2C7V - JenaLib

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

Asym./Biol. Unit (Jmol Viewer)

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

Title :   STRUCTURE OF TRYPANOSOMA BRUCEI PTERIDINE REDUCTASE (PTR1) IN TERNARY COMPLEX WITH COFACTOR AND THE ANTIFOLATE METHOTREXATE

Authors :   A. Dawson, F. Gibellini, N. Sienkiewicz, P. K. Fyfe, K. Mcluskey, A. H. Fairlamb, W. N. Hunter

Date :   29 Nov 05 (Deposition) - 19 Sep 06 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.20

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

Keywords :   Pteridine Reductase, Trypanosomatids, Drug Resistance, Short-Chain Dehydrogenase/Reductase, Methotrexate Resistance, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. Dawson, F. Gibellini, N. Sienkiewicz, L. B. Tulloch, P. K. Fyfe, K. Mcluskey, A. H. Fairlamb, W. N. Hunter
Structure And Reactivity Of Trypanosoma Brucei Pteridine Reductase: Inhibition By The Archetypal Antifolate Methotrexate
Mol. Microbiol. V. 61 1457 2006
PubMed-ID: 16968221 | Reference-DOI: 10.1111/J.1365-2958.2006.05332.X

Molecule 1 - PTERIDINE REDUCTASE
	Chains	:	A, B, C, D
	EC Number	:	1.5.1.33
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Plasmid	:	PET-TBPTR1H
	Expression System Strain	:	BL21(DE3)
	Expression System Taxid	:	469008
	Expression System Vector	:	PET15B
	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 (5, 20)

No.	Name	Count	Type	Full Name
1	ACT	2	Ligand/Ion	ACETATE ION
2	CAF	8	Mod. Amino Acid	S-DIMETHYLARSINOYL-CYSTEINE
3	MTX	4	Ligand/Ion	METHOTREXATE
4	NAP	4	Ligand/Ion	NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
5	NI	2	Ligand/Ion	NICKEL (II) ION

Asymmetric Unit (12, 12)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	HIS A:179 , HIS C:179	BINDING SITE FOR RESIDUE NI A1273
02	AC2	SOFTWARE	GLU A:215 , LYS A:218 , ARG A:222	BINDING SITE FOR RESIDUE ACT A1274
03	AC3	SOFTWARE	HIS B:179 , HIS D:179	BINDING SITE FOR RESIDUE NI B1273
04	AC4	SOFTWARE	MET B:213 , GLY B:214 , GLU B:215 , HOH B:2159 , HOH B:2217	BINDING SITE FOR RESIDUE ACT B1274
05	AC5	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 , MTX A:1272 , HOH A:2008 , HOH A:2127 , HOH A:2188 , HOH A:2189 , HOH A:2190 , HOH A:2191 , HOH A:2192 , HOH A:2193 , HOH A:2194 , HOH A:2195	BINDING SITE FOR RESIDUE NAP A1271
06	AC6	SOFTWARE	ARG A:14 , SER A:95 , PHE A:97 , PRO A:99 , CAF A:168 , TYR A:174 , LEU A:208 , MET A:213 , NAP A:1271 , HOH A:2141 , HOH A:2198 , HOH A:2199 , HOH A:2200 , HOH A:2201 , HOH A:2202 , HOH A:2203	BINDING SITE FOR RESIDUE MTX A1272
07	AC7	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 , TYR B:174 , LYS B:178 , PRO B:204 , GLY B:205 , SER B:207 , LEU B:208 , MTX B:1272 , HOH B:2004 , HOH B:2031 , HOH B:2142 , HOH B:2205 , HOH B:2206 , HOH B:2207 , HOH B:2208 , HOH B:2210	BINDING SITE FOR RESIDUE NAP B1271
08	AC8	SOFTWARE	ARG B:14 , SER B:95 , PHE B:97 , PRO B:99 , CAF B:168 , TYR B:174 , LEU B:208 , MET B:213 , GLU B:217 , TRP B:221 , NAP B:1271 , HOH B:2139 , HOH B:2157 , HOH B:2211 , HOH B:2212 , HOH B:2213 , HOH B:2214 , HOH B:2215 , HOH B:2216	BINDING SITE FOR RESIDUE MTX B1272
09	AC9	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 , VAL C:206 , SER C:207 , LEU C:208 , MTX C:1272 , HOH C:2117 , HOH C:2180 , HOH C:2181 , HOH C:2183 , HOH C:2184 , HOH C:2185 , HOH C:2186	BINDING SITE FOR RESIDUE NAP C1271
10	BC1	SOFTWARE	ARG C:14 , SER C:95 , PHE C:97 , PRO C:99 , TYR C:174 , LEU C:208 , MET C:213 , TRP C:221 , NAP C:1271 , HOH C:2124 , HOH C:2187 , HOH C:2188 , HOH C:2189 , HOH C:2190 , HOH C:2191 , HOH C:2192	BINDING SITE FOR RESIDUE MTX C1272
11	BC2	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 , CYS D:160 , TYR D:174 , LYS D:178 , PRO D:204 , GLY D:205 , SER D:207 , LEU D:208 , MTX D:1272 , HOH D:2114 , HOH D:2175 , HOH D:2176 , HOH D:2177 , HOH D:2179 , HOH D:2181 , HOH D:2182 , HOH D:2183	BINDING SITE FOR RESIDUE NAP D1271
12	BC3	SOFTWARE	ARG D:14 , SER D:95 , PHE D:97 , PRO D:99 , TYR D:174 , LEU D:208 , PRO D:210 , MET D:213 , TRP D:221 , NAP D:1271 , HOH D:2109 , HOH D:2184 , HOH D:2185 , HOH D:2186 , HOH D:2187	BINDING SITE FOR RESIDUE MTX D1272

(no "SS Bond" information available for 2C7V)

(no "Cis Peptide Bond" information available for 2C7V)

(no "SAP(SNP)/Variant" information available for 2C7V)

(no "PROSITE Motif" information available for 2C7V)

(no "Exon" information available for 2C7V)

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:253
 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 d2c7va_ A: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2c7vA00 A:2-268 NAD(P)-binding Rossmann-like Domain                                                                                                                                                                                                                         CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhhh.eeeeee..hhhhhhhhhhhhhhhh...eeeee.......hhhhhhhhhhhhhhhhhh...eeee............--------..hhhhhhhhhhhhhhhhhhhhhhhhhhhhh.------...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c7v A   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQ--------GKTVETQVAELIGTNAIAPFLLTMSFAQRQKG------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       
                                                                                    59-CAF                                      104      113                            144    151              168-CAF

Chain B from PDB  Type:PROTEIN  Length:254
 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 d2c7vb_ B: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2c7vB00 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............-------...hhhhhhhhhhhhhhhhhhhhhhhhhhhhh------.....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c7v B   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQ-------NGKTVETQVAELIGTNAIAPFLLTMSFAQRQK------TSSNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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       
                                                                                    59-CAF                                      104     112                            143    150               168-CAF

Chain C from PDB  Type:PROTEIN  Length:260
 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 d2c7vc_ C: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2c7vC00 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.............-------..hhhhhhhhhhhhhhhhhhhhhhhhhhhh............eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c7v C   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQG-------GKTVETQVAELIGTNAIAPFLLTMSFAQRQKGTNPNCTSSNLSIVNLCDAMVDQPcMAFSLYNMGKHALVGLTQSAALELAPYGIRVNGVAPGVSLLPVAMGEEEKDKWRRKVPLGRREASAEQIADAVIFLVSGSAQYITGSIIKVDGGLSLVHA 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       
                                                                                    59-CAF                                       105     113                                                    168-CAF

Chain D from PDB  Type:PROTEIN  Length:257
 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 d2c7vd_ D: automated matches                                                                                                                                                                                                                                                SCOP domains
               CATH domains 2c7vD00 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...............----...hhhhhhhhhhhhhhhhhhhhhhhhhhh...------....eeeee...........hhhhhhhhhhhhhhhhhhhhhhhhhh.eeeeeee.........hhhhhhhhhh.........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2c7v D   2 EAPAAVVTGAAKRIGRAIAVKLHQTGYRVVIHYHNSAEAAVSLADELNKERSNTAVVcQADLTNSNVLPASCEEIINSCFRAFGRCDVLVNNASAFYPTPLVQGDH----NGKTVETQVAELIGTNAIAPFLLTMSFAQRQKG------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       
                                                                                    59-CAF                                         107  112                             144    151              168-CAF

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: automated matches (114)

Trypanosoma brucei [TaxId: 5702] (4)

1a	d2c7va_	A:
1b	d2c7vb_	B:
1c	d2c7vc_	C:
1d	d2c7vd_	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. (7)

1a	2c7vA00	A:2-268
1b	2c7vB00	B:2-268
1c	2c7vD00	D:2-268
1d	2c7vC00	C:2-268

(no "Pfam Domain" information available for 2C7V)

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 2c7v)

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	2c7v
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	O76290_TRYBB \| O76290
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(no "Related Entries Specified in the PDB File" available for 2C7V)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (5, 20)

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)

CATH Domains (1, 4)

Pfam Domains (0, 0)

Gene Ontology (4, 4)

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