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 :  THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CB3717
 
Authors :  Z. Newby, T. T. Lee, J. Finer-Moore, R. M. Stroud
Date :  10 May 13  (Deposition) - 22 May 13  (Release) - 05 Jun 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.30
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Protein, Methyltransferase, Methylenetetrahydrofolate, Antifolate, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  Z. Wang, P. J. Sapienza, T. Abeysinghe, C. Luzum, A. L. Lee, J. S. Finer-Moore, R. M. Stroud, A. Kohen
Mg(2+) Binds To The Surface Of Thymidylate Synthase And Affects Hydride Transfer At The Interior Active Site.
J. Am. Chem. Soc. V. 135 7583 2013
PubMed-ID: 23611499  |  Reference-DOI: 10.1021/JA400761X
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    Chains: A, B
    EC Number: 2.1.1.45
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: B2827, JW2795, THYA
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 83333
    Strain: K12
    Synonym: TS, TSASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 7)

Asymmetric/Biological Unit (4, 7)
No.NameCountTypeFull Name
1CB32Ligand/Ion10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
2CXM2Mod. Amino AcidN-CARBOXYMETHIONINE
3NA1Ligand/IonSODIUM ION
4UMC2Ligand/Ion2'-DEOXY-5'-URIDYLIC ACID

(-) Sites  (5, 5)

Asymmetric Unit (5, 5)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:21 , CYS A:146 , HIS A:147 , GLN A:165 , ARG A:166 , SER A:167 , CYS A:168 , ASP A:169 , ASN A:177 , HIS A:207 , TYR A:209 , CB3 A:902 , HOH A:1020 , HOH A:1059 , ARG B:126 , ARG B:127BINDING SITE FOR RESIDUE UMC A 901
2AC2SOFTWAREGLU A:58 , ILE A:79 , TRP A:80 , TRP A:83 , LEU A:143 , ASP A:169 , GLY A:173 , PHE A:176 , ASN A:177 , TYR A:209 , VAL A:262 , ALA A:263 , UMC A:901 , HOH A:1014 , HOH A:1031 , HOH A:1054 , HOH A:1061 , HOH A:1064 , HOH A:1077 , HOH A:1117 , HOH A:1130 , HOH A:1140 , HOH A:1263 , HOH A:1317 , HOH A:1383 , HOH A:1412BINDING SITE FOR RESIDUE CB3 A 902
3AC3SOFTWAREHIS A:51 , ARG A:53 , ASN A:76 , HOH A:1054 , HOH A:1298 , HOH A:1317 , HOH A:1345 , HOH A:1464 , HOH A:1465BINDING SITE FOR RESIDUE NA A 903
4AC4SOFTWAREARG A:126 , ARG A:127 , ARG B:21 , CYS B:146 , HIS B:147 , GLN B:165 , ARG B:166 , SER B:167 , CYS B:168 , ASP B:169 , ASN B:177 , HIS B:207 , TYR B:209 , CB3 B:302 , HOH B:411 , HOH B:415BINDING SITE FOR RESIDUE UMC B 301
5AC5SOFTWAREGLU B:58 , ILE B:79 , TRP B:80 , TRP B:83 , LEU B:143 , ASP B:169 , GLY B:173 , PHE B:176 , ASN B:177 , TYR B:209 , ILE B:258 , VAL B:262 , ALA B:263 , UMC B:301 , HOH B:422 , HOH B:431 , HOH B:458 , HOH B:460 , HOH B:462 , HOH B:464 , HOH B:480 , HOH B:501 , HOH B:546 , HOH B:594 , HOH B:713 , HOH B:766BINDING SITE FOR RESIDUE CB3 B 302

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4KNZ)

(-) 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
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4knza_ A: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhhh...hhhhhhh....hhhhh........hhhhhhhheee...eeehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4knz A   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                            |       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    
                            |                                                                                                                                                                                                                                                                       
                            1-CXM                                                                                                                                                                                                                                                                   


Chain B from PDB  Type:PROTEIN  Length:264
                                                                                                                                                                                                                                                                                                        
               SCOP domains d4knzb_ B: Thymidylate synthase                                                                                                                                                                                                                                          SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhheee.......eeeeeeeeeeee.hhh.........hhhhhhhhhhhhhh....hhhhhhh....hhhhh........hhhhhhhhee.....eehhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhhh.......eeee..........hhh.eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4knz B   1 mKQYLELMQKVLDEGTQKNDRTGTGTLSIFGHQMRFNLQDGFPLVTTKRCHLRSIIHELLWFLQGDTNIAYLHENNVTIWDEWADENGDLGPVYGKQWRAWPTPDGRHIDQITTVLNQLKNDPDSRRIIVSAWNVGELDKMALAPCHAFFQFYVADGKLSCQLYQRSCDVFLGLPFNIASYALLVHMMAQQCDLEVGDFVWTGGDTHLYSNHMDQTHLQLSREPRPLPKLIIKRKPESIFDYRFEDFEIEGYDPHPGIKAPVAI 264
                            |       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    
                            1-CXM
   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/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (11, 11)

Asymmetric/Biological Unit(hide GO term definitions)

 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
    CB3  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    CXM  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UMC  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4knz)
 

(-) 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
  4knz
    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
  TYSY_ECOLI | P0A884
    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)
  2.1.1.45
    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
  TYSY_ECOLI | P0A884
    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
        TYSY_ECOLI | P0A884: 1aiq 1ajm 1an5 1aob 1axw 1bdu 1bid 1bjg 1bq1 1bq2 1ddu 1dna 1ev5 1ev8 1evf 1evg 1f4b 1f4c 1f4d 1f4e 1f4f 1f4g 1ffl 1fwm 1jg0 1jtq 1jtu 1jut 1kce 1kzi 1kzj 1nce 1qqq 1syn 1tdu 1tjs 1tlc 1tls 1trg 1tsd 1tsn 1tys 1zpr 2a9w 2bbq 2ftn 2fto 2ftq 2g8x 2kce 2tsc 2vet 2vf0 3b5b 3b9h 3bfi 3bgx 3bhl 3bhr 3tms 4f2v 4gev 4isk

(-) Related Entries Specified in the PDB File

4gev E. COLI Y209W THYMIDYLATE SYNTHASE TERNARY COMPLEX WITH DUMP AND CB3717