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
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)

(-) Description

Title :  STRUCTURE OF CITRATE SYNTHASE FROM THE THERMOACIDOPHILIC EURYARCHAEON THERMOLASMA ACIDOPHILUM
 
Authors :  J. R. Murphy, S. Donini, T. J. Kappock
Date :  19 Feb 15  (Deposition) - 02 Sep 15  (Release) - 14 Oct 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Tricarboxylic Acid Cycle, Transferase, Carbohydrate Metabolism (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. R. Murphy, S. Donini, T. J. Kappock
An Active Site-Tail Interaction In The Structure Of Hexahistidine-Tagged Thermoplasma Acidophilum Citrate Synthase
Acta Crystallogr. , Sect. F V. 71 1292 2015
PubMed: search  |  Reference-DOI: 10.1107/S2053230X15015939

(-) Compounds

Molecule 1 - CITRATE SYNTHASE
    Atcc: 25905
    Chains: A, B, C, D
    EC Number: 2.3.3.16
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET24A
    Expression System Strain: C41(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: GLTA, TA0169
    Organism Scientific: THERMOPLASMA ACIDOPHILUM (STRAIN ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165)
    Organism Taxid: 273075
    Strain: ATCC 25905 / DSM 1728 / JCM 9062 / NBRC 15155 / AMRC-C165

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): AB  
Biological Unit 2 (1x):   CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
1BCT2Ligand/IonBICARBONATE ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1BCT1Ligand/IonBICARBONATE ION

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS B:286 , PRO B:287 , GLU B:288 , VAL B:289binding site for residue BCT B 400
2AC2SOFTWARELYS C:286 , PRO C:287 , GLU C:288binding site for residue BCT C 400

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4YBO)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4YBO)

(-) 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:395
                                                                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhh..eeeee..eeee....eeee..eehhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.........hhhhh..hhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybo A   5 EISKGLEDVNIKWTRLTTIDGNKGILRYGGYSVEDIIASGAQDEEIQYLFLYGNLPTEQELRKYKETVQKGYKIPDFVINAIRQLPRESDAVAMQMAAVAAMAASETKFKWNKDTDRDVAAEMIGRMSAITVNVYRHIMNMPAELPKPSDSYAESFLNAAFGRKATKEEIDAMNTALILYTDHEVPASTTAGLVAVSTLSDMYSGITAALAALKGPLHGGAAEAAIAQFDEIKDPAMVEKWFNDNIINGKKRLMGFGHRVYKTYDPRAKIFKGIAEKLSSKKPEVHKVYEIATKLEDFGIKAFGSKGIYPNTDYFSGIVYMSIGFPLRNNIYTALFALSRVTGWQAHFIEYVEEQQRLIRPRAVYVGPAERKYVPIAERKVDKLAAALEHHHHHH 399
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394     


Chain B from PDB  Type:PROTEIN  Length:381
                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeeee..eeee....eeee..eehhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhh...hhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.........hhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybo B   4 EEISKGLEDVNIKWTRLTTIDGNKGILRYGGYSVEDIIASGAQDEEIQYLFLYGNLPTEQELRKYKETVQKGYKIPDFVINAIRQLPRESDAVAMQMAAVAAMAASETKFKWNKDTDRDVAAEMIGRMSAITVNVYRHIMNMPAELPKPSDSYAESFLNAAFGRKATKEEIDAMNTALILYTDHEVPASTTAGLVAVSTLSDMYSGITAALAALKGPLHGGAAEAAIAQFDEIKDPAMVEKWFNDNIINGKKRLMGFGHRVYKTYDPRAKIFKGIAEKLSSKKPEVHKVYEIATKLEDFGIKAFGSKGIYPNTDYFSGIVYMSIGFPLRNNIYTALFALSRVTGWQAHFIEYVEEQQRLIRPRAVYVGPAERKYVPIAERK 384
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383 


Chain C from PDB  Type:PROTEIN  Length:380
                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhh..eeeee..eeee....eeee..eehhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeee.........hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybo C   4 EEISKGLEDVNIKWTRLTTIDGNKGILRYGGYSVEDIIASGAQDEEIQYLFLYGNLPTEQELRKYKETVQKGYKIPDFVINAIRQLPRESDAVAMQMAAVAAMAASETKFKWNKDTDRDVAAEMIGRMSAITVNVYRHIMNMPAELPKPSDSYAESFLNAAFGRKATKEEIDAMNTALILYTDHEVPASTTAGLVAVSTLSDMYSGITAALAALKGPLHGGAAEAAIAQFDEIKDPAMVEKWFNDNIINGKKRLMGFGHRVYKTYDPRAKIFKGIAEKLSSKKPEVHKVYEIATKLEDFGIKAFGSKGIYPNTDYFSGIVYMSIGFPLRNNIYTALFALSRVTGWQAHFIEYVEEQQRLIRPRAVYVGPAERKYVPIAER 383
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373       383


Chain D from PDB  Type:PROTEIN  Length:397
                                                                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhh..eeeee..eeee....eeee..eehhhhhhh..hhhhhhhhhhhh...hhhhhhhhhhhhhhh...hhhhhhhhhh.....hhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhh...hhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhh.hhhhhhhhhhhhh..................hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....eeee.........hhhhh..hhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ybo D   3 TEEISKGLEDVNIKWTRLTTIDGNKGILRYGGYSVEDIIASGAQDEEIQYLFLYGNLPTEQELRKYKETVQKGYKIPDFVINAIRQLPRESDAVAMQMAAVAAMAASETKFKWNKDTDRDVAAEMIGRMSAITVNVYRHIMNMPAELPKPSDSYAESFLNAAFGRKATKEEIDAMNTALILYTDHEVPASTTAGLVAVSTLSDMYSGITAALAALKGPLHGGAAEAAIAQFDEIKDPAMVEKWFNDNIINGKKRLMGFGHRVYKTYDPRAKIFKGIAEKLSSKKPEVHKVYEIATKLEDFGIKAFGSKGIYPNTDYFSGIVYMSIGFPLRNNIYTALFALSRVTGWQAHFIEYVEEQQRLIRPRAVYVGPAERKYVPIAERKVDKLAAALEHHHHHH 399
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       382       392
   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 4YBO)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (6, 6)

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
    BCT  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ybo)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ 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 ](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
  4ybo
    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
  CISY_THEAC | P21553
    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)
  2.3.3.16
    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
  CISY_THEAC | P21553
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        CISY_THEAC | P21553: 2ifc 2r26 2r9e

(-) Related Entries Specified in the PDB File

2ifc 2IFC CONTAINS AN UNTAGGED VERSION OF THE SAME PROTEIN COMPLEXED WITH OXALOACETATE.
2r26 2R26 CONTAINS AN UNTAGGED VERSION OF THE SAME PROTEIN COMPLEXED WITH OXALOACETATE AND CARBOXYMETHYL-COA.
2r9e 2R9E CONTAINS AN UNTAGGED VERSION OF THE SAME PROTEIN COMPLEXED WITH DETHIACITRYL-COA.