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(-) Description

Title :  S. CEREVISIAE OROTATE PHOSPHORIBOSYLTRANSFERASE COMPLEXED WITH OMP
 
Authors :  L. Gonzalez-Segura, T. D. Hurley, R. W. Mcclard
Date :  04 May 07  (Deposition) - 15 Jan 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.90
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Keywords :  Alpha Beta, Oprtase-Omp Complex, Transferase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Gonzalez-Segura, J. F. Witte, R. W. Mcclard, T. D. Hurley
Ternary Complex Formation And Induced Asymmetry In Orotate Phosphoribosyltransferase.
Biochemistry V. 46 14075 2007
PubMed-ID: 18020427  |  Reference-DOI: 10.1021/BI701023Z
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - OROTATE PHOSPHORIBOSYLTRANSFERASE 1
    ChainsA, B, C, D
    EC Number2.4.2.10
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPREJ2
    Expression System StrainCS101-4UI
    Expression System Taxid562
    Expression System Vector TypePTRC99A
    GeneURA5, PYR5
    Organism CommonBAKER'S YEAST
    Organism ScientificSACCHAROMYCES CEREVISIAE
    Organism Taxid4932
    SynonymOPRT 1, OPRTASE 1

 Structural Features

(-) Chains, Units

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

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 8)

Asymmetric Unit (2, 8)
No.NameCountTypeFull Name
1CL4Ligand/IonCHLORIDE ION
2OMP4Ligand/IonOROTIDINE-5'-MONOPHOSPHATE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2OMP2Ligand/IonOROTIDINE-5'-MONOPHOSPHATE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1CL-1Ligand/IonCHLORIDE ION
2OMP2Ligand/IonOROTIDINE-5'-MONOPHOSPHATE

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:75 , LYS A:76 , ARG B:105BINDING SITE FOR RESIDUE CL A 1
2AC2SOFTWARETYR C:75 , LYS C:76BINDING SITE FOR RESIDUE CL C 2
3AC3SOFTWAREARG C:105 , TYR D:75 , LYS D:76BINDING SITE FOR RESIDUE CL D 225
4AC4SOFTWAREARG A:105 , TYR B:75 , LYS B:76BINDING SITE FOR RESIDUE CL B 225
5AC5SOFTWARELEU A:28 , LYS A:29 , PHE A:37 , PHE A:38 , ASP A:132 , VAL A:133 , MET A:134 , THR A:135 , ALA A:136 , GLY A:137 , THR A:138 , ALA A:139 , ARG A:163 , HOH A:453 , HOH A:457 , HOH A:458 , HOH A:465 , HOH A:482 , HOH A:501BINDING SITE FOR RESIDUE OMP A 450
6AC6SOFTWARELEU B:28 , LYS B:29 , PHE B:37 , PHE B:38 , ASP B:132 , VAL B:133 , MET B:134 , THR B:135 , ALA B:136 , GLY B:137 , THR B:138 , ALA B:139 , ARG B:163 , HOH B:554 , HOH B:559 , HOH B:560 , HOH B:577BINDING SITE FOR RESIDUE OMP B 550
7AC7SOFTWARELEU C:28 , LYS C:29 , PHE C:37 , PHE C:38 , ASP C:132 , VAL C:133 , MET C:134 , THR C:135 , ALA C:136 , GLY C:137 , THR C:138 , ALA C:139 , ARG C:163 , HOH C:652 , HOH C:654 , HOH C:671 , HOH C:698 , HOH C:718 , HOH C:728BINDING SITE FOR RESIDUE OMP C 650
8AC8SOFTWARELEU D:28 , LYS D:29 , PHE D:37 , PHE D:38 , ASP D:132 , VAL D:133 , MET D:134 , THR D:135 , ALA D:136 , GLY D:137 , THR D:138 , ALA D:139 , ARG D:163 , HOH D:753 , HOH D:754 , HOH D:756 , HOH D:787 , HOH D:815 , HOH D:835BINDING SITE FOR RESIDUE OMP D 750

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Ala A:74 -Tyr A:75
2Ala B:74 -Tyr B:75
3Ala C:74 -Tyr C:75
4Ala D:74 -Tyr D:75

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (1, 4)

Asymmetric Unit (1, 4)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.PYRE_YEAST128-140
 
 
 
  4A:127-139
B:127-139
C:127-139
D:127-139
Biological Unit 1 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.PYRE_YEAST128-140
 
 
 
  2A:127-139
B:127-139
-
-
Biological Unit 2 (1, 2)
 PROSITEUniProtKBPDB
No.IDACDescriptionIDLocationCountLocation
1PUR_PYR_PR_TRANSFERPS00103 Purine/pyrimidine phosphoribosyl transferases signature.PYRE_YEAST128-140
 
 
 
  2-
-
C:127-139
D:127-139

(-) Exons   (1, 4)

Asymmetric Unit (1, 4)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1YML106W1YML106W.1XIII:56773-57453681PYRE_YEAST1-2262264A:4-224 (gaps)
B:2-224 (gaps)
C:4-224 (gaps)
D:2-224 (gaps)
221
223
221
223

(-) 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:215
 aligned with PYRE_YEAST | P13298 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:221
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
           PYRE_YEAST     5 LEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 225
               SCOP domains d2prza_ A: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2przA00 A:4-224  [code=3.40.50.2020, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhh..eeeee....------..ee.......eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............hhhhhhhhhhh..eeeeeehhhhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: A:4-224 (gaps) UniProt: 1-226 [INCOMPLETE]                                                                                                                                                                     Transcript 1
                 2prz A   4 LEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEA------GIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 224
                                    13        23        33        43        53        63        73        83        93       103    |    - |     123       133       143       153       163       173       183       193       203       213       223 
                                                                                                                                  108    115                                                                                                             

Chain B from PDB  Type:PROTEIN  Length:216
 aligned with PYRE_YEAST | P13298 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           PYRE_YEAST     3 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 225
               SCOP domains d2przb_ B: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2przB00 B:2-224  [code=3.40.50.2020, no name defined]                                                                                                                                                                           CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eee....hhhhhhhhhhhhhhhhhhhhhh..eeeee....-------.ee.......eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............hhhhhhhhhhh..eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: B:2-224 (gaps) UniProt: 1-226 [INCOMPLETE]                                                                                                                                                                       Transcript 1
                 2prz B   2 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEA-------IIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 224
                                    11        21        31        41        51        61        71        81        91       101      |  -    |  121       131       141       151       161       171       181       191       201       211       221   
                                                                                                                                    108     116                                                                                                            

Chain C from PDB  Type:PROTEIN  Length:215
 aligned with PYRE_YEAST | P13298 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:221
                                    14        24        34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224 
           PYRE_YEAST     5 LEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 225
               SCOP domains d2przc_ C: automated matches                                                                                                                                                                                                  SCOP domains
               CATH domains 2przC00 C:4-224  [code=3.40.50.2020, no name defined]                                                                                                                                                                         CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhh.....eeee...hhhhhhhhhhhhhhhhhhhhhh..eeeee....------..ee.......eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............hhhhhhhhhhh..eeeeeehhhhhhhh....hhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: C:4-224 (gaps) UniProt: 1-226 [INCOMPLETE]                                                                                                                                                                     Transcript 1
                 2prz C   4 LEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEA------GIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 224
                                    13        23        33        43        53        63        73        83        93       103    |    - |     123       133       143       153       163       173       183       193       203       213       223 
                                                                                                                                  108    115                                                                                                             

Chain D from PDB  Type:PROTEIN  Length:217
 aligned with PYRE_YEAST | P13298 from UniProtKB/Swiss-Prot  Length:226

    Alignment length:223
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222   
           PYRE_YEAST     3 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEAKDHGEGGIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 225
               SCOP domains d2przd_ D: automated matches                                                                                                                                                                                                    SCOP domains
               CATH domains 2przD00 D:2-224  [code=3.40.50.2020, no name defined]                                                                                                                                                                           CATH domains
           Pfam domains (1) --------------------------------------Pribosyltran-2przD01 D:40-161                                                                                             --------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------Pribosyltran-2przD02 D:40-161                                                                                             --------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------Pribosyltran-2przD03 D:40-161                                                                                             --------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------Pribosyltran-2przD04 D:40-161                                                                                             --------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...hhhhhhhhhhhhhh..eeeeeee.....eeeeee.hhhh.hhhhhhhhhhhhhhhhhhhh....eeee...hhhhhhhhhhhhhhhhhhhhhh..eeeee....------..ee.......eeeeeeeee..hhhhhhhhhhhhhh..eeeeeeeeee.............hhhhhhhhhh...eeeeeehhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------PUR_PYR_PR_TR------------------------------------------------------------------------------------- PROSITE
               Transcript 1 Exon 1.1  PDB: D:2-224 (gaps) UniProt: 1-226 [INCOMPLETE]                                                                                                                                                                       Transcript 1
                 2prz D   2 IMLEDYQKNFLELAIECQALRFGSFKLKSGRESPYFFNLGLFNTGKLLSNLATAYAIAIIQSDLKFDVIFGPAYKGIPLAAIVCVKLAEIGGSKFQNIQYAFNRKEA------GIIVGSALENKRILIIDDVMTAGTAINEAFEIISNAKGQVVGSIIALDRQEVVSTDDKEGLSATQTVSKKYGIPVLSIVSLIHIITYLEGRITAEEKSKIEQYLQTYGAS 224
                                    11        21        31        41        51        61        71        81        91       101      |  -   |   121       131       141       151       161       171       181       191       201       211       221   
                                                                                                                                    108    115                                                                                                             

   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  (1, 4)

Asymmetric Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (1, 4)

Asymmetric Unit

(-) Gene Ontology  (8, 8)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D   (PYRE_YEAST | P13298)
molecular function
    GO:0004588    orotate phosphoribosyltransferase activity    Catalysis of the reaction: orotidine 5'-phosphate + diphosphate = orotate + 5-phospho-alpha-D-ribose 1-diphosphate.
    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).
biological process
    GO:0044205    'de novo' UMP biosynthetic process    The chemical reactions and pathways resulting in the formation of UMP, uridine monophosphate, starting with the synthesis of (S)-dihydroorotate from bicarbonate; UMP biosynthesis may either occur via reduction by quinone, NAD(+) or oxygen.
    GO:0006207    'de novo' pyrimidine nucleobase biosynthetic process    The chemical reactions and pathways resulting in the formation of pyrimidine nucleobases, 1,3-diazine, organic nitrogenous bases, beginning with the synthesis of a pyrimidine ring from simpler precursors.
    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:0006221    pyrimidine nucleotide biosynthetic process    The chemical reactions and pathways resulting in the formation of a pyrimidine nucleotide, a compound consisting of nucleoside (a pyrimidine base linked to a deoxyribose or ribose sugar) esterified with a phosphate group at either the 3' or 5'-hydroxyl group of the sugar.
    GO:0046132    pyrimidine ribonucleoside biosynthetic process    The chemical reactions and pathways resulting in the formation of any ribonucleoside, a nucleoside in which a pyrimidine base is linked to a ribose (beta-D-ribofuranose) molecule.

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 Related Entries

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

UniProtKB/Swiss-Prot
        PYRE_YEAST | P132982pry 2ps1 4wml 4wn3

(-) Related Entries Specified in the PDB File

2pry THE SAME PROTEIN IN THE APO FORM
2ps1 THE SAME PROTEIN COMPLEXED WITH ORO AND PRPP