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Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF PTERIDINE REDUCTASE 1 (PTR1) FROM TRYPANOSOMA BRUCEI IN TERNARY COMPLEX WITH COFACTOR (NADP+) AND INHIBITOR (DDD00067116)

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

Date :   16 Mar 09 (Deposition) - 29 Dec 09 (Release) - 07 Sep 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

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

Keywords :   Pteridine Reductase, Ptr1, Trypanosoma Brucei, Short Chain Dehydrogenase, Inhibitor, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   C. P. Mpamhanga, D. Spinks, L. B. Tulloch, E. J. Shanks, D. A. Robinson, I. T. Collie, A. H. Fairlamb, P. G. Wyatt, J. A. Frearson, W. N. Hunter, I. H. Gilbert, R. Brenk
One Scaffold, Three Binding Modes: Novel And Selective Pteridine Reductase 1 Inhibitors Derived From Fragment Hits Discovered By Virtual Screening.
J. Med. Chem. V. 52 4454 2009
PubMed-ID: 19527033 | Reference-DOI: 10.1021/JM900414X

Molecule 1 - PTERIDINE REDUCTASE
	Chains	:	A, B, C, D
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET15B
	Expression System Strain	:	BL21(DE3)
	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 (4, 13)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	AX7	3	Ligand/Ion	1H-BENZIMIDAZOL-2-AMINE
3	CSX	4	Mod. Amino Acid	S-OXY CYSTEINE
4	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE

Asymmetric Unit (9, 9)

No.	Name	Evidence	Residues	Description
1	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 , ASP A:161 , TYR A:174 , LYS A:178 , PRO A:204 , GLY A:205 , VAL A:206 , SER A:207 , LEU A:208 , AX7 A:271 , HOH A:293 , HOH A:296 , HOH A:315 , HOH A:320 , HOH A:329 , HOH A:372 , HOH A:384 , HOH A:417 , HOH A:471	BINDING SITE FOR RESIDUE NAP A 269
2	AC2	SOFTWARE	PHE A:97 , ASP A:161 , TYR A:174 , NAP A:269 , HOH A:430	BINDING SITE FOR RESIDUE AX7 A 271
3	AC3	SOFTWARE	LYS A:13 , ARG A:14 , ARG A:17 , HOH A:375 , HOH A:385 , HOH A:400	BINDING SITE FOR RESIDUE ACT A 270
4	AC4	SOFTWARE	ARG B:14 , ILE B:15 , HIS B:33 , 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 , ASP B:161 , TYR B:174 , LYS B:178 , PRO B:204 , GLY B:205 , VAL B:206 , SER B:207 , LEU B:208 , HOH B:490 , HOH B:494 , HOH B:498 , HOH B:517 , HOH B:522 , HOH B:544 , HOH B:556 , HOH B:573 , HOH B:584 , HOH B:622	BINDING SITE FOR RESIDUE NAP B 269
5	AC5	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 , ASP C:161 , TYR C:174 , LYS C:178 , PRO C:204 , GLY C:205 , VAL C:206 , SER C:207 , LEU C:208 , AX7 C:271 , HOH C:479 , HOH C:480 , HOH C:497 , HOH C:570 , HOH C:608 , HOH C:613 , HOH C:615 , HOH C:675	BINDING SITE FOR RESIDUE NAP C 269
6	AC6	SOFTWARE	PHE C:97 , ASP C:161 , TYR C:174 , NAP C:269 , HOH C:615 , HOH C:676	BINDING SITE FOR RESIDUE AX7 C 271
7	AC7	SOFTWARE	TYR B:34 , VAL B:58 , HOH B:695 , VAL C:57 , VAL C:58 , HOH C:463	BINDING SITE FOR RESIDUE ACT C 270
8	AC8	SOFTWARE	ARG D:14 , ILE D:15 , HIS D:33 , 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 , VAL D:206 , SER D:207 , LEU D:208 , AX7 D:270 , HOH D:387 , HOH D:395 , HOH D:423 , HOH D:453 , HOH D:514 , HOH D:520 , HOH D:527 , HOH D:536 , HOH D:553 , HOH D:563	BINDING SITE FOR RESIDUE NAP D 269
9	AC9	SOFTWARE	PHE D:97 , ASP D:161 , TYR D:174 , NAP D:269 , HOH D:514 , HOH D:546	BINDING SITE FOR RESIDUE AX7 D 270

(no "SS Bond" information available for 3GN1)

(no "Cis Peptide Bond" information available for 3GN1)

(no "SAP(SNP)/Variant" information available for 3GN1)

(no "PROSITE Motif" information available for 3GN1)

(no "Exon" information available for 3GN1)

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:249
 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 d3gn1a_ A: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains 3gn1A00 A:2-268 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee...........---------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh---------..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gn1 A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ---------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       113                          142       152             168-CSX

Chain B 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 d3gn1b_ B: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains 3gn1B00 B:2-268 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                         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
                 3gn1 B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ----------NLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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       113                          142        153            168-CSX

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 d3gn1c_ C: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains 3gn1C00 C:2-268 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                         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
                 3gn1 C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLV---------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ----------NLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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       113                          142        153            168-CSX

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 d3gn1d_ D: Dihydropteridin reductase (pteridine reductase)                                                                                                                                                                                                                  SCOP domains
               CATH domains 3gn1D00 D:2-268 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh---------..eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3gn1 D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVCQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQ--------GKTVETQVAELIGTNAIAPFLLTMSFAQRQ---------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       
                                                                                                                                104      113                          142       152             168-CSX

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	d3gn1a_	A:
1b	d3gn1b_	B:
1c	d3gn1c_	C:
1d	d3gn1d_	D:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 3-Layer(aba) Sandwich (12045)

Topology: Rossmann fold (7312)

Homologous Superfamily: NAD(P)-binding Rossmann-like Domain (1244)

Trypanosoma brucei brucei. Organism_taxid: 5702. (6)

1a	3gn1B00	B:2-268
1b	3gn1C00	C:2-268
1c	3gn1A00	A:2-268
1d	3gn1D00	D:2-268

(no "Pfam Domain" information available for 3GN1)

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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	Ligands, Modified Residues, Ions
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	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 3gn1)

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	3gn1
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	O76290_TRYBB \| O76290
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3bmc	SAME PROTEIN COMPLEXED WITH COFACTOR (NADP+) AND SUBSTRATE (FOLATE)
3bmd	SAME PROTEIN COMPLEXED WITH LIGAND DX1
3bme	SAME PROTEIN COMPLEXED WITH LIGAND DX2
3bmf	SAME PROTEIN COMPLEXED WITH LIGAND DX3
3bmg	SAME PROTEIN COMPLEXED WITH LIGAND DX4
3bmh	SAME PROTEIN COMPLEXED WITH LIGAND DX6
3gn2	SAME PROTEIN COMPLEXED WITH LIGAND AX8

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 13)

Sites (9, 9)

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)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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