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Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

Title :   STRUCTURE OF PTR1 FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH 2,4-DIAMINO-5-[2-(2,5-DIMETHOXYPHENYL)ETHYL]THIENO[2,3-D]-PYRIMIDINE AND NADP+

Authors :   L. B. Tulloch, W. N. Hunter

Date :   29 Mar 10 (Deposition) - 02 Jun 10 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.70

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

Keywords :   Pteridine Reductase, Antifolate, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dawson, L. B. Tulloch, K. L. Barrack, W. N. Hunter
High-Resolution Structures Of Trypanosoma Brucei Pteridine Reductase Ligand Complexes Inform On The Placement Of New Molecular Entities In The Active Site Of A Potential Drug Target.
Acta Crystallogr. , Sect. D V. 66 1334 2010
PubMed-ID: 21123874 | Reference-DOI: 10.1107/S0907444910040886

Molecule 1 - PTERIDINE REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.5.1.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Taxid	:	562
	Expression System Vector Type	:	PLASMID
	Gene	:	PTR1
	Organism Scientific	:	TRYPANOSOMA BRUCEI BRUCEI
	Organism Taxid	:	5702

		1	2	3	4
Asymmetric/Biological Unit	:	A	B	C	D

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 12)

No.	Name	Count	Type	Full Name
1	ACT	4	Ligand/Ion	ACETATE ION
2	MCV	4	Ligand/Ion	5-[2-(2,5-DIMETHOXYPHENYL)ETHYL]THIENO[2,3-D]PYRIMIDINE-2,4-DIAMINE
3	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ARG A:14 , ILE A:15 , TYR A:34 , HIS A:35 , ASN A:36 , SER A:37 , ALA A:61 , ASP A:62 , LEU A:63 , THR A:64 , ASN A:93 , ALA A:94 , SER A:95 , THR A:126 , LEU A:159 , CYS A:160 , TYR A:174 , LYS A:178 , PRO A:204 , GLY A:205 , SER A:207 , LEU A:208 , MCV A:300 , HOH A:306 , HOH A:307 , HOH A:321 , HOH A:331 , HOH A:362 , HOH A:368 , HOH A:383 , HOH A:409 , HOH A:448 , HOH A:454	BINDING SITE FOR RESIDUE NAP A 269
02	AC2	SOFTWARE	ARG A:14 , SER A:95 , PHE A:97 , ASP A:161 , CYS A:168 , TYR A:174 , GLY A:205 , MET A:213 , TRP A:221 , NAP A:269 , HOH A:409 , HOH A:510	BINDING SITE FOR RESIDUE MCV A 300
03	AC3	SOFTWARE	ARG A:222 , ARG A:230 , GLU A:231 , HOH A:388 , HOH A:519	BINDING SITE FOR RESIDUE ACT A 270
04	AC4	SOFTWARE	ARG B:14 , ILE B:15 , TYR B:34 , HIS B:35 , ASN B:36 , SER B:37 , ALA B:61 , ASP B:62 , LEU B:63 , THR B:64 , ASN B:93 , ALA B:94 , SER B:95 , THR B:126 , LEU B:159 , CYS B:160 , TYR B:174 , LYS B:178 , PRO B:204 , GLY B:205 , SER B:207 , LEU B:208 , MCV B:300 , HOH B:303 , HOH B:307 , HOH B:315 , HOH B:337 , HOH B:339 , HOH B:348 , HOH B:374 , HOH B:381 , HOH B:493 , HOH B:512 , HOH B:513	BINDING SITE FOR RESIDUE NAP B 269
05	AC5	SOFTWARE	ARG B:14 , SER B:95 , PHE B:97 , TYR B:174 , GLY B:205 , VAL B:206 , MET B:213 , TRP B:221 , NAP B:269 , HOH B:386 , HOH B:493	BINDING SITE FOR RESIDUE MCV B 300
06	AC6	SOFTWARE	ALA B:212 , MET B:213 , GLY B:214 , GLU B:215 , HOH B:399 , HOH B:425	BINDING SITE FOR RESIDUE ACT B 270
07	AC7	SOFTWARE	TYR B:34 , VAL B:58 , VAL C:57 , VAL C:58 , HOH C:418	BINDING SITE FOR RESIDUE ACT B 271
08	AC8	SOFTWARE	ARG C:14 , ILE C:15 , TYR C:34 , HIS C:35 , ASN C:36 , SER C:37 , ALA C:61 , ASP C:62 , LEU C:63 , THR C:64 , ASN C:93 , ALA C:94 , SER C:95 , THR C:126 , LEU C:159 , CYS C:160 , TYR C:174 , LYS C:178 , PRO C:204 , GLY C:205 , SER C:207 , LEU C:208 , MCV C:300 , HOH C:314 , HOH C:315 , HOH C:341 , HOH C:357 , HOH C:364 , HOH C:373 , HOH C:393 , HOH C:394 , HOH C:395 , HOH C:435	BINDING SITE FOR RESIDUE NAP C 269
09	AC9	SOFTWARE	ARG C:14 , SER C:95 , PHE C:97 , ASP C:161 , CYS C:168 , TYR C:174 , GLY C:205 , VAL C:206 , PRO C:210 , MET C:213 , TRP C:221 , NAP C:269 , HOH C:364	BINDING SITE FOR RESIDUE MCV C 300
10	BC1	SOFTWARE	LYS D:13 , ARG D:14 , ILE D:15 , TYR D:34 , HIS D:35 , ASN D:36 , SER D:37 , ALA D:61 , ASP D:62 , LEU D:63 , THR D:64 , ASN D:93 , ALA D:94 , SER D:95 , THR D:126 , LEU D:159 , CYS D:160 , TYR D:174 , LYS D:178 , PRO D:204 , GLY D:205 , SER D:207 , LEU D:208 , MCV D:300 , HOH D:304 , HOH D:305 , HOH D:328 , HOH D:348 , HOH D:360 , HOH D:376 , HOH D:402 , HOH D:439 , HOH D:459	BINDING SITE FOR RESIDUE NAP D 269
11	BC2	SOFTWARE	ARG D:14 , SER D:95 , PHE D:97 , ASP D:161 , CYS D:168 , TYR D:174 , GLY D:205 , VAL D:206 , MET D:213 , TRP D:221 , NAP D:269 , HOH D:439 , HOH D:487	BINDING SITE FOR RESIDUE MCV D 300
12	BC3	SOFTWARE	HIS A:267 , CYS D:168 , MET D:169 , TRP D:221	BINDING SITE FOR RESIDUE ACT D 270

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

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

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

(no "PROSITE Motif" information available for 3MCV)

(no "Exon" information available for 3MCV)

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:251
 aligned with O76290_TRYBB | O76290 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         O76290_TRYBB     2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
               SCOP domains d3mcva_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............--------..hhhhhhhhhhhhhhhhhhhhhhhhhhh.--------...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcv A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQ--------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ--------SSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101  |      - |     121       131       141|      151       161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                                104      113                          142      151

Chain B from PDB  Type:PROTEIN  Length:251
 aligned with O76290_TRYBB | O76290 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         O76290_TRYBB     2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
               SCOP domains d3mcvb_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............---------.hhhhhhhhhhhhhhhhhhhhhhhhhhh..-------....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcv B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQ---------KTVETQVAELIGTNAIAPFLLTMSFAQRQK-------SSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101  |      -  |    121       131       141 |     151       161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                                104       114                          143     151

Chain C from PDB  Type:PROTEIN  Length:248
 aligned with O76290_TRYBB | O76290 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         O76290_TRYBB     2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
               SCOP domains d3mcvc_ C: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee...........----------.hhhhhhhhhhhhhhhhhhhhhhhhhhh.---------..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcv C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV----------KTVETQVAELIGTNAIAPFLLTMSFAQRQ---------SNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 |       -  |    121       131       141|        -|      161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                               103        114                         142       152

Chain D from PDB  Type:PROTEIN  Length:250
 aligned with O76290_TRYBB | O76290 from UniProtKB/TrEMBL  Length:268

    Alignment length:267
                                    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       
         O76290_TRYBB     2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDHEDNSNGKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
               SCOP domains d3mcvd_ D: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) --------adh_short_C2-3mcvD01 D:10-264                                                                                                                                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) --------adh_short_C2-3mcvD02 D:10-264                                                                                                                                                                                                                                  ---- Pfam domains (2)
           Pfam domains (3) --------adh_short_C2-3mcvD03 D:10-264                                                                                                                                                                                                                                  ---- Pfam domains (3)
           Pfam domains (4) --------adh_short_C2-3mcvD04 D:10-264                                                                                                                                                                                                                                  ---- Pfam domains (4)
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee...........---------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh--------...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3mcv D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ--------SSNLSIVNLCDAMVDQPCMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 268
                                    11        21        31        41        51        61        71        81        91       101 |       - |     121       131       141|      151       161       171       181       191       201       211       221       231       241       251       261       
                                                                                                                               103       113                          142      151

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 '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: Alpha and beta proteins (a/b) (23833)

Fold: NAD(P)-binding Rossmann-fold domains (1604)

Superfamily: NAD(P)-binding Rossmann-fold domains (1604)

Family: Tyrosine-dependent oxidoreductases (503)

Protein domain: Dihydropteridin reductase (pteridine reductase) (24)

Trypanosoma brucei [TaxId: 5702] (7)

1a	d3mcva_	A:
1b	d3mcvb_	B:
1c	d3mcvc_	C:
1d	d3mcvd_	D:

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: NADP_Rossmann (1239)

Family: adh_short_C2 (98)

Trypanosoma brucei brucei (6)

1a	adh_short_C2-3mcvD01	D:10-264
1b	adh_short_C2-3mcvD02	D:10-264
1c	adh_short_C2-3mcvD03	D:10-264
1d	adh_short_C2-3mcvD04	D:10-264

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D (O76290_TRYBB | O76290)

molecular function
	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: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:0047040	pteridine reductase activity	Catalysis of the reaction: 5,6,7,8-tetrahydrobiopterin + 2 NADP(+) = biopterin + 2 H(+) + 2 NADPH.
biological process
	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.

Asymmetric/Biological Unit
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3mcv)

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	3mcv
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	O76290_TRYBB \| O76290
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	1.5.1.33
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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 12)

Sites (12, 12)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

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SCOP Domains (1, 4)

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Pfam Domains (1, 4)

Gene Ontology (4, 4)

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