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(-) Description

Title :  TRYPANOSOMA CRUZI DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE COMPLEXED WITH NADPH, DUMP AND C-448 ANTIFOLATE
 
Authors :  P. Chitnumsub, J. Yuvaniyama, Y. Yuthavong
Date :  13 Aug 09  (Deposition) - 28 Jul 10  (Release) - 02 Mar 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.37
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Dhfr-Ts Antifolate Complex, Methyltransferase, Multifunctional Enzyme, Nadp, Nucleotide Biosynthesis, One-Carbon Metabolism, Oxidoreductase, Transferase, Oxidoreductase-Transferase Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P Chitnumsub, J Yuvaniyama, T Vilaivan, J Vanichtanankul, S Kamchonwongpaisan, Y Yuthavong
Structural Basis Of Antifolate Inhibition Of Trypanosoma Cruzi Dihydrofolate Reductase-Thymidylate Synthase
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - BIFUNCTIONAL DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
    ChainsA, B
    EC Number1.5.1.3, 2.1.1.45
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET11C
    Expression System StrainBL21(DE3) PLYSS
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    Organism ScientificTRYPANOSOMA CRUZI
    Organism Taxid5693
    StrainY
    SynonymDHFR-TS, DIHYDROFOLATE REDUCTASE, THYMIDYLATE SYNTHASE

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 11)

Asymmetric/Biological Unit (4, 11)
No.NameCountTypeFull Name
1C502Ligand/Ion1-[3-(2,3-DICHLOROPHENOXY)PROPOXY]-6,6-DIMETHYL-1,6-DIHYDRO-1,3,5-TRIAZINE-2,4-DIAMINE
2GOL5Ligand/IonGLYCEROL
3NDP2Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4UMP2Ligand/Ion2'-DEOXYURIDINE 5'-MONOPHOSPHATE

(-) Sites  (11, 11)

Asymmetric Unit (11, 11)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREVAL A:26 , VAL A:27 , ILE A:41 , ASP A:48 , MET A:49 , PHE A:52 , THR A:80 , PHE A:88 , ILE A:154 , TYR A:160 , NDP A:602BINDING SITE FOR RESIDUE C50 A 601
02AC2SOFTWAREVAL A:27 , ALA A:28 , ILE A:35 , GLY A:36 , ASP A:37 , GLY A:38 , ARG A:39 , SER A:40 , ILE A:41 , GLY A:77 , ARG A:78 , LYS A:79 , THR A:80 , LEU A:99 , SER A:100 , SER A:101 , THR A:102 , GLY A:130 , GLY A:131 , ILE A:154 , GLY A:155 , GLY A:156 , GLY A:157 , SER A:158 , VAL A:159 , TYR A:160 , C50 A:601 , HOH A:1073 , HOH A:1156BINDING SITE FOR RESIDUE NDP A 602
03AC3SOFTWAREARG A:257 , CYS A:403 , HIS A:404 , GLN A:422 , ARG A:423 , SER A:424 , CYS A:425 , ASP A:426 , GLY A:430 , ASN A:434 , HIS A:464 , TYR A:466 , GOL A:701 , GOL A:705 , HOH A:1036 , HOH A:1160 , ARG B:383 , ARG B:384BINDING SITE FOR RESIDUE UMP A 603
04AC4SOFTWARELEU A:429 , PHE A:433 , UMP A:603 , GOL A:705BINDING SITE FOR RESIDUE GOL A 701
05AC5SOFTWAREGLU A:295 , TYR A:343 , HIS A:404 , PHE A:433 , UMP A:603 , GOL A:701 , HOH A:1197BINDING SITE FOR RESIDUE GOL A 705
06AC6SOFTWAREVAL B:26 , VAL B:27 , ILE B:41 , ASP B:48 , PHE B:52 , ILE B:84 , PRO B:85 , PHE B:88 , ILE B:154 , TYR B:160 , THR B:178 , NDP B:602BINDING SITE FOR RESIDUE C50 B 601
07AC7SOFTWAREALA B:28 , ILE B:35 , ASP B:37 , GLY B:38 , ARG B:39 , SER B:40 , ILE B:41 , GLY B:77 , ARG B:78 , LYS B:79 , THR B:80 , LEU B:99 , SER B:100 , SER B:101 , THR B:102 , GLY B:130 , GLY B:131 , ILE B:154 , GLY B:155 , GLY B:156 , GLY B:157 , SER B:158 , VAL B:159 , TYR B:160 , C50 B:601 , HOH B:1274BINDING SITE FOR RESIDUE NDP B 602
08AC8SOFTWAREARG A:383 , ARG A:384 , CYS B:403 , HIS B:404 , GLN B:422 , ARG B:423 , SER B:424 , ASP B:426 , GLY B:430 , ASN B:434 , HIS B:464 , TYR B:466 , GOL B:703 , GOL B:704 , HOH B:1146 , HOH B:1218BINDING SITE FOR RESIDUE UMP B 603
09AC9SOFTWAREGLY A:267 , GLN B:239 , GLN B:269 , ARG B:271 , HOH B:1031BINDING SITE FOR RESIDUE GOL B 702
10BC1SOFTWAREGLY B:430 , UMP B:603 , GOL B:704BINDING SITE FOR RESIDUE GOL B 703
11BC2SOFTWAREGLU B:295 , ILE B:316 , TYR B:343 , HIS B:404 , UMP B:603 , GOL B:703 , HOH B:1067 , HOH B:1111BINDING SITE FOR RESIDUE GOL B 704

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Arg A:89 -Pro A:90
2Thr A:145 -Pro A:146
3Pro A:166 -Pro A:167
4Arg B:89 -Pro B:90
5Thr B:145 -Pro B:146
6Pro B:166 -Pro B:167

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (3, 6)

Asymmetric/Biological Unit (3, 6)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1DHFR_2PS51330 Dihydrofolate reductase (DHFR) domain profile.DRTS_TRYCR22-232
 
  2A:22-232
B:22-232
2DHFR_1PS00075 Dihydrofolate reductase (DHFR) domain signature.DRTS_TRYCR34-56
 
  2A:34-56
B:34-56
3THYMIDYLATE_SYNTHASEPS00091 Thymidylate synthase active site.DRTS_TRYCR383-411
 
  2A:383-411
B:383-411

(-) Exons   (0, 0)

(no "Exon" information available for 3INV)

(-) 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:514
 aligned with DRTS_TRYCR | Q27793 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:514
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511    
           DRTS_TRYCR     2 SLFKIRMPETVAEGTRLALRAFSLVVAVDEHGGIGDGRSIPWNVPEDMKFFRDLTTKLRGKNVKPSPAKRNAVVMGRKTWDSIPPKFRPLPGRLNVVLSSTLTTQHLLDGLPDEEKRNLHADSIVAVNGGLEQALRLLASPNYTPSIETVYCIGGGSVYAEALRPPCVHLLQAIYRTTIRASESSCSVFFRVPESGTEAAAGIEWQRETISEELTSANGNETKYYFEKLIPRNREEEQYLSLVDRIIREGNVKHDRTGVGTLSIFGAQMRFSLRNNRLPLLTTKRVFWRGVCEELLWFLRGETYAKKLSDKGVHIWDDNGSRAFLDSRGLTEYEEMDLGPVYGFQWRHFGAAYTHHDANYDGQGVDQIKAIVETLKTNPDDRRMLFTAWNPSALPRMALPPCHLLAQFYVSNGELSCMLYQRSCDMGLGVPFNIASYALLTILIAKATGLRPGELVHTLGDAHVYSNHVEPCNEQLKRVPRAFPYLVFRREREFLEDYEEGDMEVIDYAPYPPI 515
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....................eeeeeeee...eee........hhhhhhhhhhhhhh............eeeeeeehhhhhhhhhhhh....eeeeee....hhhhhhhh..hhhhhhhh...eeee..hhhhhhhhhh.......eeeeee..hhhhhhhhh..hhhh.eeeeeeeeee.......ee.......hhhhh...eeeeee...ee.......eeeeeeeee.hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhh....hhhhhh.....hhhhhhhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) --------------------DHFR_2  PDB: A:22-232 UniProt: 22-232                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) --------------------------------DHFR_1  PDB: A:34-56   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3inv A   2 SLFKIRMPETVAEGTRLALRAFSLVVAVDEHGGIGDGRSIPWNVPEDMKFFRDLTTKLRGKNVKPSPAKRNAVVMGRKTWDSIPPKFRPLPGRLNVVLSSTLTTQHLLDGLPDEEKRNLHADSIVAVNGGLEQALRLLASPNYTPSIETVYCIGGGSVYAEALRPPCVHLLQAIYRTTIRASESSCSVFFRVPESGTEAAAGIEWQRETISEELTSANGNETKYYFEKLIPRNREEEQYLSLVDRIIREGNVKHDRTGVGTLSIFGAQMRFSLRNNRLPLLTTKRVFWRGVCEELLWFLRGETYAKKLSDKGVHIWDDNGSRAFLDSRGLTEYEEMDLGPVYGFQWRHFGAAYTHHDANYDGQGVDQIKAIVETLKTNPDDRRMLFTAWNPSALPRMALPPCHLLAQFYVSNGELSCMLYQRSCDMGLGVPFNIASYALLTILIAKATGLRPGELVHTLGDAHVYSNHVEPCNEQLKRVPRAFPYLVFRREREFLEDYEEGDMEVIDYAPYPPI 515
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371       381       391       401       411       421       431       441       451       461       471       481       491       501       511    

Chain B from PDB  Type:PROTEIN  Length:513
 aligned with DRTS_TRYCR | Q27793 from UniProtKB/Swiss-Prot  Length:521

    Alignment length:513
                                    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       402       412       422       432       442       452       462       472       482       492       502       512   
           DRTS_TRYCR     3 LFKIRMPETVAEGTRLALRAFSLVVAVDEHGGIGDGRSIPWNVPEDMKFFRDLTTKLRGKNVKPSPAKRNAVVMGRKTWDSIPPKFRPLPGRLNVVLSSTLTTQHLLDGLPDEEKRNLHADSIVAVNGGLEQALRLLASPNYTPSIETVYCIGGGSVYAEALRPPCVHLLQAIYRTTIRASESSCSVFFRVPESGTEAAAGIEWQRETISEELTSANGNETKYYFEKLIPRNREEEQYLSLVDRIIREGNVKHDRTGVGTLSIFGAQMRFSLRNNRLPLLTTKRVFWRGVCEELLWFLRGETYAKKLSDKGVHIWDDNGSRAFLDSRGLTEYEEMDLGPVYGFQWRHFGAAYTHHDANYDGQGVDQIKAIVETLKTNPDDRRMLFTAWNPSALPRMALPPCHLLAQFYVSNGELSCMLYQRSCDMGLGVPFNIASYALLTILIAKATGLRPGELVHTLGDAHVYSNHVEPCNEQLKRVPRAFPYLVFRREREFLEDYEEGDMEVIDYAPYPPI 515
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........hhhhh.....eeeeeeee...eee........hhhhhhhhhhhhhh............eeeeeeehhhhhhhhhhhh....eeeeee....hhhhhhhh........hhhh.eeee..hhhhhhhhhhh......eeeeee..hhhhhhhhh..hhhh.eeeeeeeeee.......ee.......hhhhh...eeeeee...ee.......eeeeeeeee.hhhhhhhhhhhhhhhhhheeee.....eeeeeeeeeeeee.hhhh.........hhhhhhhhhhhhhh....hhhhhh..........hhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeeee..eeeeeeeeeeee...hhhhhhhhhhhhhhhhhhh...eeeeeeeeeeeeeee..hhhhhhhhh........eeee.....hhhhhhhh.eeee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                PROSITE (1) -------------------DHFR_2  PDB: B:22-232 UniProt: 22-232                                                                                                                                                                              ------------------------------------------------------------------------------------------------------------------------------------------------------THYMIDYLATE_SYNTHASE         -------------------------------------------------------------------------------------------------------- PROSITE (1)
                PROSITE (2) -------------------------------DHFR_1  PDB: B:34-56   --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE (2)
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3inv B   3 LFKIRMPETVAEGTRLALRAFSLVVAVDEHGGIGDGRSIPWNVPEDMKFFRDLTTKLRGKNVKPSPAKRNAVVMGRKTWDSIPPKFRPLPGRLNVVLSSTLTTQHLLDGLPDEEKRNLHADSIVAVNGGLEQALRLLASPNYTPSIETVYCIGGGSVYAEALRPPCVHLLQAIYRTTIRASESSCSVFFRVPESGTEAAAGIEWQRETISEELTSANGNETKYYFEKLIPRNREEEQYLSLVDRIIREGNVKHDRTGVGTLSIFGAQMRFSLRNNRLPLLTTKRVFWRGVCEELLWFLRGETYAKKLSDKGVHIWDDNGSRAFLDSRGLTEYEEMDLGPVYGFQWRHFGAAYTHHDANYDGQGVDQIKAIVETLKTNPDDRRMLFTAWNPSALPRMALPPCHLLAQFYVSNGELSCMLYQRSCDMGLGVPFNIASYALLTILIAKATGLRPGELVHTLGDAHVYSNHVEPCNEQLKRVPRAFPYLVFRREREFLEDYEEGDMEVIDYAPYPPI 515
                                    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       402       412       422       432       442       452       462       472       482       492       502       512   

   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 3INV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (14, 14)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (DRTS_TRYCR | Q27793)
molecular function
    GO:0003824    catalytic activity    Catalysis of a biochemical reaction at physiological temperatures. In biologically catalyzed reactions, the reactants are known as substrates, and the catalysts are naturally occurring macromolecular substances known as enzymes. Enzymes possess specific binding sites for substrates, and are usually composed wholly or largely of protein, but RNA that has catalytic activity (ribozyme) is often also regarded as enzymatic.
    GO:0004146    dihydrofolate reductase activity    Catalysis of the reaction: 5,6,7,8-tetrahydrofolate + NADP+ = 7,8-dihydrofolate + NADPH + H+.
    GO:0008168    methyltransferase activity    Catalysis of the transfer of a methyl group to an acceptor molecule.
    GO:0016491    oxidoreductase activity    Catalysis of an oxidation-reduction (redox) reaction, a reversible chemical reaction in which the oxidation state of an atom or atoms within a molecule is altered. One substrate acts as a hydrogen or electron donor and becomes oxidized, while the other acts as hydrogen or electron acceptor and becomes reduced.
    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:0006231    dTMP biosynthetic process    The chemical reactions and pathways resulting in the formation of dTMP, deoxyribosylthymine monophosphate (2'-deoxyribosylthymine 5'-phosphate).
    GO:0006545    glycine biosynthetic process    The chemical reactions and pathways resulting in the formation of glycine, aminoethanoic acid.
    GO:0008152    metabolic process    The chemical reactions and pathways, including anabolism and catabolism, by which living organisms transform chemical substances. Metabolic processes typically transform small molecules, but also include macromolecular processes such as DNA repair and replication, and protein synthesis and degradation.
    GO:0032259    methylation    The process in which a methyl group is covalently attached to a molecule.
    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:0006730    one-carbon metabolic process    The chemical reactions and pathways involving the transfer of one-carbon units in various oxidation states.
    GO:0055114    oxidation-reduction process    A metabolic process that results in the removal or addition of one or more electrons to or from a substance, with or without the concomitant removal or addition of a proton or protons.
    GO:0046654    tetrahydrofolate biosynthetic process    The chemical reactions and pathways resulting in the formation of tetrahydrofolate, 5,6,7,8-tetrahydrofolic acid, a folate derivative bearing additional hydrogens on the pterin group.

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 Related Entries

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

UniProtKB/Swiss-Prot
        DRTS_TRYCR | Q277932h2q 3cl9 3clb 3hbb 3irm 3irn 3iro

(-) Related Entries Specified in the PDB File

2h2q THE SAME PROTEIN IN FOLATE-FREE STATE
3cl9 THE SAME PROTEIN COMPLEXED WITH MTX
3clb THE SAME PROTEIN COMPLEXED WITH TMQ
3hbb THE SAME PROTEIN COMPLEXED WITH TMQ
3irm TCDHFR-TS PROTEIN IN COMPLEX WITH CYCLOGUANIL
3irn TCDHFR-TS PROTEIN IN COMPLEX WITH NADPH AND CYCLOGUANIL
3iro TCDHFR-TS PROTEIN IN COMPLEX WITH NADPH NADPH AND Q-8 ANTIFOLATE