5T0L - JenaLib

Asym./Biol. Unit (Jmol Viewer)

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Title :   CRYSTAL STRUCTURE OF TOXOPLASMA GONDII TS-DHFR COMPLEXED WITH NADPH, DUMP, PDDF AND 5-(4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL)PYRIMIDINE-2, 4-DIAMINE (TRC-15)

Authors :   S. B. Thomas, Z. Chen, H. Lu, Y. Li

Date :   16 Aug 16 (Deposition) - 28 Sep 16 (Release) - 04 Jan 17 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   3.13

Chains :   Asym./Biol. Unit : A,B

Keywords :   Toxoplasma Gondii, Dhfr, Inhibitor, Oxidoreductase-Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   M. E. Welsch, J. Zhou, Y. Gao, Y. Yan, G. Porter, G. Agnihotri, Y. Li, H. Lu, Z. Chen, S. B. Thomas
Discovery Of Potent And Selective Leads Against Toxoplasma Gondii Dihydrofolate Reductase Via Structure-Based Design.
Acs Med Chem Lett V. 7 1124 2016
PubMed-ID: 27994750 | Reference-DOI: 10.1021/ACSMEDCHEMLETT.6B00328

Molecule 1 - BIFUNCTIONAL DIHYDROFOLATE REDUCTASE-THYMIDYLATE SYNTHASE
	Chains	:	A, B
	EC Number	:	1.5.1.3, 2.1.1.45
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	TOXOPLASMA GONDII
	Organism Taxid	:	5811
	Synonym	:	DHFR-TS

		1	2
Asymmetric/Biological Unit	:	A	B

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (4, 8)

No.	Name	Count	Type	Full Name
1	73X	2	Ligand/Ion	5-[4-(3,4-DICHLOROPHENYL)PIPERAZIN-1-YL]PYRIMIDINE-2,4-DIAMINE
2	CB3	2	Ligand/Ion	10-PROPARGYL-5,8-DIDEAZAFOLIC ACID
3	NDP	2	Ligand/Ion	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
4	UMP	2	Ligand/Ion	2'-DEOXYURIDINE 5'-MONOPHOSPHATE

Asymmetric Unit (8, 8)

No.	Name	Evidence	Residues	Description
1	AC1	SOFTWARE	ARG A:344 , LEU A:486 , CYS A:489 , HIS A:490 , GLN A:509 , ARG A:510 , SER A:511 , ASP A:513 , GLY A:517 , ASN A:521 , HIS A:551 , TYR A:553 , CB3 A:703 , ARG B:469 , ARG B:470	binding site for residue UMP A 701
2	AC2	SOFTWARE	ALA A:10 , ILE A:17 , ASN A:21 , GLY A:22 , GLY A:80 , ARG A:81 , LYS A:82 , THR A:83 , SER A:86 , VAL A:102 , SER A:103 , SER A:104 , SER A:105 , ALA A:128 , VAL A:151 , GLY A:152 , GLY A:153 , ALA A:154 , GLY A:155 , LEU A:156 , TYR A:157 , 73X A:704	binding site for residue NDP A 702
3	AC3	SOFTWARE	LYS A:371 , ARG A:372 , PHE A:374 , ILE A:402 , TRP A:403 , ASN A:406 , ASP A:513 , LEU A:516 , GLY A:517 , PHE A:520 , ASN A:521 , ARG A:603 , MET A:608 , ALA A:609 , UMP A:701	binding site for residue CB3 A 703
4	AC4	SOFTWARE	VAL A:8 , VAL A:9 , ASP A:31 , PHE A:32 , PHE A:35 , MET A:87 , PRO A:88 , VAL A:151 , THR A:172 , NDP A:702	binding site for residue 73X A 704
5	AC5	SOFTWARE	ARG A:469 , ARG A:470 , ARG B:344 , LEU B:486 , CYS B:489 , HIS B:490 , GLN B:509 , ARG B:510 , SER B:511 , ASP B:513 , GLY B:517 , ASN B:521 , HIS B:551 , TYR B:553 , CB3 B:703	binding site for residue UMP B 701
6	AC6	SOFTWARE	VAL B:9 , ALA B:10 , ILE B:17 , ASN B:21 , GLY B:22 , LEU B:23 , TRP B:25 , GLY B:80 , ARG B:81 , LYS B:82 , THR B:83 , VAL B:102 , SER B:103 , SER B:104 , SER B:105 , ALA B:128 , VAL B:151 , GLY B:153 , ALA B:154 , GLY B:155 , TYR B:157 , VAL B:182 , 73X B:704	binding site for residue NDP B 702
7	AC7	SOFTWARE	LYS B:371 , PHE B:374 , GLU B:381 , ILE B:402 , TRP B:403 , ASN B:406 , ASP B:513 , LEU B:516 , GLY B:517 , PHE B:520 , ASN B:521 , ARG B:603 , MET B:608 , ALA B:609 , UMP B:701	binding site for residue CB3 B 703
8	AC8	SOFTWARE	VAL B:8 , VAL B:9 , ALA B:10 , ASP B:31 , PHE B:32 , PHE B:35 , SER B:86 , PRO B:88 , VAL B:151 , TYR B:157 , THR B:172 , NDP B:702	binding site for residue 73X B 704

(no "SS Bond" information available for 5T0L)

Asymmetric/Biological Unit

No.	Residues
1	Arg A:92	-	Pro A:93
2	Gly A:152	-	Gly A:153
3	Arg B:92	-	Pro B:93
4	Gly B:152	-	Gly B:153

(no "SAP(SNP)/Variant" information available for 5T0L)

(no "PROSITE Motif" information available for 5T0L)

(no "Exon" information available for 5T0L)

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:508
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                            
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeee....eee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhh....eeeeee....hhhhhhhhh.........eee.hhhhhhhhhhhh....eeeeeeeehhhhhhhhhhhh.eeeeeeeee.......ee.....hhhhh.....eeeeee...eee..eeeeeeeeee.....hhhhhhhhh..........ee...hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhhh...hhhhhh..........hhhhhhhh............hhhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee................eeee.............. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t0l A   4 PVCLVVAMTPKRGIGINNGLPWPHLTTDFKHFSRVTKTTPASRFNAVVMGRKTWESMPRKFRPLVDRLNIVVSSSLKEEDIAAEKPQAEGQQRVRVCASLPAALSLLEEEYKDSVDQIFVVGGAGLYEAALSLGVASHLYITRVAREFPCDVFFPAFPGDDILSNKATYRPIFISKTFSDNGVPYDFVVLEKRRAAAIAPVLAWMDELIRAVPHVHFRGHEEFQYLDLIADIINNGRTMDDRTGVGVISKFGCTMRYSLDQAFPLLTTKRVFWKGVLEELLWFIRGDTNANHLSEKGVKIWDKNVTREFLDSRNLPHREVGDIGPGYGFQWRHFGAAYKDMHTDYTGQGVDQLKNVIQMLRTNPTDRRMLMTAWNPAALDEMALPPCHLLCQFYVNDQKELSCIMYQRSCDVGLGVPFNIASYSLLTLMVAHVCNLKPKEFIHFMGNTHVYTNHVEALKEQLRREPRPFPIVNILNKERIKEIDDFTAEDFEVVGYVPHGRIQMEMAV 610
                                    13        23        33        43| ||    80        90       100       110       120       130       140       150       160       170       180       190     ||228       238       248   ||  292      |312       322       332       342       352       362       372       382       392       402       412       422       432       442       452       462       472       482       492       502       512       522       532       542       552       562       572       582       592       602        
                                                                  43| ||                                                                                                                       196|                        252|         299|                                                                                                                                                                                                                                                                                                            
                                                                   46 ||                                                                                                                        225                         287          310                                                                                                                                                                                                                                                                                                            
                                                                     48|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                
                                                                      74

Chain B from PDB  Type:PROTEIN  Length:510
                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .eeeeeee....eee.........hhhhhhhhhhhhhh.....eeeeeeehhhhhhhhhhhh....eeeeee....hhhhhhhhh.........eee.hhhhhhhhhhhh....eeeeeeeehhhhhhhhhhh..eeeeeeeee.......ee.....hhhhh.....eeeeee...eee..eeeeeeeeee.......hhhhhhhhh..........ee...hhhhhhhhhhhhhhheee.......eeeeeeeeeeee.............hhhhhhhhhhhhhhh...hhhhhh.....hhhhhhhhhhhhh.............hhhhhhhh................hhhhhhhhhhhhh......eee.....hhhhh.....eeeeeeee....eeeeeeeeeeee..hhhhhhhhhhhhhhhhhhhhh..eeeeeeeeeeeeeee..hhhhhhhhh........eeee................eeee.............. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5t0l B   4 PVCLVVAMTPKRGIGINNGLPWPHLTTDFKHFSRVTKTTPASRFNAVVMGRKTWESMPRKFRPLVDRLNIVVSSSLKEEDIAAEKPQAEGQQRVRVCASLPAALSLLEEEYKDSVDQIFVVGGAGLYEAALSLGVASHLYITRVAREFPCDVFFPAFPGDDILSNKATYRPIFISKTFSDNGVPYDFVVLEKRRSSAAAIAPVLAWMDELIRAVPHVHFRGHEEFQYLDLIADIINNGRTMDDRTGVGVISKFGCTMRYSLDQAFPLLTTKRVFWKGVLEELLWFIRGDTNANHLSEKGVKIWDKNVTREFLDSRNLPHREVGDIGPGYGFQWRHFGAAYKDMHTDYTGQGVDQLKNVIQMLRTNPTDRRMLMTAWNPAALDEMALPPCHLLCQFYVNDQKELSCIMYQRSCDVGLGVPFNIASYSLLTLMVAHVCNLKPKEFIHFMGNTHVYTNHVEALKEQLRREPRPFPIVNILNKERIKEIDDFTAEDFEVVGYVPHGRIQMEMAV 610
                                    13        23        33        43| ||    80        90       100       110       120       130       140       150       160       170       180       190     ||228       238       248   ||  290       310       320       330       340       350       360       370       380       390       400       410       420       430       440       450       460       470       480       490       500       510       520       530       540       550       560       570       580       590       600       610
                                                                  43| ||                                                                                                                       196|                        252|           299|                                                                                                                                                                                                                                                                                                            
                                                                   46 ||                                                                                                                        225                         285            310                                                                                                                                                                                                                                                                                                            
                                                                     48|                                                                                                                                                                                                                                                                                                                                                                                                                                                                                  
                                                                      74

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 '\|'

(no "SCOP Domain" information available for 5T0L)

(no "CATH Domain" information available for 5T0L)

(no "Pfam Domain" information available for 5T0L)

Asymmetric/Biological Unit(hide GO term definitions)

Asymmetric/Biological Unit
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	Ligands, Modified Residues, Ions
		73X	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		CB3	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Arg A:92 - Pro A:93	[ RasMol ]
		Arg B:92 - Pro B:93	[ RasMol ]
		Gly A:152 - Gly A:153	[ RasMol ]
		Gly B:152 - Gly B:153	[ RasMol ]

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(no "Related Entries Specified in the PDB File" available for 5T0L)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 8)

Sites (8, 8)

SS Bonds (0, 0)

Cis Peptide Bonds (4, 4)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Gene Ontology (14, 14)

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