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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF GLUCOSE 1-PHOSPHATE THYMIDYLYLTRANSFERASE FROM ANEURINIBACILLUS THERMOAEROPHILUS COMPLEXED WITH UDP-N-ACETYLGLUCOSAMINE
 
Authors :  T. J. Chen, W. T. Chien, C. C. Lin, W. C. Wang
Date :  22 Oct 12  (Deposition) - 23 Oct 13  (Release) - 23 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.20
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  A,B  (2x)
Keywords :  Thymidylyltransferase, Nucleotide Binding, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. J. Chen, W. T. Chien, C. C. Lin, W. C. Wang
Crystal Structure Of Glucose 1-Phosphate Thymidylyltransferase From Aneurinibacillus Thermoaerophilu Complexed With Udp-N-Acetylglucosamine
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - GLUCOSE-1-PHOSPHATE THYMIDYLYLTRANSFERASE
    Chains: A, B
    EC Number: 2.7.7.24
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PTXB1
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: RMLA
    Organism Scientific: ANEURINIBACILLUS THERMOAEROPHILUS
    Organism Taxid: 143495

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B
Biological Unit 3 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 6)

Asymmetric Unit (2, 6)
No.NameCountTypeFull Name
1SO44Ligand/IonSULFATE ION
2UD12Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 1 (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1SO42Ligand/IonSULFATE ION
2UD11Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE
Biological Unit 3 (2, 12)
No.NameCountTypeFull Name
1SO48Ligand/IonSULFATE ION
2UD14Ligand/IonURIDINE-DIPHOSPHATE-N-ACETYLGLUCOSAMINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:6 , GLY A:8 , GLY A:9 , GLN A:80 , PRO A:83 , ASP A:84 , GLY A:85 , LEU A:86 , LEU A:106 , ASP A:108 , ASN A:109 , PHE A:143 , GLY A:144 , GLU A:159 , LYS A:160 , VAL A:170 , GLY A:172 , HOH A:422 , HOH A:428BINDING SITE FOR RESIDUE UD1 A 300
2AC2SOFTWAREGLY A:67 , GLY A:68 , SER A:69 , HOH A:434BINDING SITE FOR RESIDUE SO4 A 301
3AC3SOFTWAREASN A:125 , ARG A:126 , LYS A:127 , SER A:128 , LYS A:268BINDING SITE FOR RESIDUE SO4 A 302
4AC4SOFTWARELEU B:6 , GLY B:8 , GLY B:9 , GLN B:80 , PRO B:83 , ASP B:84 , GLY B:85 , LEU B:86 , LEU B:106 , ASP B:108 , ASN B:109 , PHE B:143 , GLY B:144 , GLU B:159 , LYS B:160 , VAL B:170 , GLY B:172 , HOH B:449 , HOH B:451 , HOH B:472BINDING SITE FOR RESIDUE UD1 B 300
5AC5SOFTWAREGLY B:66 , GLY B:67 , GLY B:68 , SER B:69BINDING SITE FOR RESIDUE SO4 B 301
6AC6SOFTWAREARG B:126 , LYS B:127 , SER B:128 , LYS B:268BINDING SITE FOR RESIDUE SO4 B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Tyr A:15 -Pro A:16
2Glu A:150 -Lys A:151
3Arg A:217 -Gly A:218
4Tyr B:15 -Pro B:16

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4HOC)

(-) 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:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hoca_ A: RmlA (RfbA)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhh......hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee...eeee.hhhhhhhhhhhh...eeeeeee..hhhh.eeee........eeee........eeeeeeeee..hhhhhhhhh......hhhhhhhhhhhh..eeeeee...eeee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhhhhhh...hhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hoc A   1 MKGIILSGGSGTRLYPLTKVVSKQLLPVYDKPMVYYPLSVLMLAGIKDILIISTPEDTPRFEQLLGGGSELGISLSYAVQSSPDGLAQAFIIGEEFIGDDNVALVLGDNIFYGHGFTELLQRAANRKSGATIFGYNVKDPQRFGVVEFDEKGKVISIEEKPEEPKSSYAVTGLYFYDNRVVDIAKNITPSGELEITDVNKAYLELGELHVELLGRGFAWLDTGTHESLLQASQFIETIEKRQSLKVACLEEIAYRMGYISREQLIKLAEPLMKNEYGQYLMNLAHR 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190|      202       212       222       232       242       252       262       272       282      
                                                                                                                                                                                                                       190|                                                                                               
                                                                                                                                                                                                                        193                                                                                               


Chain B from PDB  Type:PROTEIN  Length:286
                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4hocb_ B: RmlA (RfbA)                                                                                                                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee....hhhhh......hhhh.ee..ee.hhhhhhhhhhh...eeeeee...hhhhhhhhhh.hhhhh.eeeeee.......hhhhhhhhhhhh...eeeee...eeee.hhhhhhhhhhhh...eeeeeee..hhhh.eeeee.....eeeeee........eeeeeeeee..hhhhhhhhh......hhhhhhhhhhhh..eeeeee...eeee...hhhhhhhhhhhhhhhhhhhh....hhhhhhhhh...hhhhhhhhh.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4hoc B   1 MKGIILSGGSGTRLYPLTKVVSKQLLPVYDKPMVYYPLSVLMLAGIKDILIISTPEDTPRFEQLLGGGSELGISLSYAVQSSPDGLAQAFIIGEEFIGDDNVALVLGDNIFYGHGFTELLQRAANRKSGATIFGYNVKDPQRFGVVEFDEKGKVISIEEKPEEPKSSYAVTGLYFYDNRVVDIAKNITPSAELEITDVNKAYLELGELHVELLGRGFAWLDTGTHESLLQASQFIETIEKRQSLKVACLEEIAYRMGYISREQLIKLAEPLMKNEYGQYLMNLAHR 288
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190||     202       212       222       232       242       252       262       272       282      
                                                                                                                                                                                                                        191|                                                                                              
                                                                                                                                                                                                                         194
   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) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (7, 7)

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
    SO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UD1  [ 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 ]
 
  Cis Peptide Bonds
    Arg A:217 - Gly A:218   [ RasMol ]  
    Glu A:150 - Lys A:151   [ RasMol ]  
    Tyr A:15 - Pro A:16   [ RasMol ]  
    Tyr B:15 - Pro B:16   [ RasMol ]  
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ 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 | Biol. Unit 3 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
  4hoc
    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
  Q9AGY4_ANETH | Q9AGY4
    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)
  2.7.7.24
    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
  Q9AGY4_ANETH | Q9AGY4
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/TrEMBL
        Q9AGY4_ANETH | Q9AGY4: 4ho0 4ho2 4ho3 4ho4 4ho5 4ho6 4ho8 4ho9

(-) Related Entries Specified in the PDB File

4ho0 4ho2 4ho3 4ho4 4ho5 4ho6 4ho8 4ho9