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
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)

(-) Description

Title :  X-RAY CRYSTAL STRUCTURE OF THE "CLOSED" CONFORMATION OF CTP-INHIBITED E. COLI CYTIDINE TRIPHOSPHATE (CTP) SYNTHETASE
 
Authors :  E. P. Baldwin, J. A. Endrizzi
Date :  07 Oct 16  (Deposition) - 26 Apr 17  (Release) - 14 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A,B  (2x)
Keywords :  Pyrimidine Biosynthesis, Enzyme Regulation Via Polymerization, Feedback Inhibition, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Lynch, D. R. Hicks, M. Shepherd, J. A. Endrizzi, A. Maker, J. M. Hansen, R. M. Barry, Z. Gitai, E. P. Baldwin, J. M. Kollman
Human Ctp Synthase Filament Structure Reveals The Active Enzyme Conformation.
Nat. Struct. Mol. Biol. V. 24 507 2017
PubMed-ID: 28459447  |  Reference-DOI: 10.1038/NSMB.3407

(-) Compounds

Molecule 1 - CTP SYNTHASE
    Chains: A, B
    EC Number: 6.3.4.2
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28B
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PYRG, B2780, JW2751
    Organism Scientific: ESCHERICHIA COLI (STRAIN K12)
    Organism Taxid: 83333
    Synonym: CYTIDINE 5'-TRIPHOSPHATE SYNTHASE,CYTIDINE TRIPHOSPHATE SYNTHETASE,CTPS,UTP--AMMONIA LIGASE

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (2x): AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 18)

Asymmetric Unit (6, 18)
No.NameCountTypeFull Name
1CTP2Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2GLN2Mod. Amino AcidGLUTAMINE
3MG2Ligand/IonMAGNESIUM ION
4MPD2Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD2Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
6SO48Ligand/IonSULFATE ION
Biological Unit 1 (5, 32)
No.NameCountTypeFull Name
1CTP4Ligand/IonCYTIDINE-5'-TRIPHOSPHATE
2GLN4Mod. Amino AcidGLUTAMINE
3MG-1Ligand/IonMAGNESIUM ION
4MPD4Ligand/Ion(4S)-2-METHYL-2,4-PENTANEDIOL
5MRD4Ligand/Ion(4R)-2-METHYLPENTANE-2,4-DIOL
6SO416Ligand/IonSULFATE ION

(-) Sites  (17, 17)

Asymmetric Unit (17, 17)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:351 , GLY A:352 , PHE A:353 , CYS A:379 , LEU A:380 , GLN A:383 , GLU A:403 , ARG A:468 , HIS A:469 , ARG A:470 , TYR A:471 , HIS A:515 , HOH A:799binding site for residue GLN A 601
02AC2SOFTWARELEU A:16 , GLY A:17 , LYS A:18 , GLY A:19 , SO4 A:603 , HOH A:701 , HOH A:779binding site for residue SO4 A 602
03AC3SOFTWARELYS A:18 , LYS A:40 , GLU A:140 , GLY A:142 , GLY A:143 , SO4 A:602 , HOH A:702 , HOH A:770binding site for residue SO4 A 603
04AC4SOFTWAREARG A:211 , VAL A:241 , ILE A:247binding site for residue MPD A 604
05AC5SOFTWAREARG A:391 , HIS A:392binding site for residue SO4 A 605
06AC6SOFTWARELYS A:297 , PHE A:353 , ARG A:356 , HOH A:704binding site for residue SO4 A 606
07AC7SOFTWARECTP B:603 , HOH B:788 , HOH B:821 , HOH B:841binding site for residue MG A 607
08AC8SOFTWARESER A:14 , GLN A:114 , ILE A:116 , ASP A:147 , ILE A:148 , GLU A:149 , HOH A:730 , LYS B:187 , THR B:188 , LYS B:189 , GLN B:192 , LYS B:223 , MG B:602 , HOH B:759 , HOH B:771 , HOH B:785 , HOH B:796 , HOH B:799 , HOH B:812 , HOH B:837binding site for residue CTP B 601
09AC9SOFTWARECTP B:601 , HOH B:796 , HOH B:812 , HOH B:837binding site for residue MG B 602
10AD1SOFTWARELYS A:187 , THR A:188 , LYS A:189 , GLN A:192 , LYS A:223 , MG A:607 , SER B:14 , GLN B:114 , VAL B:115 , ILE B:116 , ASP B:147 , ILE B:148 , GLU B:149 , HOH B:728 , HOH B:740 , HOH B:788 , HOH B:795 , HOH B:809 , HOH B:821 , HOH B:841binding site for residue CTP B 603
11AD2SOFTWAREGLY B:351 , GLY B:352 , PHE B:353 , CYS B:379 , LEU B:380 , GLN B:383 , GLU B:403 , HIS B:469 , ARG B:470 , TYR B:471 , HIS B:515binding site for residue GLN B 604
12AD3SOFTWARESER B:15 , LEU B:16 , GLY B:17 , LYS B:18 , GLY B:19 , SO4 B:606 , HOH B:704 , HOH B:738binding site for residue SO4 B 605
13AD4SOFTWARELYS B:18 , LYS B:40 , GLU B:140 , GLY B:142 , GLY B:143 , SO4 B:605 , HOH B:703 , HOH B:705 , HOH B:847binding site for residue SO4 B 606
14AD5SOFTWAREARG B:211 , LEU B:238 , LYS B:239 , ASP B:240 , VAL B:241 , ILE B:247binding site for residue MPD B 607
15AD6SOFTWAREARG B:391 , HIS B:392binding site for residue SO4 B 608
16AD7SOFTWARELYS B:297 , ARG B:356 , HOH B:701binding site for residue SO4 B 609
17AD8SOFTWAREGLU B:283binding site for residue MRD B 611

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5TKV)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Ile A:116 -Pro A:117
2Ile B:116 -Pro B:117

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5TKV)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5TKV)

(-) Exons   (0, 0)

(no "Exon" information available for 5TKV)

(-) 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:533
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.....hhhhh........ee.....ee.hhhhhhhh......hhh.eeehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhh.hhhhhhhhhh........hhhhhhhhhhhhh..eeeeeeeee....hhhhhhhhhhhhhhhhhhh.eeeeeeeeehhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......ee.........eeee..............eeeeeeeee...hhhhhhh...eeeeeeee..ee...hhhhhhhh..eeeee......eeeee......eeee..hhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkv A   1 MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVLRKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIESLPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLSIGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGLLKSQGLDDYICKRFSLNAPEANLSEWEQVIFEEANPVSEVTIGMVGKYIELPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVPGGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENANSTEFVPDCKYPVVALITEWRDENGNVEMRLGAQQCQLVDDSLVRQLYNAPTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQQ 601
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420      |441       451       461       471       481       491       501       511       521       531       541 ||
                                                                                                                                                                                                                                                                                                                                                                                                                                                                    427|                                                                                                     543|
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     439                                                                                                      601


Chain B from PDB  Type:PROTEIN  Length:535
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeee......hhhhhhhhhhhhhhh....eeeeeee.....hhhhhhhhhhh..ee.....ee.hhhhhhhhhh....hhh.eeehhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh...eeeeee........hhhhhhhhhhhhhhhh...eeeeeeee..ee....ee.hhhhhhhhhhhhhh.....eeeeee....hhhhhhhhhhhhh.hhh.eeeee...hhhhhhhhhhh.hhhhhhhhhh........hhhhhhhhhhhhh...eeeeeeee....hhhhhhhhhhhhhhhhhhh..eeeeeeeehhhhhhhhhhhhh...eeee.......hhhhhhhhhhhhhhh...eeeehhhhhhhhhhhhhhh......ee.........eeeehhhhh...........eeeeeeeee...hhhhhhh...eeeeeeee..ee...hhhhhhh...eeeee......eeeee......eeee..hhhhhh.....hhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5tkv B   1 MTTNYIFVTGGVVSSLGKGIAAASLAAILEARGLNVTIMKLDPYINVDPGTMSPIQHGEVFVTEDGAETDLDLGHYERFIRTKMSRRNNFTTGRIYSDVLRKERRGDYLGATVQVIPHITNAIKERVLEGGEGHDVVLVEIGGTVGDIESLPFLEAIRQMAVEIGREHTLFMHLTLVPYMAASGEVKTKPTQHSVKELLSIGIQPDILICRSDRAVPANERAKIALFCNVPEKAVISLKDVDSIYKIPGLLKSQGLDDYICKRFSLNAPEANLSEWEQVIFEEANPVSEVTIGMVGKYIELPDAYKSVIEALKHGGLKNRVSVNIKLIDSQDVETRGVEILKGLDAILVPGGFGYRGVEGMITTARFARENNIPYLGICLGMQVALIDYARHVANMENANSTEFVPDCKYPVVALITEWRDENGNVEVTMRLGAQQCQLVDDSLVRQLYNAPTIVERHRHRYEVNNMLLKQIEDAGLRVAGRSGDDQLVEIIEVPNHPWFVACQFHPEFTSTPRDGHPLFAGFVKAASEFQKRQA 544
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370       380       390       400       410       420       439       449       459       469       479       489       499       509       519       529       539     
                                                                                                                                                                                                                                                                                                                                                                                                                                                                     428|                                                                                                          
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      438
   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 5TKV)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5TKV)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5TKV)

(-) Gene Ontology  (10, 10)

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
    CTP  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GLN  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MPD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    MRD  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    SO4  [ 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 ]
    AC9  [ RasMol ]  +environment [ RasMol ]
    AD1  [ RasMol ]  +environment [ RasMol ]
    AD2  [ RasMol ]  +environment [ RasMol ]
    AD3  [ RasMol ]  +environment [ RasMol ]
    AD4  [ RasMol ]  +environment [ RasMol ]
    AD5  [ RasMol ]  +environment [ RasMol ]
    AD6  [ RasMol ]  +environment [ RasMol ]
    AD7  [ RasMol ]  +environment [ RasMol ]
    AD8  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
    Ile A:116 - Pro A:117   [ RasMol ]  
    Ile B:116 - Pro B:117   [ RasMol ]  
 
Biological Unit
  Complete Structure
    Biological Unit 1  [ 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 ](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
  5tkv
    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_ECOLI | P0A7E5
    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_ECOLI | P0A7E5
    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
        PYRG_ECOLI | P0A7E5: 1s1m 2ad5

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5TKV)