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(-) Description

Title :  CO-CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE INOSINE MONOPHOSPHATE DEHYDROGENASE FROM CRYPTOSPORIDIUM PARVUM WITH INHIBITOR N109
 
Authors :  Y. Kim, M. Makowska-Grzyska, M. Gu, L. Hedstrom, W. F. Anderson, A. Joac Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  03 Jun 14  (Deposition) - 06 Aug 14  (Release) - 06 Aug 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.42
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, Alpha-Beta Fold, Tim Barrel, Oxidoreductase- Oxidoreductase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  Y. Kim, M. Makowska-Grzyska, M. Gu, L. Hedstrom, W. F. Anderson, A. Joachimiak
Co-Crystal Structure Of The Catalytic Domain Of The Inosine Monophosphate Dehydrogenase From Cryptosporidium Parvum Wit Inhibitor N109
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    ChainsA, B, C, D
    EC Number1.1.1.205
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG7
    Expression System StrainBL21(DE3) GOLD
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentSEE REMARK 999
    Gene56K.02, CGD6_20
    MutationYES
    Organism ScientificCRYPTOSPORIDIUM PARVUM
    Organism Taxid5807
    SynonymIMPDH

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 13)

Asymmetric/Biological Unit (5, 13)
No.NameCountTypeFull Name
1ACY1Ligand/IonACETIC ACID
2EDO3Ligand/Ion1,2-ETHANEDIOL
3FMT1Ligand/IonFORMIC ACID
4IMP4Ligand/IonINOSINIC ACID
5N094Ligand/IonN-(4-CHLORO-3-METHOXYPHENYL)-2-(4-OXOCHROMENO[4,3-C]PYRAZOL-1(4H)-YL)ACETAMIDE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:48 , MET A:50 , ASN A:191 , GLY A:216 , SER A:217 , ILE A:218 , CYS A:219 , ASP A:252 , GLY A:254 , MET A:273 , GLY A:275 , SER A:276 , TYR A:299 , GLY A:301 , MET A:302 , GLY A:303 , GLU A:329 , GLY A:330 , N09 A:502 , HOH A:601 , HOH A:605 , HOH A:632BINDING SITE FOR RESIDUE IMP A 501
02AC2SOFTWAREALA A:165 , HIS A:166 , THR A:221 , MET A:302 , GLY A:303 , GLU A:329 , IMP A:501 , SER D:354 , GLY D:357 , TYR D:358BINDING SITE FOR RESIDUE N09 A 502
03AC3SOFTWARESER B:48 , MET B:50 , ASN B:191 , GLY B:216 , SER B:217 , ILE B:218 , CYS B:219 , ASP B:252 , GLY B:254 , MET B:273 , GLY B:275 , SER B:276 , TYR B:299 , GLY B:301 , MET B:302 , GLY B:303 , GLU B:329 , GLY B:330 , N09 B:502 , HOH B:611 , HOH B:616 , HOH B:628BINDING SITE FOR RESIDUE IMP B 501
04AC4SOFTWARESER A:354 , GLY A:357 , TYR A:358 , SER B:164 , ALA B:165 , HIS B:166 , THR B:221 , MET B:302 , GLY B:303 , GLU B:329 , IMP B:501BINDING SITE FOR RESIDUE N09 B 502
05AC5SOFTWARESER B:354 , GLY B:357 , TYR B:358 , ALA C:165 , HIS C:166 , MET C:302 , GLY C:303 , GLU C:329 , IMP C:501BINDING SITE FOR RESIDUE N09 B 503
06AC6SOFTWAREGLU B:375 , ILE B:376 , LYS C:8BINDING SITE FOR RESIDUE ACY B 504
07AC7SOFTWAREN09 B:503 , SER C:48 , MET C:50 , ASN C:191 , GLY C:216 , SER C:217 , ILE C:218 , CYS C:219 , ASP C:252 , GLY C:253 , GLY C:254 , MET C:273 , ILE C:274 , GLY C:275 , SER C:276 , TYR C:299 , GLY C:301 , MET C:302 , GLY C:303 , GLU C:329 , GLY C:330 , HOH C:604 , HOH C:614BINDING SITE FOR RESIDUE IMP C 501
08AC8SOFTWARETHR C:377 , THR C:378 , SER C:379 , GLU D:13 , ASP D:14 , ILE D:376 , THR D:377 , THR D:378BINDING SITE FOR RESIDUE EDO C 502
09AC9SOFTWARESER D:48 , MET D:50 , ASN D:191 , GLY D:216 , SER D:217 , ILE D:218 , CYS D:219 , ASP D:252 , GLY D:254 , MET D:273 , GLY D:275 , SER D:276 , TYR D:299 , GLY D:301 , MET D:302 , GLY D:303 , GLU D:329 , GLY D:330 , N09 D:502 , HOH D:605 , HOH D:623 , HOH D:624BINDING SITE FOR RESIDUE IMP D 501
10BC1SOFTWARELEU C:25 , SER C:354 , GLY C:357 , TYR C:358 , ALA D:165 , HIS D:166 , MET D:302 , GLY D:303 , GLU D:329 , IMP D:501BINDING SITE FOR RESIDUE N09 D 502
11BC2SOFTWAREILE D:277 , LYS D:338 , MET D:396 , ASN D:397BINDING SITE FOR RESIDUE EDO D 503
12BC3SOFTWAREARG D:256 , ILE D:277 , SER D:399BINDING SITE FOR RESIDUE FMT D 504
13BC4SOFTWARELYS D:8BINDING SITE FOR RESIDUE EDO D 505

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4QJ1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1Gly A:190 -Asn A:191
2Gly B:190 -Asn B:191
3Gly C:190 -Asn C:191
4Gly D:190 -Asn D:191

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4QJ1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4QJ1)

(-) Exons   (0, 0)

(no "Exon" information available for 4QJ1)

(-) 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:342
                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...eeee..hhh.eee...............ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eee....eeeeee...hhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee........ Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4qj1 A   2 GTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKNKMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIVKEVMNYS 399
                                    11        21        31        41        51        61        71        81        91||     143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303     ||327       337       347       357       367       377       387       397  
                                                                                                                     92|                                                                                                                                                                           309|                                                                           
                                                                                                                     135                                                                                                                                                                            324                                                                           

Chain B from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eee....eeeeee...hhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qj1 B   0 AMGTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSNKMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIVKEVMNYS 399
                                     9        19        29        39        49        59        69        79        89  ||   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       324       334       344       354       364       374       384       394     
                                                                                                                       92|                                                                                                                                                                            310|                                                                           
                                                                                                                       135                                                                                                                                                                             324                                                                           

Chain C from PDB  Type:PROTEIN  Length:345
                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeee..hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhhh..eeeehhhhhh.......eee....eeeeee...hhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee........ Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qj1 C   0 AMGTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSNKMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIVKEVMNYS 399
                                     9        19        29        39        49        59        69        79        89  ||   141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       324       334       344       354       364       374       384       394     
                                                                                                                       92|                                                                                                                                                                            310|                                                                           
                                                                                                                       135                                                                                                                                                                             324                                                                           

Chain D from PDB  Type:PROTEIN  Length:346
                                                                                                                                                                                                                                                                                                                                                                                          
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......eeee..hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhhh.eeee....hhhhhhhhhhhhhh......eeee...hhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eee....eeeeee...hhhhhhh........eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee........ Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4qj1 D  -1 NAMGTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSNKMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIVKEVMNYS 399
                                     8        18        28        38        48        58        68        78        88   ||  140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310|      333       343       353       363       373       383       393      
                                                                                                                        92|                                                                                                                                                                            310|                                                                           
                                                                                                                        135                                                                                                                                                                             324                                                                           

   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 '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 4QJ1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4QJ1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4QJ1)

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IMDH_CRYPV | Q8T6T23ffs 4ixh 4rv8

(-) Related Entries Specified in the PDB File

3ffs INOSINE MONOPHOSPHATE DEHYDROGENASE WITHOUT LIGANDS
4ixh INOSINE MONOPHOSPHATE DEHYDROGENASE WITH INHIBITOR Q21 RELATED ID: CSGID-IDP92622 RELATED DB: TARGETTRACK