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(-) Description

Title :  LEISHMANIA MAJOR PTERIDINE REDUCTASE 1 (PTR1) IN COMPLEX WITH COMPOUND 3
 
Authors :  L. Dello Iacono, F. Di Pisa, C. Pozzi, G. Landi, S. Mangani
Date :  24 May 16  (Deposition) - 03 May 17  (Release) - 03 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Leishmania Major, Pteridine Reductase 1, Ptr1, Oxidoreductase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Dello Iacono, F. Di Pisa, C. Pozzi, G. Landi, S. Mangani
Leishmania Major Pteridine Reductase 1 (Ptr1) In Complex With Compound 3
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - PTERIDINE REDUCTASE 1
    Chains: A, B, C, D
    EC Number: 1.5.1.33
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET-15B
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: PTR1, HMTXR, L1063.01, LMJF23.0270, LMJF_23_0270
    Organism Scientific: LEISHMANIA MAJOR
    Organism Taxid: 5664
    Synonym: H REGION METHOTREXATE RESISTANCE PROTEIN

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 28)

Asymmetric/Biological Unit (7, 28)
No.NameCountTypeFull Name
16J64Ligand/Ion(2~{R})-2-[3,4-BIS(OXIDANYL)PHENYL]-6-OXIDANYL-2,3-DIHYDROCHROMEN-4-ONE
2ACT4Ligand/IonACETATE ION
3CSX4Mod. Amino AcidS-OXY CYSTEINE
4EDO5Ligand/Ion1,2-ETHANEDIOL
5GOL6Ligand/IonGLYCEROL
6NDP4Ligand/IonNADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDEPHOSPHATE
7PGE1Ligand/IonTRIETHYLENE GLYCOL

(-) Sites  (24, 24)

Asymmetric Unit (24, 24)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREARG A:17 , SER A:111 , PHE A:113 , LEU A:188 , TYR A:194 , GLY A:225 , LEU A:226 , TYR A:283 , NDP A:302 , ACT A:307 , HOH A:466 , HOH A:486 , ARG D:287 , HOH D:456binding site for residue 6J6 A 301
02AC2SOFTWAREARG A:17 , LEU A:18 , HIS A:36 , TYR A:37 , HIS A:38 , ARG A:39 , SER A:40 , ALA A:64 , ASP A:65 , LEU A:66 , SER A:67 , ASN A:109 , ALA A:110 , SER A:111 , SER A:112 , ASP A:142 , MET A:179 , VAL A:180 , ASP A:181 , TYR A:194 , LYS A:198 , PRO A:224 , GLY A:225 , LEU A:226 , SER A:227 , 6J6 A:301 , ACT A:307 , HOH A:402 , HOH A:409 , HOH A:421 , HOH A:427 , HOH A:431 , HOH A:436 , HOH A:451 , HOH A:507binding site for residue NDP A 302
03AC3SOFTWARETYR A:97 , ARG A:161 , THR A:165binding site for residue GOL A 303
04AC4SOFTWAREGLN A:216 , LYS A:270 , ARG C:250 , ARG D:54binding site for residue GOL A 304
05AC5SOFTWAREHIS A:99 , TRP A:100 , GLY A:101binding site for residue ACT A 305
06AC6SOFTWAREARG A:20 , THR A:50 , HOH A:475 , ARG B:20 , THR B:50binding site for residue ACT A 306
07AC7SOFTWAREARG A:17 , 6J6 A:301 , NDP A:302 , HOH A:497binding site for residue ACT A 307
08AC8SOFTWARETYR A:248 , ARG A:250 , HOH A:415 , HOH A:416 , GLN C:216 , LYS C:270binding site for residue PGE A 308
09AC9SOFTWAREPRO A:166 , LYS A:168binding site for residue EDO A 309
10AD1SOFTWAREVAL A:6 , ASN A:57 , SER A:58 , HOH A:438binding site for residue EDO A 310
11AD2SOFTWAREARG B:17 , SER B:111 , PHE B:113 , TYR B:194 , GLY B:225 , LEU B:226 , TYR B:283 , NDP B:302 , HOH B:491 , HOH B:493 , HOH B:539 , ARG C:287 , HOH C:572binding site for residue 6J6 B 301
12AD3SOFTWAREARG B:17 , LEU B:18 , HIS B:36 , TYR B:37 , HIS B:38 , ARG B:39 , SER B:40 , ALA B:64 , ASP B:65 , LEU B:66 , ASN B:109 , ALA B:110 , SER B:111 , SER B:112 , ASP B:142 , MET B:179 , VAL B:180 , ASP B:181 , TYR B:194 , LYS B:198 , PRO B:224 , GLY B:225 , LEU B:226 , SER B:227 , 6J6 B:301 , GOL B:305 , HOH B:408 , HOH B:421 , HOH B:443 , HOH B:445 , HOH B:449 , HOH B:459 , HOH B:473 , HOH B:517binding site for residue NDP B 302
13AD4SOFTWAREGLN B:216 , LYS B:270 , HOH B:450 , TYR D:248 , ARG D:250binding site for residue GOL B 303
14AD5SOFTWAREVAL B:228 , ARG B:242 , ARG B:250 , ASP B:251 , SER B:252 , HOH B:544binding site for residue GOL B 304
15AD6SOFTWAREVAL A:230 , ASP A:231 , ASP A:232 , NDP B:302 , HOH B:421 , HOH B:427 , HOH B:443 , HOH B:449 , HOH B:507binding site for residue GOL B 305
16AD7SOFTWARETYR B:248 , ARG B:250 , HOH B:489 , GLN D:216 , LYS D:270binding site for residue ACT B 306
17AD8SOFTWAREARG B:287 , ARG C:17 , SER C:111 , PHE C:113 , LEU C:188 , TYR C:194 , LEU C:226 , LEU C:229 , NDP C:302 , GOL C:303 , HOH C:423 , HOH C:523binding site for residue 6J6 C 301
18AD9SOFTWAREARG C:17 , LEU C:18 , HIS C:36 , TYR C:37 , HIS C:38 , ARG C:39 , SER C:40 , ALA C:64 , ASP C:65 , LEU C:66 , SER C:67 , ASN C:109 , ALA C:110 , SER C:111 , SER C:112 , ASP C:142 , SER C:146 , MET C:179 , VAL C:180 , ASP C:181 , TYR C:194 , LYS C:198 , PRO C:224 , GLY C:225 , LEU C:226 , SER C:227 , 6J6 C:301 , GOL C:303 , HOH C:416 , HOH C:421 , HOH C:458 , HOH C:465 , HOH C:472 , HOH C:490 , HOH C:506 , HOH C:536binding site for residue NDP C 302
19AE1SOFTWAREARG C:17 , PHE C:113 , VAL C:230 , 6J6 C:301 , NDP C:302binding site for residue GOL C 303
20AE2SOFTWAREHOH C:414 , HOH C:509binding site for residue EDO C 304
21AE3SOFTWAREARG A:287 , ARG D:17 , SER D:111 , PHE D:113 , TYR D:194 , LEU D:226 , LEU D:229 , HIS D:241 , NDP D:302 , EDO D:304 , HOH D:444 , HOH D:534binding site for residue 6J6 D 301
22AE4SOFTWAREARG D:17 , LEU D:18 , TYR D:37 , HIS D:38 , ARG D:39 , SER D:40 , ALA D:64 , ASP D:65 , LEU D:66 , SER D:67 , ASN D:109 , ALA D:110 , SER D:111 , SER D:112 , ASP D:142 , MET D:179 , VAL D:180 , ASP D:181 , TYR D:194 , LYS D:198 , PRO D:224 , GLY D:225 , LEU D:226 , SER D:227 , 6J6 D:301 , EDO D:304 , HOH D:412 , HOH D:418 , HOH D:423 , HOH D:434 , HOH D:455 , HOH D:468 , HOH D:470 , HOH D:485binding site for residue NDP D 302
23AE5SOFTWAREHIS D:169 , HOH D:471 , HOH D:562binding site for residue EDO D 303
24AE6SOFTWARE6J6 D:301 , NDP D:302 , HOH D:527binding site for residue EDO D 304

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5L42)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5L42)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5L42)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5L42)

(-) Exons   (0, 0)

(no "Exon" information available for 5L42)

(-) 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
(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:265
                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l42 A   5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRREAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTcVKVDGGYSLTRA 288
                                    14        24        34        44        54        64        81        91       101       111       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273  |    283     
                                                                                               73|                                    120|                                                                                                                                            276-CSX        
                                                                                                81                                     133                                                                                                                                                           


Chain B from PDB  Type:PROTEIN  Length:266
                                                                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee.........hhhhhhhhhhh........hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l42 B   5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRDREAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVDDMPPAVWEGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTcVKVDGGYSLTRA 288
                                    14        24        34        44        54        64        81        91       101       111       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272   |   282      
                                                                                               73|                                    120|                                                                                                                                             276-CSX        
                                                                                                81                                     132                                                                                                                                                            


Chain C from PDB  Type:PROTEIN  Length:257
                                                                                                                                                                                                                                                                                                 
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee..............hhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l42 C   5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPSAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRREAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTcVKVDGGYSLTRA 288
                                    14        24        34        44        54        64        80        90       100       110       120|      142       152       162       172       182       192       202       212       222       241       251       261       271    |  281       
                                                                                               73|                                     120|                                                                                              230|                                 276-CSX        
                                                                                                80                                      133                                                                                               240                                                


Chain D from PDB  Type:PROTEIN  Length:254
                                                                                                                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee....hhhhhhhhhhhhhh..eeeeee..hhhhhhhhhhhhhhhh...eeeee.............hhhhhhhhhhhhhhhhhh...eeee.............hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...eeeeee...........hhhhhhhhhhhhhhhhhhhhhhh...eeeeeeee......hhhhhh.......hhhhhhhhhhhhhhhhhh.....eeee..hhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5l42 D   5 TVPVALVTGAAKRLGRSIAEGLHAEGYAVCLHYHRSAAEANALSATLNARRPNSAITVQADLSNVATAPAPVTLFTRCAELVAACYTHWGRCDVLVNNASSFYPTPLLRAMETATADLFGSNAIAPYFLIKAFAHRVAGTPAKHRGTNYSIINMVDAMTNQPLLGYTIYTMAKGALEGLTRSAALELAPLQIRVNGVGPGLSVLVGHRSKVPLYQRDSSAAEVSDVVIFLCSSKAKYITGTcVKVDGGYSLTRA 288
                                    14        24        34        44        54        64        81        91       101       111       135       145       155       165       175       185       195       205       215       225    || 244       254       264       274 |     284    
                                                                                               73|                                    120|                                                                                            230|                                 276-CSX        
                                                                                                81                                     135                                                                                             240
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  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 5L42)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5L42)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5L42)

(-) Gene Ontology  (9, 9)

Asymmetric/Biological Unit(hide GO term definitions)

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  5l42
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  PTR1_LEIMA | Q01782
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 Related Entries

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

UniProtKB/Swiss-Prot
        PTR1_LEIMA | Q01782: 1e7w 1e92 1w0c 2bf7 2bfa 2bfm 2bfo 2bfp 2qhx 3h4v 5l4n

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5L42)