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(-) Description

Title :  HUMAN GAR TRANSFORMYLASE IN COMPLEX WITH GAR AND (S)-2-({4-[4-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]-PYRIMIDIN-6-YL) BUTYL]THIOPHENE-2-CARBONYL}AMINO)PENTANEDIOIC ACID (AGF117)
 
Authors :  S. M. Deis, C. E. Dann Iii
Date :  22 May 15  (Deposition) - 20 Apr 16  (Release) - 22 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.65
Chains :  Asym./Biol. Unit :  A
Keywords :  Gar Transformylase, Antifolate, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  S. M. Deis, A. Doshi, Z. Hou, L. H. Matherly, A. Gangjee, C. E. Dann
Structural And Enzymatic Analysis Of Tumor-Targeted Antifolates That Inhibit Glycinamide Ribonucleotide Formyltransferase.
Biochemistry V. 55 4574 2016
PubMed-ID: 27439469  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B00412

(-) Compounds

Molecule 1 - TRIFUNCTIONAL PURINE BIOSYNTHETIC PROTEIN ADENOSINE-3
    ChainsA
    EC Number2.1.2.2
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPET22B
    Expression System StrainROSETTA(DE3)PLYSS
    Expression System Taxid562
    Expression System Vector TypePLASMID
    FragmentGAR TRANSFORMYLASE DOMAIN
    GeneGART, PGFT, PRGS
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit A

Summary Information (see also Sequences/Alignments below)

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

Asymmetric/Biological Unit (2, 2)
No.NameCountTypeFull Name
13YB1Ligand/IonN-({4-[4-(2-AMINO-4-OXO-4,7-DIHYDRO-3H-PYRROLO[2,3-D]PYRIMIDIN-6-YL)BUTYL]THIOPHEN-2-YL}CARBONYL)-L-GLUTAMIC ACID
2GAR1Ligand/IonGLYCINAMIDE RIBONUCLEOTIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETHR A:817 , GLY A:818 , SER A:819 , ASN A:820 , GLY A:894 , ILE A:914 , PRO A:916 , LYS A:977 , GLU A:980 , 3YB A:1102 , HOH A:1209 , HOH A:1228 , HOH A:1245 , HOH A:1247 , HOH A:1248 , HOH A:1251 , HOH A:1289 , HOH A:1299 , HOH A:1304binding site for residue GAR A 1101
2AC2SOFTWAREARG A:871 , PHE A:895 , MET A:896 , ARG A:897 , ILE A:898 , LEU A:899 , VAL A:904 , GLY A:924 , HIS A:944 , VAL A:946 , ALA A:947 , GLU A:948 , VAL A:950 , ASP A:951 , GAR A:1101 , HOH A:1238 , HOH A:1326binding site for residue 3YB A 1102

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Leu A:919 -Pro A:920

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4ZYX)

(-) 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
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Chain A from PDB  Type:PROTEIN  Length:200
                                                                                                                                                                                                                                         
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeee...hhhhhhhhhhhh......eeeeeee....hhhhhhhhhh...eee.hhhhh.hhhhhhhhhhhhhhhh...eeee.......hhhhhhhh...eeeee..........hhhhhhhhhh..eeeeeeee.........eeeeeeee.....hhhhhhhhhhhhhhhhhhhhhhhhhh..eee.....eee. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                4zyx A  808 ARVAVLISGTGSNLQALIDSTREPNSSAQIDIVISNKAAVAGLDKAERAGIPTRVINHKLYKNRVEFDSAIDLVLEEFSIDIVCLAGFMRILSGPFVQKWNGKMLNIHPSLLPSFKGSNAHEQALETGVTVTGCTVHFVAEDVDAGQIILQEAVPVKRGDTVATLSERVKLAEHKIFPAALQLVASGTVQLGENGKICWV 1007
                                   817       827       837       847       857       867       877       887       897       907       917       927       937       947       957       967       977       987       997      1007

   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 4ZYX)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (27, 27)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        PUR2_HUMAN | P221021mej 1men 1meo 1njs 1rbm 1rbq 1rby 1rbz 1rc0 1rc1 1zlx 1zly 2qk4 2v9y 4ew1 4ew2 4ew3 4zyt 4zyu 4zyv 4zyw 4zyy 4zyz 4zz0 4zz1 4zz2 4zz3 5j9f

(-) Related Entries Specified in the PDB File

1mej 1MEJ IS THE SAME PROTEIN IN APO FORM AT PH 8.5
1men 1MEN IS THE SAME PROTEIN COMPLEXED WITH BETA-GAR
1meo 1MEO IS THE SAME PROTEIN IN APO FORM AT PH 4.2
1njs 1NJS IS THE SAME PROTEIN COMPLEXED WITH A HYDROLYZED FORM OF 10- (TRIFLUOROACETYL)-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
1rbm 1RBM IS THE SAME PROTEIN COMPLEXED WITH POLYGLUTAMINATED 10- (TRIFLUOROACETYL)-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
1rbq 1RBQ IS THE SAME PROTEIN COMPLEXED WITH 10-(TRIFLUOROACETYL)-5,10- DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
1rby 1RBY IS THE SAME PROTEIN COMPLEXED WITH 10-(TRIFLUOROACETYL)-5,10- DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID AND BETA-GAR
1rbz 1RBZ IS THE SAME PROTEIN COMPLEXED WITH POLYGLUTAMINATED 10- (TRIFLUOROACETYL)-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
1rc0 1RC0 IS THE SAME PROTEIN COMPLEXED WITH POLYGLUTAMINATED 10- (TRIFLUOROACETYL)-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
1rc1 1RC1 IS THE SAME PROTEIN COMPLEXED WITH POLYGLUTAMINATED 10- (TRIFLUOROACETYL)-5,10-DIDEAZAACYCLIC-5,6,7,8-TETRAHYDROFOLIC ACID
1zlx 1ZLX IS THE SAME PROTEIN IN APO FORM
1zly 1ZLY IS THE SAME PROTEIN COMPLEXED WITH 4-[(4-{[(2-AMINO-4-OXO-3,4- DIHYDROQUINAZOLIN- 6-YL)METHYL]AMINO}BENZOYL)AMINO]BUTANOIC ACID AND 5-O-PHOSPHONO-BETA-D-RIBOFURANOSYLAMINE
4ew2 4EW2 IS THE SAME PROTEIN COMPLEXED WITH 10S-METHYLTHIO-DDATHF
4ew3 4EW3 IS THE SAME PROTEIN COMPLEXED WITH 10R-METHYLTHIO-DDATHF
4zyt
4zyu
4zyv
4zyw
4zyy
4zyz
4zz0
4zz1
4zz2
4zz3