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(-) Description

Title :  CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF THE INOSINE MONOPHOSPHATE DEHYDROGENASE FROM CRYPTOSPORIDIUM PARVUM
 
Authors :  Y. Kim, M. Makowska-Grzyska, M. Gu, M. Kavitha, L. Hedstrom, W. F. Ander A. Joachimiak, Center For Structural Genomics Of Infectious D (Csgid)
Date :  25 Jan 13  (Deposition) - 03 Apr 13  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.10
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 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. K. Gorla, M. Kavitha, M. Zhang, J. E. Chin, X. Liu, B. Striepen, M. Makowska-Grzyska, Y. Kim, A. Joachimiak, L. Hedstrom, G. D. Cuny
Optimization Of Benzoxazole-Based Inhibitors Of Cryptosporidium Parvum Inosine 5'-Monophosphate Dehydrogenase.
J. Med. Chem. V. 56 4028 2013
PubMed-ID: 23668331  |  Reference-DOI: 10.1021/JM400241J

(-) Compounds

Molecule 1 - INOSINE-5'-MONOPHOSPHATE DEHYDROGENASE
    Chains: A, B, C, D
    EC Number: 1.1.1.205
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PMCSG7
    Expression System Strain: BM21 MAGIC
    Expression System Taxid: 511693
    Expression System Vector Type: PLASMID
    Gene: 56K.02, CGD6_20
    Organism Scientific: CRYPTOSPORIDIUM PARVUM
    Organism Taxid: 5807
    Synonym: IMP DEHYDROGENASE, IMPD, IMPDH

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 13)

Asymmetric/Biological Unit (3, 13)
No.NameCountTypeFull Name
1EDO5Ligand/Ion1,2-ETHANEDIOL
2IMP4Ligand/IonINOSINIC ACID
3Q214Ligand/Ion(2S)-2-(NAPHTHALEN-1-YLOXY)-N-[2-(PYRIDIN-4-YL)-1,3-BENZOXAZOL-5-YL]PROPANAMIDE

(-) Sites  (13, 13)

Asymmetric Unit (13, 13)
No.NameEvidenceResiduesDescription
01AC1SOFTWARESER A:48 , MET A:50 , GLY A:216 , SER A:217 , ILE A:218 , CYS A:219 , ASP A:252 , GLY A:253 , 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 , HOH A:604 , HOH A:608 , HOH A:609 , HOH A:628 , Q21 B:501BINDING SITE FOR RESIDUE IMP A 501
02AC2SOFTWARETHR A:33 , LYS A:34 , SER A:270BINDING SITE FOR RESIDUE EDO A 502
03AC3SOFTWAREVAL A:224 , VAL A:327 , PRO A:328 , HOH A:646 , HOH A:659 , GLN B:347BINDING SITE FOR RESIDUE EDO A 503
04AC4SOFTWARESER A:22 , VAL A:24 , LEU A:25 , PRO A:26 , SER A:354 , TYR A:358 , HOH A:706 , ALA D:165 , SER D:169 , THR D:221 , MET D:302 , GLY D:303 , MET D:308 , GLU D:329 , IMP D:501BINDING SITE FOR RESIDUE Q21 A 504
05AC5SOFTWAREGLN A:347 , HOH A:656 , VAL D:224 , VAL D:327 , PRO D:328 , HOH D:646BINDING SITE FOR RESIDUE EDO A 505
06AC6SOFTWAREALA A:165 , SER A:169 , ASN A:171 , THR A:221 , MET A:302 , GLY A:303 , VAL A:327 , GLU A:329 , IMP A:501 , SER B:22 , VAL B:24 , LEU B:25 , SER B:354 , TYR B:358 , HOH B:638BINDING SITE FOR RESIDUE Q21 B 501
07AC7SOFTWARESER B:48 , MET B:50 , GLY B:216 , SER B:217 , ILE B:218 , CYS B:219 , ASP B:252 , GLY B:253 , 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 , Q21 B:503 , HOH B:602 , HOH B:608 , HOH B:614 , HOH B:639BINDING SITE FOR RESIDUE IMP B 502
08AC8SOFTWAREALA B:165 , SER B:169 , ASN B:171 , THR B:221 , MET B:302 , GLY B:303 , VAL B:327 , GLU B:329 , IMP B:502 , HOH B:659 , SER C:22 , VAL C:24 , LEU C:25 , PRO C:26 , SER C:354 , TYR C:358BINDING SITE FOR RESIDUE Q21 B 503
09AC9SOFTWARESER C:48 , MET C:50 , GLY C:216 , SER C:217 , ILE C:218 , CYS C:219 , ASP C:252 , GLY C:253 , GLY C:254 , MET C:273 , GLY C:275 , SER C:276 , TYR C:299 , GLY C:301 , MET C:302 , GLY C:303 , GLU C:329 , GLY C:330 , Q21 C:502 , HOH C:601 , HOH C:605 , HOH C:620 , HOH C:622BINDING SITE FOR RESIDUE IMP C 501
10BC1SOFTWAREALA C:165 , SER C:169 , THR C:221 , MET C:302 , GLY C:303 , VAL C:327 , GLU C:329 , IMP C:501 , HOH C:630 , HOH C:712 , SER D:22 , VAL D:24 , LEU D:25 , PRO D:26 , SER D:354 , TYR D:358BINDING SITE FOR RESIDUE Q21 C 502
11BC2SOFTWARESER C:239 , SER C:243 , GLY C:268 , TRP C:368 , HOH C:642 , HOH C:664BINDING SITE FOR RESIDUE EDO C 503
12BC3SOFTWARETHR C:33 , LYS C:34 , SER C:270 , TRP C:368BINDING SITE FOR RESIDUE EDO C 504
13BC4SOFTWAREQ21 A:504 , SER D:48 , MET D:50 , GLY D:216 , SER D:217 , ILE D:218 , CYS D:219 , ASP D:252 , GLY D:253 , 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 , HOH D:606 , HOH D:609 , HOH D:611 , HOH D:612BINDING SITE FOR RESIDUE IMP D 501

(-) SS Bonds  (0, 0)

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

(-) 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 4IXH)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4IXH)

(-) 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:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ixha_ A: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eeee..eeeeeee...hhhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixh A   1 MGTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSGMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIV 392
                                    10        20        30        40        50        60        70        80        90 ||    142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       326       336       346       356       366       376       386      
                                                                                                                      92|                                                                                                                                                                             311|                                                                  
                                                                                                                      135                                                                                                                                                                              326                                                                  


Chain B from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4ixhb_ B: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee...hhhhhhhhhhh...eeee......hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeee.............eeee..eeeeeee...hhhhhh.......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ixh B   2 GTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIV 392
                                    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      |328       338       348       358       368       378       388    
                                                                                                                     92|                                                                                                                                                                            310|                                                                  
                                                                                                                     135                                                                                                                                                                             326                                                                  


Chain C from PDB  Type:PROTEIN  Length:336
                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains d4ixhc_ C: automated matches                                                                                                                                                                                                                                                                                                                     SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ....eeee..hhh.eee.......hhhhh...eeee..eee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhh.....eeee....hhhhhhhhhhh...eeeehhhhhh.......eeee..eeeeeee...hhhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ixh C   1 MGTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSGMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIV 392
                                    10        20        30        40        50        60        70        80        90 ||    142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       326       336       346       356       366       376       386      
                                                                                                                      92|                                                                                                                                                                             311|                                                                  
                                                                                                                      135                                                                                                                                                                              326                                                                  


Chain D from PDB  Type:PROTEIN  Length:334
                                                                                                                                                                                                                                                                                                                                                                              
               SCOP domains d4ixhd_ D: automated matches                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..hhh.eee.......hhhhh...ee.....ee...eee.......hhhhhhhhhhh..eeee....hhhhhhhhhhhhhh......eeee...hhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhh..eeeeeee.hhhhhhhhhhh...eeee........hhhhhh....hhhhhhhhhhhhhhhhh..eeee....hhhhhhhhhhh...eeeehhhhhh.......eeee..eeeeeee...hhhhhhh......eeeee...hhhhhhhhhhhhhhhhhhhh...hhhhhhhhh.eee.hhhhhhhhh....ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ixh D   2 GTKNIGKGLTFEDILLVPNYSEVLPREVSLETKLTKNVSLKIPLISSAMDTVTEHLMAVGMARLGGIGIIHKNMDMESQVNEVLKVKNSGGLRVGAAIGVNEIERAKLLVEAGVDVIVLDSAHGHSLNIIRTLKEIKSKMNIDVIVGNVVTEEATKELIENGADGIKVGIGPGSICTTRIVAGVGVPQITAIEKCSSVASKFGIPIIADGGIRYSGDIGKALAVGASSVMIGSILAGTEESPGEKELIGDTVYKYYRGMGSVGAMKSMVPEGIEGRVKYKGEMEGVVYQLVGGLRSCMGYLGSASIEELWKKSSYVEITTSGLRESHVHDVEIV 392
                                    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      |328       338       348       358       368       378       388    
                                                                                                                     92|                                                                                                                                                                            310|                                                                  
                                                                                                                     135                                                                                                                                                                             326
   Legend:   → Mismatch (orange background)
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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  (1, 4)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (8, 8)

Asymmetric/Biological Unit(hide GO term definitions)

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  4ixh
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  IMDH_CRYPV | Q8T6T2
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 Related Entries

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

UniProtKB/Swiss-Prot
        IMDH_CRYPV | Q8T6T2: 3ffs 4qj1 4rv8

(-) Related Entries Specified in the PDB File

3ffs THE SAME PROTEIN WITHOUT LIGANDS RELATED ID: CSGID-IDP92622 RELATED DB: TARGETTRACK