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(-) Description

Title :  CRYSTAL STRUCTURE OF PLASMODIUM FALCIPARUM HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH S-SERME-IMMH PHOSPHONATE
 
Authors :  M. Ho, K. Z. Hazleton, S. C. Almo, V. L. Schramm
Date :  24 Sep 10  (Deposition) - 28 Sep 11  (Release) - 11 Jul 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.99
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (2x)
Biol. Unit 2:  C,D  (2x)
Keywords :  Hypoxanthine, Transferase-Transferase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  K. Z. Hazleton, M. C. Ho, M. B. Cassera, K. Clinch, D. R. Crump, I. Rosario, E. F. Merino, S. C. Almo, P. C. Tyler, V. L. Schramm
Acyclic Immucillin Phosphonates: Second-Generation Inhibitors Of Plasmodium Falciparum Hypoxanthine- Guanine-Xanthine Phosphoribosyltransferase.
Chem. Biol. V. 19 721 2012
PubMed-ID: 22726686  |  Reference-DOI: 10.1016/J.CHEMBIOL.2012.04.012

(-) Compounds

Molecule 1 - HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE
    ChainsA, B, C, D
    EC Number2.4.2.-
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPDEST14
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneLACZ
    Organism ScientificPLASMODIUM FALCIPARUM FCR-3/GAMBIA
    Organism Taxid5838
    SynonymHGXPRTASE, HGXPRT, HGPRT

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (2x)AB  
Biological Unit 2 (2x)  CD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric Unit (3, 12)
No.NameCountTypeFull Name
1MG4Ligand/IonMAGNESIUM ION
2POP4Ligand/IonPYROPHOSPHATE 2-
3SSI4Ligand/Ion[(3S)-4-HYDROXY-3-{[(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]AMINO}BUTYL]PHOSPHONIC ACID
Biological Unit 1 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2POP4Ligand/IonPYROPHOSPHATE 2-
3SSI4Ligand/Ion[(3S)-4-HYDROXY-3-{[(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]AMINO}BUTYL]PHOSPHONIC ACID
Biological Unit 2 (2, 8)
No.NameCountTypeFull Name
1MG-1Ligand/IonMAGNESIUM ION
2POP4Ligand/IonPYROPHOSPHATE 2-
3SSI4Ligand/Ion[(3S)-4-HYDROXY-3-{[(4-OXO-4,5-DIHYDRO-3H-PYRROLO[3,2-D]PYRIMIDIN-7-YL)METHYL]AMINO}BUTYL]PHOSPHONIC ACID

(-) Sites  (12, 12)

Asymmetric Unit (12, 12)
No.NameEvidenceResiduesDescription
01AC1SOFTWARETYR A:116 , GLU A:144 , ASP A:145 , ILE A:146 , ASP A:148 , THR A:149 , GLY A:150 , LYS A:151 , THR A:152 , LYS A:176 , PHE A:197 , VAL A:198 , ASP A:204 , POP A:233 , HOH A:237 , HOH A:250 , HOH A:269 , HOH A:291BINDING SITE FOR RESIDUE SSI A 232
02AC2SOFTWARELYS A:77 , GLY A:78 , ARG A:112 , VAL A:113 , LYS A:114 , SER A:115 , TYR A:116 , ASP A:204 , ARG A:210 , SSI A:232 , MG A:234 , HOH A:252 , HOH A:289 , HOH A:290 , HOH A:291 , HOH A:292BINDING SITE FOR RESIDUE POP A 233
03AC3SOFTWAREASP A:204 , POP A:233 , HOH A:269 , HOH A:289 , HOH A:290BINDING SITE FOR RESIDUE MG A 234
04AC4SOFTWAREASP B:204 , POP B:234 , HOH B:256 , HOH B:283 , HOH B:284BINDING SITE FOR RESIDUE MG B 232
05AC5SOFTWARETYR B:116 , GLU B:144 , ASP B:145 , ILE B:146 , ASP B:148 , THR B:149 , GLY B:150 , LYS B:151 , THR B:152 , LYS B:176 , PHE B:197 , VAL B:198 , ASP B:204 , POP B:234 , HOH B:256 , HOH B:266 , HOH B:280 , HOH B:285BINDING SITE FOR RESIDUE SSI B 233
06AC6SOFTWARELYS B:77 , GLY B:78 , ARG B:112 , VAL B:113 , LYS B:114 , SER B:115 , TYR B:116 , ASP B:204 , ARG B:210 , MG B:232 , SSI B:233 , HOH B:279 , HOH B:283 , HOH B:285 , HOH B:286BINDING SITE FOR RESIDUE POP B 234
07AC7SOFTWARETYR C:116 , GLU C:144 , ASP C:145 , ILE C:146 , ASP C:148 , THR C:149 , GLY C:150 , LYS C:151 , THR C:152 , LYS C:176 , PHE C:197 , VAL C:198 , LEU C:203 , ASP C:204 , POP C:233 , HOH C:265 , HOH C:270BINDING SITE FOR RESIDUE SSI C 232
08AC8SOFTWARELEU C:76 , LYS C:77 , GLY C:78 , ARG C:112 , VAL C:113 , LYS C:114 , SER C:115 , TYR C:116 , ASP C:204 , ARG C:210 , SSI C:232 , MG C:234 , HOH C:256 , HOH C:265 , HOH C:268 , HOH C:269 , HOH C:271 , HOH C:272BINDING SITE FOR RESIDUE POP C 233
09AC9SOFTWAREASP C:204 , POP C:233 , HOH C:268 , HOH C:269 , HOH C:270BINDING SITE FOR RESIDUE MG C 234
10BC1SOFTWARETYR D:116 , GLU D:144 , ASP D:145 , ILE D:146 , ASP D:148 , THR D:149 , GLY D:150 , LYS D:151 , THR D:152 , LYS D:176 , PHE D:197 , VAL D:198 , LEU D:203 , ASP D:204 , POP D:233 , HOH D:264 , HOH D:267 , HOH D:268 , HOH D:269 , HOH D:275BINDING SITE FOR RESIDUE SSI D 232
11BC2SOFTWARELYS D:77 , GLY D:78 , ARG D:112 , VAL D:113 , LYS D:114 , SER D:115 , TYR D:116 , ASP D:204 , ARG D:210 , SSI D:232 , MG D:234 , HOH D:244 , HOH D:265 , HOH D:266 , HOH D:268 , HOH D:269BINDING SITE FOR RESIDUE POP D 233
12BC3SOFTWAREASP D:204 , POP D:233 , HOH D:263 , HOH D:266 , HOH D:267BINDING SITE FOR RESIDUE MG D 234

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Leu A:76 -Lys A:77
2Leu B:76 -Lys B:77
3Leu C:76 -Lys C:77
4Leu D:76 -Lys D:77

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.HGXR_PLAFG140-152
 
 
 
  4A:140-152
B:140-152
C:140-152
D:140-152
Biological Unit 1 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.HGXR_PLAFG140-152
 
 
 
  4A:140-152
B:140-152
-
-
Biological Unit 2 (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.HGXR_PLAFG140-152
 
 
 
  4-
-
C:140-152
D:140-152

(-) Exons   (0, 0)

(no "Exon" information available for 3OZG)

(-) Sequences/Alignments

Asymmetric 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:227
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:227
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       
           HGXR_PLAFG     2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
               SCOP domains d3ozga_ A: automated matches                                                                                                                                                                                                        SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee.......hhhhh..hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee..eeeeeeeeee.hhhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozg A   2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       

Chain B from PDB  Type:PROTEIN  Length:228
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           HGXR_PLAFG     1 MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
               SCOP domains d3ozgb_ B: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................ee.......hhhhh.....hhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee..eeeeeeee....hhhhh..eeeeeeeee..hhhhhhhhhhhhh....eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ozg B   1 MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

Chain C from PDB  Type:PROTEIN  Length:230
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:230
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231
           HGXR_PLAFG     2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKATSL 231
               SCOP domains d3ozgc_ C: automated matches                                                                                                                                                                                                           SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...............ee.......hhhhh..hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee..eeeeeeeee...hhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ozg C   2 PIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKATSL 231
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231

Chain D from PDB  Type:PROTEIN  Length:228
 aligned with HGXR_PLAFG | P20035 from UniProtKB/Swiss-Prot  Length:231

    Alignment length:228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        
           HGXR_PLAFG     1 MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
               SCOP domains d3ozgd_ D: automated matches                                                                                                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ................ee.......hhhhh..hhhhhh.eeeeeehhhhhhhhhhhhhhhhhhhhh...eeeeeee..hhhhhhhhhhhhhhhhhhh........eeeeeeeeeeee..eeeeeeeee...hhhhh..eeeeeeeee..hhhhhhhhhhhhhhh..eeeeeeeeee...........eeeeee....ee...............eeeehhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR---------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3ozg D   1 MPIPNNPGAGENAFDPVFVNDDDGYDLDSFMIPAHYKKYLTKVLVPNGVIKNRIEKLAYDIKKVYNNEEFHILCLLKGSRGFFTALLKHLSRIHNYSAVETSKPLFGEHYVRVKSYCNDQSTGTLEIVSEDLSCLKGKHVLIVEDIIDTGKTLVKFCEYLKKFEIKTVAIACLFIKRTPLWNGFKADFVGFSIPDHFVVGYSLDYNEIFRDLDHCCLVNDEGKKKYKA 228
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220        

   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  (1, 4)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3OZG)

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (13, 13)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (HGXR_PLAFG | P20035)
molecular function
    GO:0052657    guanine phosphoribosyltransferase activity    Catalysis of the reaction: GMP + diphosphate = guanine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0004422    hypoxanthine phosphoribosyltransferase activity    Catalysis of the reaction: IMP + diphosphate = hypoxanthine + 5-phospho-alpha-D-ribose 1-diphosphate.
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
    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:0016740    transferase activity    Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
    GO:0016757    transferase activity, transferring glycosyl groups    Catalysis of the transfer of a glycosyl group from one compound (donor) to another (acceptor).
    GO:0000310    xanthine phosphoribosyltransferase activity    Catalysis of the reaction: 5-phospho-alpha-D-ribose 1-diphosphate + xanthine = (9-D-ribosylxanthine)-5'-phosphate + diphosphate.
biological process
    GO:0032263    GMP salvage    Any process which produces guanosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0032264    IMP salvage    Any process which produces inosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0032265    XMP salvage    Any process which produces xanthosine monophosphate from derivatives of it, without de novo synthesis.
    GO:0009116    nucleoside metabolic process    The chemical reactions and pathways involving a nucleoside, a nucleobase linked to either beta-D-ribofuranose (a ribonucleoside) or 2-deoxy-beta-D-ribofuranose, (a deoxyribonucleoside), e.g. adenosine, guanosine, inosine, cytidine, uridine and deoxyadenosine, deoxyguanosine, deoxycytidine and thymidine (= deoxythymidine).
    GO:0006166    purine ribonucleoside salvage    Any process which produces a purine nucleoside from derivatives of it, without de novo synthesis.
cellular component
    GO:0005737    cytoplasm    All of the contents of a cell excluding the plasma membrane and nucleus, but including other subcellular structures.

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 Related Entries

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

UniProtKB/Swiss-Prot
        HGXR_PLAFG | P200351cjb 2vfa 3ozf

(-) Related Entries Specified in the PDB File

3ozf HYPOXANTHINE-GUANINE-XANTHINE PHOSPHORIBOSYLTRANSFERASE IN COMPLEX WITH HYPOXANTHINE