPLDDLLRTDISDYILAAASH-------------------DYYNSGLLLINLKRAREEIDPDEIFSFV--------LPDQDILNAmYGDRIYPLDDLIYNYDARNYSSYLIRSKKQADLAWLmDHTVVLHFCGRDKPWKKNHRNKFTSLYKHYmSLTKRYLA 273
                                    11     |  21        31        41        51        61     |   -         -| |     91       101      |111       121       131|        -         -|      161       171       | -      |191     | 201       211       221       231  |    241       251       261   |   271  
                                          17-MSE                                            67             82 |                     108-MSE                 132                 152                        179      188      197-MSE                              234-MSE                        265-MSE    
                                              21-MSE                                                         84-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: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (2, 2)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (C7RG54_ANAPD | C7RG54)
molecular function
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).

 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
    CIT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    EDO  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3tzt)
 

(-) 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
  3tzt
    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
  C7RG54_ANAPD | C7RG54
    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
  C7RG54_ANAPD | C7RG54
    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 3TZT)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 3TZT)