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
(-)Biological Unit 3
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)
Image Biological Unit 3
Biological Unit 3  (Jmol Viewer)

(-) Description

Title :  STRUCTURES OF THYMIDYLATE SYNTHASE R163K WITH SUBSTRATES AND INHIBITORS SHOW SUBUNIT ASYMMETRY
 
Authors :  L. M. Gibson, L. L. Lovelace, L. Lebioda
Date :  30 Apr 09  (Deposition) - 12 May 10  (Release) - 27 Mar 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.65
Chains :  Asym. Unit :  A,B,C,D,E
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C  (2x)
Biol. Unit 3:  D,E  (1x)
Keywords :  Transferase, Methyltransferase, Nucleotide Biosynthesis (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. M. Gibson, L. R. Celeste, L. L. Lovelace, L. Lebioda
Structures Of Human Thymidylate Synthase R163K With Dump, Fdump And Glutathione Show Asymmetric Ligand Binding.
Acta Crystallogr. , Sect. D V. 67 60 2011
PubMed-ID: 21206062  |  Reference-DOI: 10.1107/S0907444910044732

(-) Compounds

Molecule 1 - THYMIDYLATE SYNTHASE
    ChainsA, B, C, D, E
    EC Number2.1.1.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneTYMS, TS, OK/SW-CL.29
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymTSASE, TS

 Structural Features

(-) Chains, Units

  12345
Asymmetric Unit ABCDE
Biological Unit 1 (1x)AB   
Biological Unit 2 (2x)  C  
Biological Unit 3 (1x)   DE

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric Unit (3, 7)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PO42Ligand/IonPHOSPHATE ION
3UFP3Ligand/Ion5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1EDO2Ligand/Ion1,2-ETHANEDIOL
2PO4-1Ligand/IonPHOSPHATE ION
3UFP2Ligand/Ion5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2PO42Ligand/IonPHOSPHATE ION
3UFP-1Ligand/Ion5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE
Biological Unit 3 (2, 2)
No.NameCountTypeFull Name
1EDO-1Ligand/Ion1,2-ETHANEDIOL
2PO41Ligand/IonPHOSPHATE ION
3UFP1Ligand/Ion5-FLUORO-2'-DEOXYURIDINE-5'-MONOPHOSPHATE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREARG A:50 , CYS A:195 , GLN A:214 , ARG A:215 , SER A:216 , GLY A:217 , ASP A:218 , ASN A:226 , HIS A:256 , EDO A:401 , ARG B:175 , ARG B:176BINDING SITE FOR RESIDUE UFP A 400
2AC2SOFTWAREPHE A:225 , UFP A:400BINDING SITE FOR RESIDUE EDO A 401
3AC3SOFTWAREARG A:175 , ARG A:176 , ARG B:50 , CYS B:195 , ARG B:215 , SER B:216 , ASP B:218 , ASN B:226 , TYR B:258 , EDO B:401BINDING SITE FOR RESIDUE UFP B 400
4AC4SOFTWARELEU B:221 , UFP B:400BINDING SITE FOR RESIDUE EDO B 401
5AC5SOFTWAREARG C:50 , ARG C:175 , ARG C:176 , ARG C:215BINDING SITE FOR RESIDUE PO4 C 365
6AC6SOFTWAREARG D:50 , CYS D:195 , GLN D:214 , ARG D:215 , SER D:216 , ASP D:218 , ASN D:226 , ARG E:175 , ARG E:176BINDING SITE FOR RESIDUE UFP D 565
7AC7SOFTWAREARG D:175 , ARG D:176 , ARG E:215 , SER E:216BINDING SITE FOR RESIDUE PO4 D 616

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3H9K)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3H9K)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3H9K)

(-) PROSITE Motifs  (1, 5)

Asymmetric Unit (1, 5)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_HUMAN175-203
 
 
 
 
  5A:175-203
B:175-203
C:175-203
D:175-203
E:175-203
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_HUMAN175-203
 
 
 
 
  2A:175-203
B:175-203
-
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_HUMAN175-203
 
 
 
 
  2-
-
C:175-203
-
-
Biological Unit 3 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.TYSY_HUMAN175-203
 
 
 
 
  2-
-
-
D:175-203
E:175-203

(-) Exons   (7, 35)

Asymmetric Unit (7, 35)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1aENST000003232741aENSE00001753233chr18:657604-657947344TYSY_HUMAN1-69695A:26-69
B:26-69
C:26-69
D:27-69
E:26-69
44
44
44
43
44
1.2ENST000003232742ENSE00001225644chr18:659641-65971474TYSY_HUMAN69-93255A:69-93
B:69-93
C:69-93
D:69-93
E:69-93
25
25
25
25
25
1.3ENST000003232743ENSE00001225629chr18:662146-662320175TYSY_HUMAN94-152595A:94-152
B:94-152
C:94-152
D:94-152
E:94-152
59
59
59
59
59
1.4ENST000003232744ENSE00001225690chr18:669072-669173102TYSY_HUMAN152-186355A:152-186
B:152-186
C:152-186
D:152-186
E:152-186
35
35
35
35
35
1.5ENST000003232745ENSE00001225679chr18:670692-670867176TYSY_HUMAN186-244595A:186-244
B:186-244
C:186-244
D:186-244
E:186-244
59
59
59
59
59
1.6ENST000003232746ENSE00001225668chr18:671380-67145172TYSY_HUMAN245-268245A:245-268
B:245-268
C:245-268
D:245-268
E:245-268
24
24
24
24
24
1.7bENST000003232747bENSE00001786342chr18:672860-673578719TYSY_HUMAN269-313455A:269-306
B:269-306
C:269-306
D:269-306
E:269-306
38
38
38
38
38

(-) 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:281
 aligned with TYSY_HUMAN | P04818 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:281
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 
           TYSY_HUMAN    26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
               SCOP domains d3h9ka_ A: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3h9kA00 A:26-306 Thymidylate Synthase, chain A                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: A:26-69 UniProt: 1-69       ------------------------Exon 1.3  PDB: A:94-152 UniProt: 94-152                    ---------------------------------Exon 1.5  PDB: A:186-244 UniProt: 186-244                  Exon 1.6  PDB: A:245-268Exon 1.7b  PDB: A:269-306 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.2  PDB: A:69-93   ----------------------------------------------------------Exon 1.4  PDB: A:152-186           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3h9k A  26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 

Chain B from PDB  Type:PROTEIN  Length:281
 aligned with TYSY_HUMAN | P04818 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:281
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 
           TYSY_HUMAN    26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
               SCOP domains d3h9kb_ B: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3h9kB00 B:26-306 Thymidylate Synthase, chain A                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhhh..hhhhhhh.....hhhhhhhhhhhhhh...........hhhhhhhhh................hhhhhhhhhhhhh......eee...............eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: B:26-69 UniProt: 1-69       ------------------------Exon 1.3  PDB: B:94-152 UniProt: 94-152                    ---------------------------------Exon 1.5  PDB: B:186-244 UniProt: 186-244                  Exon 1.6  PDB: B:245-268Exon 1.7b  PDB: B:269-306 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.2  PDB: B:69-93   ----------------------------------------------------------Exon 1.4  PDB: B:152-186           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3h9k B  26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 

Chain C from PDB  Type:PROTEIN  Length:281
 aligned with TYSY_HUMAN | P04818 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:281
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 
           TYSY_HUMAN    26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
               SCOP domains d3h9kc_ C: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3h9kC00 C:26-306 Thymidylate Synthase, chain A                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhh.ee........eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh......hhhhhhhhhhh.............hhhhhhhh.................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh.........eee.....hhhhhhhh.eee........ Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: C:26-69 UniProt: 1-69       ------------------------Exon 1.3  PDB: C:94-152 UniProt: 94-152                    ---------------------------------Exon 1.5  PDB: C:186-244 UniProt: 186-244                  Exon 1.6  PDB: C:245-268Exon 1.7b  PDB: C:269-306 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.2  PDB: C:69-93   ----------------------------------------------------------Exon 1.4  PDB: C:152-186           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3h9k C  26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 

Chain D from PDB  Type:PROTEIN  Length:280
 aligned with TYSY_HUMAN | P04818 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:280
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306
           TYSY_HUMAN    27 PHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
               SCOP domains d3h9kd_ D: automated matches                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 3h9kD00 D:27-306 Thymidylate Synthase, chain A                                                                                                                                                                                                                                           CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhh....hhhhhh..........hhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee..........hhh.eeee....... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: D:27-69 UniProt: 1-69      ------------------------Exon 1.3  PDB: D:94-152 UniProt: 94-152                    ---------------------------------Exon 1.5  PDB: D:186-244 UniProt: 186-244                  Exon 1.6  PDB: D:245-268Exon 1.7b  PDB: D:269-306 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) ------------------------------------------Exon 1.2  PDB: D:69-93   ----------------------------------------------------------Exon 1.4  PDB: D:152-186           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3h9k D  27 PHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206       216       226       236       246       256       266       276       286       296       306

Chain E from PDB  Type:PROTEIN  Length:281
 aligned with TYSY_HUMAN | P04818 from UniProtKB/Swiss-Prot  Length:313

    Alignment length:281
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 
           TYSY_HUMAN    26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQRVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
               SCOP domains d3h9ke_ E: automated matches                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 3h9kE00 E:26-306 Thymidylate Synthase, chain A                                                                                                                                                                                                                                            CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhh............eeeeeeeeeeee.............hhhhhhhhhhhhhh...hhhhhhh..........hhhhhhh.............hhhhhhhhh................hhhhhhhhhhhhh......eee..hhhhh........eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhh.eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee....... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         ------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1a  PDB: E:26-69 UniProt: 1-69       ------------------------Exon 1.3  PDB: E:94-152 UniProt: 94-152                    ---------------------------------Exon 1.5  PDB: E:186-244 UniProt: 186-244                  Exon 1.6  PDB: E:245-268Exon 1.7b  PDB: E:269-306 [INCOMPLETE] Transcript 1 (1)
           Transcript 1 (2) -------------------------------------------Exon 1.2  PDB: E:69-93   ----------------------------------------------------------Exon 1.4  PDB: E:152-186           ------------------------------------------------------------------------------------------------------------------------ Transcript 1 (2)
                 3h9k E  26 PPHGELQYLGQIQHILRCGVRKDDRTGTGTLSVFGMQARYSLRDEFPLLTTKRVFWKGVLEELLWFIKGSTNAKELSSKGVKIWDANGSRDFLDSLGFSTREEGDLGPVYGFQWRHFGAEYRDMESDYSGQGVDQLQKVIDTIKTNPDDRRIIMCAWNPRDLPLMALPPCHALCQFYVVNSELSCQLYQRSGDMGLGVPFNIASYALLTYMIAHITGLKPGDFIHTLGDAHIYLNHIEPLKIQLQREPRPFPKLRILRKVEKIDDFKAEDFQIEGYNPHPT 306
                                    35        45        55        65        75        85        95       105       115       125       135       145       155       165       175       185       195       205       215       225       235       245       255       265       275       285       295       305 

   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, 5)

Asymmetric Unit

(-) CATH Domains  (1, 5)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3H9K)

(-) Gene Ontology  (52, 52)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E   (TYSY_HUMAN | P04818)
molecular function
    GO:0048037    cofactor binding    Interacting selectively and non-covalently with a cofactor, a substance that is required for the activity of an enzyme or other protein. Cofactors may be inorganic, such as the metal atoms zinc, iron, and copper in certain forms, or organic, in which case they are referred to as coenzymes. Cofactors may either be bound tightly to active sites or bind loosely with the substrate.
    GO:0008144    drug binding    Interacting selectively and non-covalently with a drug, any naturally occurring or synthetic substance, other than a nutrient, that, when administered or applied to an organism, affects the structure or functioning of the organism; in particular, any such substance used in the diagnosis, prevention, or treatment of disease.
    GO:0005542    folic acid binding    Interacting selectively and non-covalently with folic acid, pteroylglutamic acid. Folic acid is widely distributed as a member of the vitamin B complex and is essential for the synthesis of purine and pyrimidines.
    GO:0003729    mRNA binding    Interacting selectively and non-covalently with messenger RNA (mRNA), an intermediate molecule between DNA and protein. mRNA includes UTR and coding sequences, but does not contain introns.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    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.
    GO:0042803    protein homodimerization activity    Interacting selectively and non-covalently with an identical protein to form a homodimer.
    GO:0004799    thymidylate synthase activity    Catalysis of the reaction: 5,10-methylenetetrahydrofolate + dUMP = 7,8-dihydrofolate + thymidylate.
    GO:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
    GO:0071897    DNA biosynthetic process    The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
    GO:0000082    G1/S transition of mitotic cell cycle    The mitotic cell cycle transition by which a cell in G1 commits to S phase. The process begins with the build up of G1 cyclin-dependent kinase (G1 CDK), resulting in the activation of transcription of G1 cyclins. The process ends with the positive feedback of the G1 cyclins on the G1 CDK which commits the cell to S phase, in which DNA replication is initiated.
    GO:0007568    aging    A developmental process that is a deterioration and loss of function over time. Aging includes loss of functions such as resistance to disease, homeostasis, and fertility, as well as wear and tear. Aging includes cellular senescence, but is more inclusive. May precede death and may succeed developmental maturation (GO:0021700).
    GO:0031100    animal organ regeneration    The regrowth of a lost or destroyed animal organ.
    GO:0051216    cartilage development    The process whose specific outcome is the progression of a cartilage element over time, from its formation to the mature structure. Cartilage elements are skeletal elements that consist of connective tissue dominated by extracellular matrix containing collagen type II and large amounts of proteoglycan, particularly chondroitin sulfate.
    GO:0016049    cell growth    The process in which a cell irreversibly increases in size over time by accretion and biosynthetic production of matter similar to that already present.
    GO:0008283    cell proliferation    The multiplication or reproduction of cells, resulting in the expansion of a cell population.
    GO:0007623    circadian rhythm    Any biological process in an organism that recurs with a regularity of approximately 24 hours.
    GO:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0006235    dTTP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTTP, deoxyribosylthymine triphosphate.
    GO:0046078    dUMP metabolic process    The chemical reactions and pathways involving dUMP, deoxyuridine (5'-)monophosphate (2'-deoxyuridine 5'-phosphate).
    GO:0009157    deoxyribonucleoside monophosphate biosynthetic process    The chemical reactions and pathways resulting in the formation of a deoxyribonucleoside monophosphate, a compound consisting of a nucleobase linked to a deoxyribose sugar esterified with phosphate on the sugar.
    GO:0048589    developmental growth    The increase in size or mass of an entire organism, a part of an organism or a cell, where the increase in size or mass has the specific outcome of the progression of the organism over time from one condition to another.
    GO:0019088    immortalization of host cell by virus    A virus-induced cellular transformation arising in immortalized cells, or cells capable of indefinite replication, due to their ability to produce their own telomerase.
    GO:0060574    intestinal epithelial cell maturation    The developmental process, independent of morphogenetic (shape) change, that is required for a columna/cuboidal epithelial cell of the intestine to attain its fully functional state. A columnar/cuboidal epithelial cell of the intestine mature as they migrate from the intestinal crypt to the villus.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    GO:0006139    nucleobase-containing compound metabolic process    Any cellular metabolic process involving nucleobases, nucleosides, nucleotides and nucleic acids.
    GO:0009165    nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of nucleotides, any nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the glycose moiety; may be mono-, di- or triphosphate; this definition includes cyclic-nucleotides (nucleoside cyclic phosphates).
    GO:0006206    pyrimidine nucleobase metabolic process    The chemical reactions and pathways involving pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases.
    GO:0046134    pyrimidine nucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of one of a family of organic molecules consisting of a pyrimidine base covalently bonded to a sugar ribose (a ribonucleoside) or deoxyribose (a deoxyribonucleoside).
    GO:0000083    regulation of transcription involved in G1/S transition of mitotic cell cycle    Any process that regulates transcription such that the target genes are involved in the transition between G1 and S phase of the mitotic cell cycle.
    GO:0034097    response to cytokine    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a cytokine stimulus.
    GO:0042493    response to drug    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a drug stimulus. A drug is a substance used in the diagnosis, treatment or prevention of a disease.
    GO:0045471    response to ethanol    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an ethanol stimulus.
    GO:0051593    response to folic acid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a folic acid stimulus.
    GO:0051384    response to glucocorticoid    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a glucocorticoid stimulus. Glucocorticoids are hormonal C21 corticosteroids synthesized from cholesterol with the ability to bind with the cortisol receptor and trigger similar effects. Glucocorticoids act primarily on carbohydrate and protein metabolism, and have anti-inflammatory effects.
    GO:0014070    response to organic cyclic compound    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organic cyclic compound stimulus.
    GO:0046683    response to organophosphorus    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of an organophosphorus stimulus. Organophosphorus is a compound containing phosphorus bound to an organic molecule; several organophosphorus compounds are used as insecticides, and they are highly toxic cholinesterase inhibitors.
    GO:0032570    response to progesterone    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a progesterone stimulus.
    GO:0009636    response to toxic substance    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a toxic stimulus.
    GO:0033189    response to vitamin A    Any process that results in a change in state or activity of a cell or an organism (in terms of movement, secretion, enzyme production, gene expression, etc.) as a result of a vitamin A stimulus.
    GO:0035999    tetrahydrofolate interconversion    The chemical reactions and pathways by which one-carbon (C1) units are transferred between tetrahydrofolate molecules, to synthesise other tetrahydrofolate molecules.
    GO:0046653    tetrahydrofolate metabolic process    The chemical reactions and pathways involving tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.
    GO:0019860    uracil metabolic process    The chemical reactions and pathways involving uracil, 2,4-dioxopyrimidine, one of the pyrimidine bases occurring in RNA, but not in DNA.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.
    GO:0005829    cytosol    The part of the cytoplasm that does not contain organelles but which does contain other particulate matter, such as protein complexes.
    GO:0016020    membrane    A lipid bilayer along with all the proteins and protein complexes embedded in it an attached to it.
    GO:0005743    mitochondrial inner membrane    The inner, i.e. lumen-facing, lipid bilayer of the mitochondrial envelope. It is highly folded to form cristae.
    GO:0005759    mitochondrial matrix    The gel-like material, with considerable fine structure, that lies in the matrix space, or lumen, of a mitochondrion. It contains the enzymes of the tricarboxylic acid cycle and, in some organisms, the enzymes concerned with fatty acid oxidation.
    GO:0005739    mitochondrion    A semiautonomous, self replicating organelle that occurs in varying numbers, shapes, and sizes in the cytoplasm of virtually all eukaryotic cells. It is notably the site of tissue respiration.
    GO:0005730    nucleolus    A small, dense body one or more of which are present in the nucleus of eukaryotic cells. It is rich in RNA and protein, is not bounded by a limiting membrane, and is not seen during mitosis. Its prime function is the transcription of the nucleolar DNA into 45S ribosomal-precursor RNA, the processing of this RNA into 5.8S, 18S, and 28S components of ribosomal RNA, and the association of these components with 5S RNA and proteins synthesized outside the nucleolus. This association results in the formation of ribonucleoprotein precursors; these pass into the cytoplasm and mature into the 40S and 60S subunits of the ribosome.
    GO:0005654    nucleoplasm    That part of the nuclear content other than the chromosomes or the nucleolus.
    GO:0005634    nucleus    A membrane-bounded organelle of eukaryotic cells in which chromosomes are housed and replicated. In most cells, the nucleus contains all of the cell's chromosomes except the organellar chromosomes, and is the site of RNA synthesis and processing. In some species, or in specialized cell types, RNA metabolism or DNA replication may be absent.

 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
    EDO  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    PO4  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UFP  [ 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 ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3h9k)
 
Biological Units
  Complete Structure
    Biological Unit 1  [ Jena3D ]
    Biological Unit 2  [ Jena3D ]
    Biological Unit 3  [ Jena3D ]

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  3h9k
    Family and Domain InformationProDom | SYSTERS
    General Structural InformationGlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in MembranesOPM
    Protein SurfaceSURFACE
    Secondary StructureDSSP (structure derived) | HSSP (homology derived)
    Structural GenomicsGeneCensus
    Structural NeighboursCE | VAST
    Structure ClassificationCATH | Dali | SCOP
    Validation and Original DataBMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  TYSY_HUMAN | P04818
    Comparative Protein Structure ModelsModBase
    Genomic InformationEnsembl
    Protein-protein InteractionDIP
    Sequence, Family and Domain InformationInterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  2.1.1.45
    General Enzyme InformationBRENDA | EC-PDB | Enzyme | IntEnz
    PathwayKEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease InformationOMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related InformationGenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain InformationXDom
    Interatomic Contacts of Structural UnitsCSU
    Ligand-protein ContactsLPC
    Protein CavitiescastP
    Sequence and Secondary StructurePDBCartoon
    Structure AlignmentSTRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence BrowserSTING
 
Access by UniProt ID/Accession number
  TYSY_HUMAN | P04818
    Protein Disorder PredictionDisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        TYSY_HUMAN | P048181hvy 1hw3 1hw4 1hzw 1i00 1ju6 1juj 1ypv 2onb 2rd8 2rda 3eaw 3ebu 3ed7 3edw 3ef9 3egy 3ehi 3ejl 3gg5 3gh0 3gh2 3hb8 3n5e 3n5g 3ob7 4e28 4fgt 4g2o 4g6w 4gd7 4gyh 4h1i 4jef 4kpw 4o1u 4o1x 4up1 5hs3 5wrn 5x4w 5x4x 5x4y 5x5a 5x5d 5x5q 5x66 5x67 5x69

(-) Related Entries Specified in the PDB File

1hvy 1hw3 2rd8 2rda