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(-) Description

Title :  STRUCTURE OF OHCU DECARBOXYLASE IN COMPLEX WITH GUANINE
 
Authors :  L. Cendron, R. Berni, C. Folli, I. Ramazzina, R. Percudani, G. Zanotti
Date :  10 Dec 06  (Deposition) - 10 Apr 07  (Release) - 02 Apr 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym. Unit :  A,B,C,D,E,F
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Keywords :  Decarboxylation, Ohcu, 2-Oxo-4-Hydroxy-4-Carboxy-5-Ureidoimidazoline, Hiu, 5-Hydroxyisourate, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  L. Cendron, R. Berni, C. Folli, I. Ramazzina, R. Percudani, G. Zanotti
The Structure Of 2-Oxo-4-Hydroxy-4-Carboxy-5-Ureidoimidazoline Decarboxylase Provides Insights Into The Mechanism Of Uric Acid Degradation.
J. Biol. Chem. V. 282 18182 2007
PubMed-ID: 17428786  |  Reference-DOI: 10.1074/JBC.M701297200

(-) Compounds

Molecule 1 - OHCU DECARBOXYLASE
    ChainsA, B, C, D, E, F
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21
    Expression System PlasmidPET28B
    Expression System StrainBL21
    Expression System Taxid511693
    Expression System Vector TypePLASMID
    Organism CommonZEBRAFISH
    Organism ScientificDANIO RERIO
    Organism Taxid7955
    Synonym2-OXO-4-HYDROXY-4-CARBOXY-5-UREIDOIMIDAZOLINE DECARBOXYLASE

 Structural Features

(-) Chains, Units

  123456
Asymmetric Unit ABCDEF
Biological Unit 1 (1x)AB    
Biological Unit 2 (1x)  CD  
Biological Unit 3 (1x)    EF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 6)

Asymmetric Unit (1, 6)
No.NameCountTypeFull Name
1GUN6Ligand/IonGUANINE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE
Biological Unit 3 (1, 2)
No.NameCountTypeFull Name
1GUN2Ligand/IonGUANINE

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREPRO A:68 , LEU A:70 , SER A:84 , GLU A:87 , GLN A:88 , PHE A:119 , VAL A:120 , ILE A:121 , ALA A:123 , ILE A:157 , HOH A:1009BINDING SITE FOR RESIDUE GUN A 1001
2AC2SOFTWAREPRO B:68 , LEU B:70 , SER B:84 , GLU B:87 , GLN B:88 , PHE B:119 , VAL B:120 , ILE B:121 , ALA B:123 , ILE B:157 , HOH B:2103BINDING SITE FOR RESIDUE GUN B 2001
3AC3SOFTWAREPRO C:68 , LEU C:70 , SER C:84 , GLU C:87 , GLN C:88 , PHE C:119 , VAL C:120 , ILE C:121 , ALA C:123 , ILE C:157BINDING SITE FOR RESIDUE GUN C 3001
4AC4SOFTWAREPRO D:68 , LEU D:70 , SER D:84 , GLU D:87 , GLN D:88 , PHE D:119 , VAL D:120 , ILE D:121 , ALA D:123 , ILE D:157 , HOH D:4045BINDING SITE FOR RESIDUE GUN D 4001
5AC5SOFTWAREPRO F:68 , LEU F:70 , SER F:84 , GLU F:87 , GLN F:88 , PHE F:119 , ILE F:121 , ALA F:123 , ILE F:157BINDING SITE FOR RESIDUE GUN F 5001
6AC6SOFTWAREPRO E:68 , LEU E:70 , SER E:84 , GLU E:87 , GLN E:88 , PHE E:119 , VAL E:120 , ILE E:121 , ALA E:123 , ILE E:157 , HOH E:6075BINDING SITE FOR RESIDUE GUN E 6001

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2O74)

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Arg A:36 -Pro A:37
2Arg B:36 -Pro B:37
3Arg C:36 -Pro C:37
4Arg D:36 -Pro D:37
5Arg E:36 -Pro E:37
6Arg F:36 -Pro F:37

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2O74)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2O74)

(-) Exons   (2, 12)

Asymmetric Unit (2, 12)
 ENSEMBLUniProtKBPDB
No.Transcript IDExonExon IDGenome LocationLengthIDLocationLengthCountLocationLength
1.1ENSDART000001059171ENSDARE00000767616chr24:22297094-22296866229URAD_DANRE1-59596A:2-59
B:2-59
C:1-59
D:2-59
E:2-59
F:1-59
58
58
59
58
58
59
1.2ENSDART000001059172ENSDARE00000767615chr24:22295753-22295224530URAD_DANRE59-1741166A:59-166
B:59-165
C:59-167
D:59-165
E:59-165
F:59-168
108
107
109
107
107
110

(-) 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:165
 aligned with URAD_DANRE | A1L259 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     
           URAD_DANRE     2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSIV 166
               SCOP domains d2o74a_ A: OHCU decarboxylase, UraD                                                                                                                                   SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: A:2-59 UniProt: 1-59 [INCOMPLETE]          ----------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.2  PDB: A:59-166 UniProt: 59-174 [INCOMPLETE]                                                         Transcript 1 (2)
                 2o74 A   2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSIV 166
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161     

Chain B from PDB  Type:PROTEIN  Length:164
 aligned with URAD_DANRE | A1L259 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           URAD_DANRE     2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSI 165
               SCOP domains d2o74b_ B: OHCU decarboxylase, UraD                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhh.hhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: B:2-59 UniProt: 1-59 [INCOMPLETE]          ---------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.2  PDB: B:59-165 UniProt: 59-174 [INCOMPLETE]                                                        Transcript 1 (2)
                 2o74 B   2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSI 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    

Chain C from PDB  Type:PROTEIN  Length:167
 aligned with URAD_DANRE | A1L259 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       
           URAD_DANRE     1 MDINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSIVL 167
               SCOP domains d2o74c_ C: OHCU decarboxylase, UraD                                                                                                                                     SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: C:1-59 UniProt: 1-59                        ------------------------------------------------------------------------------------------------------------ Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.2  PDB: C:59-167 UniProt: 59-174 [INCOMPLETE]                                                          Transcript 1 (2)
                 2o74 C   1 MDINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSIVL 167
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       

Chain D from PDB  Type:PROTEIN  Length:164
 aligned with URAD_DANRE | A1L259 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           URAD_DANRE     2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSI 165
               SCOP domains d2o74d_ D: OHCU decarboxylase, UraD                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: D:2-59 UniProt: 1-59 [INCOMPLETE]          ---------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.2  PDB: D:59-165 UniProt: 59-174 [INCOMPLETE]                                                        Transcript 1 (2)
                 2o74 D   2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSI 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    

Chain E from PDB  Type:PROTEIN  Length:164
 aligned with URAD_DANRE | A1L259 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:164
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    
           URAD_DANRE     2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSI 165
               SCOP domains d2o74e_ E: OHCU decarboxylase, UraD                                                                                                                                  SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhh..hhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
           Transcript 1 (1) Exon 1.1  PDB: E:2-59 UniProt: 1-59 [INCOMPLETE]          ---------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ---------------------------------------------------------Exon 1.2  PDB: E:59-165 UniProt: 59-174 [INCOMPLETE]                                                        Transcript 1 (2)
                 2o74 E   2 DINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSI 165
                                    11        21        31        41        51        61        71        81        91       101       111       121       131       141       151       161    

Chain F from PDB  Type:PROTEIN  Length:168
 aligned with URAD_DANRE | A1L259 from UniProtKB/Swiss-Prot  Length:174

    Alignment length:168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        
           URAD_DANRE     1 MDINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSIVLS 168
               SCOP domains d2o74f_ F: OHCU decarboxylase, UraD                                                                                                                                      SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) -----OHCU_decarbox-2o74F01 F:6-164                                                                                                                                  ---- Pfam domains (1)
           Pfam domains (2) -----OHCU_decarbox-2o74F02 F:6-164                                                                                                                                  ---- Pfam domains (2)
           Pfam domains (3) -----OHCU_decarbox-2o74F03 F:6-164                                                                                                                                  ---- Pfam domains (3)
           Pfam domains (4) -----OHCU_decarbox-2o74F04 F:6-164                                                                                                                                  ---- Pfam domains (4)
           Pfam domains (5) -----OHCU_decarbox-2o74F05 F:6-164                                                                                                                                  ---- Pfam domains (5)
           Pfam domains (6) -----OHCU_decarbox-2o74F06 F:6-164                                                                                                                                  ---- Pfam domains (6)
         Sec.struct. author .hhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhh..hhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
           Transcript 1 (1) Exon 1.1  PDB: F:1-59 UniProt: 1-59                        ------------------------------------------------------------------------------------------------------------- Transcript 1 (1)
           Transcript 1 (2) ----------------------------------------------------------Exon 1.2  PDB: F:59-168 UniProt: 59-174 [INCOMPLETE]                                                           Transcript 1 (2)
                 2o74 F   1 MDINVVNALAYEDFVKLFGNVVEKCPLISAAIWSYRPFKDLADIEARISEFIHSLPDSGKEGILRCHPDLAGRDLQSGTLTPESQEEQSQAGMTTLDSAEIVHMYRLNSEYKERFGFPFVICARLNNKADIVRQLSERLKNRRTAELECAIEEVKKICSLRLHSIVLS 168
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160        

   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, 6)

Asymmetric Unit

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 2O74)

(-) Pfam Domains  (1, 6)

Asymmetric Unit

(-) Gene Ontology  (6, 6)

Asymmetric Unit(hide GO term definitions)
Chain A,B,C,D,E,F   (URAD_DANRE | A1L259)
molecular function
    GO:0016831    carboxy-lyase activity    Catalysis of the nonhydrolytic addition or removal of a carboxyl group to or from a compound.
    GO:0016829    lyase activity    Catalysis of the cleavage of C-C, C-O, C-N and other bonds by other means than by hydrolysis or oxidation, or conversely adding a group to a double bond. They differ from other enzymes in that two substrates are involved in one reaction direction, but only one in the other direction. When acting on the single substrate, a molecule is eliminated and this generates either a new double bond or a new ring.
biological process
    GO:0019428    allantoin biosynthetic process    The chemical reactions and pathways resulting in the formation of allantoin, (2,5-dioxo-4-imidazolidinyl)urea.
    GO:0006144    purine nucleobase metabolic process    The chemical reactions and pathways involving purine nucleobases, one of the two classes of nitrogen-containing ring compounds found in DNA and RNA, which include adenine and guanine.
    GO:0019628    urate catabolic process    The chemical reactions and pathways resulting in the breakdown of urate, the anion of uric acid, 2,6,8-trioxypurine.
cellular component
    GO:0005777    peroxisome    A small organelle enclosed by a single membrane, and found in most eukaryotic cells. Contains peroxidases and other enzymes involved in a variety of metabolic processes including free radical detoxification, lipid catabolism and biosynthesis, and hydrogen peroxide metabolism.

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 Related Entries

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

UniProtKB/Swiss-Prot
        URAD_DANRE | A1L2592o70 2o73

(-) Related Entries Specified in the PDB File

2o70 OHCU DECARBOXYLASE, APO-ENZYME
2o73 OHCU DECARBOXYLASE IN COMPLEX WITH ALLANTOIN