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(-) Description

Title :  CRYSTAL STRUCTURE OF N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE FROM STAPHYLOCOCCUS AUREUS
 
Authors :  P. Brugarolas, E. M. Duguid, W. Zhang, C. B. Poor, C. He
Date :  07 Sep 10  (Deposition) - 20 Jul 11  (Release) - 28 Mar 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.45
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F,G,H
Keywords :  Isomerase, Isomerase, Biosynthetic Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  P. Brugarolas, E. M. Duguid, W. Zhang, C. B. Poor, C. He
Structural And Biochemical Characterization Of N5-Carboxyaminoimidazole Ribonucleotide Synthetase And N5-Carboxyaminoimidazole Ribonucleotide Mutase From Staphylococcus Aureus.
Acta Crystallogr. , Sect. D V. 67 707 2011
PubMed-ID: 21795812  |  Reference-DOI: 10.1107/S0907444911023821

(-) Compounds

Molecule 1 - N5-CARBOXYAMINOIMIDAZOLE RIBONUCLEOTIDE MUTASE
    ChainsA, B, C, D, E, F, G, H
    EC Number5.4.99.18
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPMCSG19
    Expression System StrainBL21(DE3)STAR
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    GeneNWMN_0933, PURE
    Organism ScientificSTAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid426430
    StrainNEWMAN
    SynonymPHOSPHORIBOSYLAMINOIMIDAZOLE CARBOXYLASE CATALYTIC SUBUNIT

 Structural Features

(-) Chains, Units

  12345678
Asymmetric/Biological Unit ABCDEFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 18)

Asymmetric/Biological Unit (1, 18)
No.NameCountTypeFull Name
1SO418Ligand/IonSULFATE ION

(-) Sites  (18, 18)

Asymmetric Unit (18, 18)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREGLY A:8 , SER A:36 , HIS A:38 , ARG A:39 , HOH A:194 , HOH A:447 , PRO F:104BINDING SITE FOR RESIDUE SO4 A 161
02AC2SOFTWARELYS A:120 , LYS A:151 , HOH A:178 , ARG C:39BINDING SITE FOR RESIDUE SO4 A 162
03AC3SOFTWARESER A:9 , ARG A:39 , HOH A:621 , MET G:155BINDING SITE FOR RESIDUE SO4 A 163
04AC4SOFTWARELYS A:2 , GLU A:31 , ARG A:54 , HOH A:170 , HOH A:187 , HOH A:620BINDING SITE FOR RESIDUE SO4 A 164
05AC5SOFTWAREASN A:134 , PRO A:135 , SER A:136BINDING SITE FOR RESIDUE SO4 A 165
06AC6SOFTWARESER B:36 , HIS B:38 , ARG B:39 , HOH B:170 , HOH B:275 , HOH B:341 , PRO D:104BINDING SITE FOR RESIDUE SO4 B 161
07AC7SOFTWAREGLY C:8 , SER C:36 , HIS C:38 , HOH C:393 , HOH C:505 , HOH C:528 , HOH C:529 , PRO H:104 , HOH H:476BINDING SITE FOR RESIDUE SO4 C 161
08AC8SOFTWARELYS C:120 , LYS C:151 , HOH C:670 , ARG D:39BINDING SITE FOR RESIDUE SO4 C 162
09AC9SOFTWAREPRO B:104 , SER D:36 , HIS D:38 , HOH D:180 , HOH D:539 , HOH D:558 , HOH D:605 , HOH D:669BINDING SITE FOR RESIDUE SO4 D 161
10BC1SOFTWARELYS D:120 , LYS D:151 , HOH D:174 , HOH D:675 , ARG G:39BINDING SITE FOR RESIDUE SO4 D 162
11BC2SOFTWAREASN D:134 , PRO D:135 , SER D:136BINDING SITE FOR RESIDUE SO4 D 163
12BC3SOFTWARELYS D:2 , GLU D:31 , ARG D:54 , HOH D:203BINDING SITE FOR RESIDUE SO4 D 164
13BC4SOFTWAREGLY E:8 , SER E:36 , HIS E:38 , ARG E:39 , HOH E:315 , HOH E:454 , PRO G:104BINDING SITE FOR RESIDUE SO4 E 161
14BC5SOFTWAREPRO A:104 , HOH A:197 , SER F:36 , HIS F:38 , ARG F:39 , HOH F:169 , HOH F:172 , HOH F:272 , HOH F:347BINDING SITE FOR RESIDUE SO4 F 161
15BC6SOFTWARESER F:9 , ARG F:39BINDING SITE FOR RESIDUE SO4 F 162
16BC7SOFTWAREPRO E:104 , SER G:36 , HIS G:38 , HOH G:184 , HOH G:245 , HOH G:285 , HOH G:425 , HOH G:494 , HOH G:577BINDING SITE FOR RESIDUE SO4 G 161
17BC8SOFTWAREASN F:142 , SER G:49 , ARG G:52 , THR G:77 , THR G:78 , HOH G:180 , HOH G:685 , HOH G:686BINDING SITE FOR RESIDUE SO4 G 162
18BC9SOFTWAREPRO C:104 , SER H:36 , HIS H:38 , ARG H:39 , HOH H:165 , HOH H:322BINDING SITE FOR RESIDUE SO4 H 161

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3ORS)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3ORS)

(-) Exons   (0, 0)

(no "Exon" information available for 3ORS)

(-) 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:161
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
               SCOP domains d3orsa_ A: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhhh...eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors A   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 

Chain B from PDB  Type:PROTEIN  Length:161
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
               SCOP domains d3orsb_ B: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors B   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 

Chain C from PDB  Type:PROTEIN  Length:161
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
               SCOP domains d3orsc_ C: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors C   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 

Chain D from PDB  Type:PROTEIN  Length:161
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
               SCOP domains d3orsd_ D: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors D   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 

Chain E from PDB  Type:PROTEIN  Length:160
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNEL 159
               SCOP domains d3orse_ E: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors E   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNEL 159
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

Chain F from PDB  Type:PROTEIN  Length:161
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
               SCOP domains d3orsf_ F: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors F   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 

Chain G from PDB  Type:PROTEIN  Length:161
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:161
                             1                                                                                                                                                               
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
               SCOP domains d3orsg_ G: automated matches                                                                                                                                      SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors G   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNELQ 160
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159 

Chain H from PDB  Type:PROTEIN  Length:160
 aligned with A0A0H3K7Y1_S | A0A0H3K7Y1 from UniProtKB/TrEMBL  Length:160

    Alignment length:160
                             1                                                                                                                                                              
                             |       9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159
         A0A0H3K7Y1_S     - -MKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNEL 159
               SCOP domains d3orsh_ H: automated matches                                                                                                                                     SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeee.hhhhhhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhh......eeeeeee...hhhhhhhhh....eeeeee......hhhhhhhhhh.......ee...hhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3ors H   0 AMKVAVIMGSSSDWKIMQESCNMLDYFEIPYEKQVVSAHRTPKMMVQFASEARERGINIIIAGAGGAAHLPGMVASLTTLPVIGVPIETKSLKGIDSLLSIVQMPGGIPVATTAIGAAGAKNAGILAARMLSIQNPSLVEKLNQYESSLIQKVEDMQNEL 159
                                     9        19        29        39        49        59        69        79        89        99       109       119       129       139       149       159

   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, 8)

Asymmetric/Biological Unit

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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3orq 3orr