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 :  TRYPANOSOMA BRUCEI CTPS - GLUTAMINASE DOMAIN WITH BOUND ACIVICIN
 
Authors :  M. Welin, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collin L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Ham A. Johansson, I. Johansson, T. Karlberg, T. Kotenyova, L. Lehtio, M. E T. Nyman, C. Persson, J. Sagemark, H. Schueler, M. I. Siponen, A. G. Tho L. Tresaugues, S. Van Den Berg, J. Weigelt, M. Wikstrom, M. Wisniews P. Nordlund, Structural Genomics Consortium (Sgc)
Date :  30 Dec 08  (Deposition) - 13 Jan 09  (Release) - 24 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A
Keywords :  Glutaminase Domain, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Welin, M. Moche, C. H. Arrowsmith, H. Berglund, C. Bountra, R. Collins, L. G. Dahlgren, A. M. Edwards, S. Flodin, A. Flores, S. Graslund, M. Hammarstrom, A. Johansson, I. Johansson, T. Karlberg T. Kotenyova, L. Lehtio, M. E. Nilsson, T. Nyman, C. Persson, J. Sagemark, H. Schueler, M. I. Siponen, A. G. Thorsell, L. Tresaugues S. Van Den Berg, J. Weigelt, M. Wikstrom, M. Wisniewska, P. Nordlund Structural Genomics Consortium (Sgc)
Trypanosoma Brucei Ctps - Glutaminase Domain With Bound Acivicin
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PUTATIVE CYTIDINE TRIPHOSPHATE SYNTHASE
    Chains: A
    EC Number: 6.3.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Variant: R3 PRARE
    Expression System Vector: PNIC-BSA4
    Expression System Vector Type: PLASMID
    Fragment: GLUTAMINASE DOMAIN, RESIDUES 319-589
    Mutation: YES
    Organism Scientific: TRYPANOSOMA BRUCEI
    Organism Taxid: 5691
    Synonym: CTP SYNTHETASE

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
15CS1Mod. Amino Acid2-AMINO-3-(CYSTEIN-S-YL)-ISOXAZOLIDIN-5-YL-ACETIC ACID
2CL2Ligand/IonCHLORIDE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:485 , ARG A:541 , HOH A:2089BINDING SITE FOR RESIDUE CL A 1588
2AC2SOFTWAREGLY A:331 , LYS A:332 , SER A:366 , ARG A:396 , LYS A:401BINDING SITE FOR RESIDUE CL A 1589

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2W7T)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 2W7T)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2W7T)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2W7T)

(-) Exons   (0, 0)

(no "Exon" information available for 2W7T)

(-) 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:264
 aligned with Q4GZ95_TRYB2 | Q4GZ95 from UniProtKB/TrEMBL  Length:589

    Alignment length:264
                                   333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583    
         Q4GZ95_TRYB2   324 TVRIAFVGKYLQDAGDTYFSVLQCFEHCQIALQVRLDILYVDSEELEGPNADEARKALLGCDGIFVPGGFGNRGVDGKCAAAQVARMNNIPYFGVCLGMQVAVIELSRNVVGWSDANSEEFNKESTHQVVRIMDCDRNKMGANMHLGACDVHIVEKSSIMAKIYSKSNIVVERHRHRYEVNTAYFEDLRKAGLCISAVTDPTFSSRCRVEAVENPSLRFFLAVQFHPEFISTPMDPAPTYLSFMAAAAKKDYVWPQKCSQRRLK 587
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee.hhhhhh..hhhhhhhhhhhhhhhh..eeeeeee.hhhh...hhhhhhhhhh..eeee.......hhhhhhhhhhhhhhhh..eee..hhhhhhhhhhhhhh......ee.........eeee.hhhh........eeeeeeeee....hhhhhhh....eeeeeeee..ee...hhhhhhhh..eeeee..........eeeee......eeee..hhhhh......hhhhhhhhhhhhh.........hhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2w7t A 324 TVRIAFVGKYLQDAGDTYFSVLQCFEHCQIALQVRLDILYVDSEELEGPNADEARKALLGCDGIFVPGGFGNRGVDGKCAAAQVARMNNIPYFGVcLGMQVAVIELSRNVVGWSDANSEEFNKESTHQVVRIMDCDRNKMGANMHLGACDVYIVEKSSIMAKIYSKSNIVVERHRHRYEVNTAYFEDLRKAGLCISAVTDPTFSSRCRVEAVENPSLRFFLAVQFHPEFISTPMDPAPTYLSFMAAAAKKDYVWPQKCSQRRLK 587
                                   333       343       353       363       373       383       393       403       413     | 423       433       443       453       463       473       483       493       503       513       523       533       543       553       563       573       583    
                                                                                                                         419-5CS
   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 2W7T)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2W7T)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 2W7T)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q4GZ95_TRYB2 | Q4GZ95)
molecular function
    GO:0005524    ATP binding    Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
    GO:0003883    CTP synthase activity    Catalysis of the reaction: ATP + UTP + NH3 = ADP + phosphate + CTP.
    GO:0016874    ligase activity    Catalysis of the joining of two substances, or two groups within a single molecule, with the concomitant hydrolysis of the diphosphate bond in ATP or a similar triphosphate.
    GO:0000166    nucleotide binding    Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
biological process
    GO:0044210    'de novo' CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of cytidine 5'-triphosphate (CTP) from simpler components.
    GO:0006241    CTP biosynthetic process    The chemical reactions and pathways resulting in the formation of CTP, cytidine 5'-triphosphate.
    GO:0006541    glutamine metabolic process    The chemical reactions and pathways involving glutamine, 2-amino-4-carbamoylbutanoic acid.
    GO:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.

 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
    5CS  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 2w7t)
 

(-) 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
  2w7t
    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
  Q4GZ95_TRYB2 | Q4GZ95
    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)
  6.3.4.2
    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
  Q4GZ95_TRYB2 | Q4GZ95
    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 2W7T)

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 2W7T)