Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)

(-) Description

Title :  DIMERIC FORM OF CTP SYNTHASE FROM SULFOLOBUS SOLFATARICUS
 
Authors :  P. Harris, M. Willemoes, I. Lauritsen, E. Johansson, K. F. Jensen
Date :  08 Jul 10  (Deposition) - 08 Sep 10  (Release) - 12 Nov 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.50
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Rossmann Fold, Ctp Synthase Activity, Nucleotide Binding, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  I. Lauritsen, M. Willemoes, K. F. Jensen, E. Johansson, P. Harris
Structure Of The Dimeric Form Of Ctp Synthase From Sulfolobus Solfataricus
Acta Crystallogr. , Sect. F V. 67 201 2011
PubMed-ID: 21301086  |  Reference-DOI: 10.1107/S1744309110052334

(-) Compounds

Molecule 1 - CTP SYNTHASE
    Chains: A, B
    EC Number: 6.3.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: PYRG, SSO0201
    Organism Scientific: SULFOLOBUS SOLFATARICUS
    Organism Taxid: 2287
    Synonym: UTP-AMMONIA LIGASE, CTP SYNTHETASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 3NVA)

(-) Sites  (0, 0)

(no "Site" information available for 3NVA)

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Ile A:116 -Pro A:117
2Lys A:427 -Asn A:428
3Ile B:116 -Pro B:117
4Lys B:427 -Asn B:428

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 3NVA)

(-) 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:533
 aligned with PYRG_SULSO | Q980S6 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:533
                                    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       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   
           PYRG_SULSO     2 PNKYIVVTGGVLSSVGKGTLVASIGMLLKRRGYNVTAVKIDPYINVDAGTMNPYMHGEVFVTEDGAETDLDLGHYERFMDVNMTKYNNITAGKVYFEVIKKEREGKYLGQTVQIIPHVTDQIKDMIRYASKINNAEITLVEIGGTVGDIESLPFLEAVRQLKLEEGEDNVIFVHIALVEYLSVTGELKTKPLQHSVQELRRIGIQPDFIVGRATLPLDDETRRKIALFTNVKVDHIVSSYDVETSYEVPIILESQKLVSKILSRLKLEDRQVDLTDWISFVNNIKGINSKKTINIALVGKYTKLKDSYISIKEAIYHASAYIGVRPKLIWIESTDLESDTKNLNEILGNVNGIIVLPGFGSRGAEGKIKAIKYAREHNIPFLGICFGFQLSIVEFARDVLGLSEANSTEINPNTKDPVITLLDEQKNVTQLGGTMRLGAQKIILKEGTIAYQLYGKKVVYERHRHRYEVNPKYVDILEDAGLVVSGISENGLVEIIELPSNKFFVATQAHPEFKSRPTNPSPIYLGFIRAVAS 534
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeeee.......hhhhhhhhhhhhhhhh...eeeeeee..........hhhhhh..ee.....ee.hhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhh..eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee...........hhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhh..hhh.eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhh.....eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeee.hhhh..............eeee.......hhhhhhhhhhhhhhhh..eeeehhhhhhhhhhhhhh.......ee.........eeee...............eeeeeeeee...hhhhhhhh..eeeeeeee..eehhhhhhhhhhh..eeeee.....eeeee......eeee..hhhhhh.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nva A   2 PNKYIVVTGGVLSSVGKGTLVASIGMLLKRRGYNVTAVKIDPYINVDAGTMNPYMHGEVFVTEDGAETDLDLGHYERFMDVNMTKYNNITAGKVYFEVIKKEREGKYLGQTVQIIPHVTDQIKDMIRYASKINNAEITLVEIGGTVGDIESLPFLEAVRQLKLEEGEDNVIFVHIALVEYLSVTGELKTKPLQHSVQELRRIGIQPDFIVGRATLPLDDETRRKIALFTNVKVDHIVSSYDVETSYEVPIILESQKLVSKILSRLKLEDRQVDLTDWISFVNNIKGINSKKTINIALVGKYTKLKDSYISIKEAIYHASAYIGVRPKLIWIESTDLESDTKNLNEILGNVNGIIVLPGFGSRGAEGKIKAIKYAREHNIPFLGICFGFQLSIVEFARDVLGLSEANSTEINPNTKDPVITLLDEQKNVTQLGGTMRLGAQKIILKEGTIAYQLYGKKVVYERHRHRYEVNPKYVDILEDAGLVVSGISENGLVEIIELPSNKFFVATQAHPEFKSRPTNPSPIYLGFIRAVAS 534
                                    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       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   


Chain B from PDB  Type:PROTEIN  Length:533
 aligned with PYRG_SULSO | Q980S6 from UniProtKB/Swiss-Prot  Length:535

    Alignment length:533
                                    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       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531   
           PYRG_SULSO     2 PNKYIVVTGGVLSSVGKGTLVASIGMLLKRRGYNVTAVKIDPYINVDAGTMNPYMHGEVFVTEDGAETDLDLGHYERFMDVNMTKYNNITAGKVYFEVIKKEREGKYLGQTVQIIPHVTDQIKDMIRYASKINNAEITLVEIGGTVGDIESLPFLEAVRQLKLEEGEDNVIFVHIALVEYLSVTGELKTKPLQHSVQELRRIGIQPDFIVGRATLPLDDETRRKIALFTNVKVDHIVSSYDVETSYEVPIILESQKLVSKILSRLKLEDRQVDLTDWISFVNNIKGINSKKTINIALVGKYTKLKDSYISIKEAIYHASAYIGVRPKLIWIESTDLESDTKNLNEILGNVNGIIVLPGFGSRGAEGKIKAIKYAREHNIPFLGICFGFQLSIVEFARDVLGLSEANSTEINPNTKDPVITLLDEQKNVTQLGGTMRLGAQKIILKEGTIAYQLYGKKVVYERHRHRYEVNPKYVDILEDAGLVVSGISENGLVEIIELPSNKFFVATQAHPEFKSRPTNPSPIYLGFIRAVAS 534
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -CTP_synth_N-3nvaB03 B:3-278                                                                                                                                                                                                                                                         -------------------------GATase-3nvaB01 B:304-531                                                                                                                                                                                                            --- Pfam domains (1)
           Pfam domains (2) -CTP_synth_N-3nvaB04 B:3-278                                                                                                                                                                                                                                                         -------------------------GATase-3nvaB02 B:304-531                                                                                                                                                                                                            --- Pfam domains (2)
         Sec.struct. author ..eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.................eee.....eeehhhhhhhhhhh...hhh.eeehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhhhh...eeeeee.....hhhhhhhhhhhhhhhhhhh...eeeeeeee..........hhhhhhhhhhhhhhhh....eeeeee....hhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhh......eeeeeeee........hhhhhhhhhhhhhhh..eeeeeeee.hhhh...............eee.......hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh.....eee........eeeee...............eeeeeeeee...hhhhhhhh..eeeeeeee..ee...hhhhhhhh..eeeeee....eeeee......eeee..hhhhhh.....hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3nva B   2 PNKYIVVTGGVLSSVGKGTLVASIGMLLKRRGYNVTAVKIDPYINVDAGTMNPYMHGEVFVTEDGAETDLDLGHYERFMDVNMTKYNNITAGKVYFEVIKKEREGKYLGQTVQIIPHVTDQIKDMIRYASKINNAEITLVEIGGTVGDIESLPFLEAVRQLKLEEGEDNVIFVHIALVEYLSVTGELKTKPLQHSVQELRRIGIQPDFIVGRATLPLDDETRRKIALFTNVKVDHIVSSYDVETSYEVPIILESQKLVSKILSRLKLEDRQVDLTDWISFVNNIKGINSKKTINIALVGKYTKLKDSYISIKEAIYHASAYIGVRPKLIWIESTDLESDTKNLNEILGNVNGIIVLPGFGSRGAEGKIKAIKYAREHNIPFLGICFGFQLSIVEFARDVLGLSEANSTEINPNTKDPVITLLDEQKNVTQLGGTMRLGAQKIILKEGTIAYQLYGKKVVYERHRHRYEVNPKYVDILEDAGLVVSGISENGLVEIIELPSNKFFVATQAHPEFKSRPTNPSPIYLGFIRAVAS 534
                                    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       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511       521       531
   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 3NVA)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Glutaminase_I (73)
(-)
Clan: P-loop_NTPase (1112)

(-) Gene Ontology  (7, 7)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (PYRG_SULSO | Q980S6)
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: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
(no "Ligands, Modified Residues, Ions" information available for 3nva)
 
  Sites
(no "Sites" information available for 3nva)
 
  Cis Peptide Bonds
    Ile A:116 - Pro A:117   [ RasMol ]  
    Ile B:116 - Pro B:117   [ RasMol ]  
    Lys A:427 - Asn A:428   [ RasMol ]  
    Lys B:427 - Asn B:428   [ RasMol ]  
 

(-) 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 ](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
  3nva
    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
  PYRG_SULSO | Q980S6
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
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
  PYRG_SULSO | Q980S6
    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 3NVA)

(-) Related Entries Specified in the PDB File

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