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(-) Description

Title :  CRYSTAL STRUCTURE OF THE P. PUTIDA TOLUENE TRANSPORTER TODX
 
Authors :  E. M. Hearn, D. R. Patel, B. Van Den Berg
Date :  21 Dec 07  (Deposition) - 10 Jun 08  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Beta Barrel, Outer Membrane Protein, Transport Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  E. M. Hearn, D. R. Patel, B. Van Den Berg
Outer-Membrane Transport Of Aromatic Hydrocarbons As A First Step In Biodegradation.
Proc. Natl. Acad. Sci. Usa V. 105 8601 2008
PubMed-ID: 18559855  |  Reference-DOI: 10.1073/PNAS.0801264105
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - TODX
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBAD22
    Expression System Strain: C43(DE3)
    Expression System Vector Type: PLASMID
    Fragment: SEQUENCE DATABASE RESIDUES 21-453
    Gene: TODX
    Organism Scientific: PSEUDOMONAS PUTIDA
    Strain: F1

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit : AB
Biological Unit 1 (1x): A 
Biological Unit 2 (1x):  B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
1C8E4Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Biological Unit 1 (1, 2)
No.NameCountTypeFull Name
1C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE
Biological Unit 2 (1, 2)
No.NameCountTypeFull Name
1C8E2Ligand/Ion(HYDROXYETHYLOXY)TRI(ETHYLOXY)OCTANE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREALA A:191 , GLY A:195BINDING SITE FOR RESIDUE C8E A 501
2AC2SOFTWAREALA B:191 , GLY B:195BINDING SITE FOR RESIDUE C8E B 502
3AC3SOFTWARELEU A:164 , LEU A:168 , PHE A:202BINDING SITE FOR RESIDUE C8E A 503
4AC4SOFTWARELEU B:164 , LEU B:166 , GLN B:172 , PHE B:202 , PHE B:275 , LEU B:326BINDING SITE FOR RESIDUE C8E B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3BS0)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3BS0)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3BS0)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3BS0)

(-) Exons   (0, 0)

(no "Exon" information available for 3BS0)

(-) 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:414
 aligned with A5W4F4_PSEP1 | A5W4F4 from UniProtKB/TrEMBL  Length:453

    Alignment length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      453   
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444        |-  
         A5W4F4_PSEP1    25 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEAKSSTRSNNRGPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMDSMNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQQALDSELILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQTPSYLAGTEMLRQSHSQINAVVSYSKNF---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bs0A00 A:5-436 Outer membrane protein transport protein (OMPP1/Fad     L/TodX)                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh.........hhhhhh.hhhhhhhh...eeeeeeeeeeeeeeeee.....eeee..-----...eeeeeeeeeee..eeeeeeeeeeeeeeee....hhhhh...........eeeeeeee..eeeee.......eeeee..eeeeeeeeeeeehhhhhhhhhh..ee.hhhhhhhhhhh...eeeeee.........eeeeee.eeeeeeee....eeeeeeee...ee..eeeeeeeeee.....eeeeeeeeee.......eeeeeeeee....eeeeeeeeee.hhhh..-...eeee..eeeee........eeeeeeeeeee....eeeeeeeee..------...........eeeeeeeeee....eeeeeeeeeeeeeeee.------....eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bs0 A   5 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEAKSST-----GPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMD-MNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQ------LILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQT------TEMLRQSHSQINAVVSYSKNFHHH 436
                                    14        24        34        44        54        64      |  -  |     84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    | |314       324       334       344       354   |     -|      374       384       394       404 |     414       424       434  
                                                                                             71    77                                                                                                                                                                                                                                     309 |                                            358    365                                      406    413                       
                                                                                                                                                                                                                                                                                                                                            311                                                                                                                             


Chain A from PDB  Type:PROTEIN  Length:414
 aligned with Q51971_PSEPU | Q51971 from UniProtKB/TrEMBL  Length:453

    Alignment length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      453   
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444        |-  
         Q51971_PSEPU    25 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEPKSSTRSNNRAPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMDSMNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQQALDSELILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQTPSYLAGTEMLRQSHSQINAVVSYSKNF---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bs0A00 A:5-436 Outer membrane protein transport protein (OMPP1/Fad     L/TodX)                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh.........hhhhhh.hhhhhhhh...eeeeeeeeeeeeeeeee.....eeee..-----...eeeeeeeeeee..eeeeeeeeeeeeeeee....hhhhh...........eeeeeeee..eeeee.......eeeee..eeeeeeeeeeeehhhhhhhhhh..ee.hhhhhhhhhhh...eeeeee.........eeeeee.eeeeeeee....eeeeeeee...ee..eeeeeeeeee.....eeeeeeeeee.......eeeeeeeee....eeeeeeeeee.hhhh..-...eeee..eeeee........eeeeeeeeeee....eeeeeeeee..------...........eeeeeeeeee....eeeeeeeeeeeeeeee.------....eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bs0 A   5 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEAKSST-----GPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMD-MNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQ------LILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQT------TEMLRQSHSQINAVVSYSKNFHHH 436
                                    14        24        34        44        54        64      |  -  |     84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    | |314       324       334       344       354   |     -|      374       384       394       404 |     414       424       434  
                                                                                             71    77                                                                                                                                                                                                                                     309 |                                            358    365                                      406    413                       
                                                                                                                                                                                                                                                                                                                                            311                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:414
 aligned with A5W4F4_PSEP1 | A5W4F4 from UniProtKB/TrEMBL  Length:453

    Alignment length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      453   
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444        |-  
         A5W4F4_PSEP1    25 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEAKSSTRSNNRGPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMDSMNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQQALDSELILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQTPSYLAGTEMLRQSHSQINAVVSYSKNF---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bs0B00 B:5-436 Outer membrane protein transport protein (OMPP1/Fad     L/TodX)                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh.........hhhhhh.hhhhhhhh...eeeeeeeeeeeeeeeee.....eeee..-----...eeeeeeeeeee..eeeeeeeeeeeeeeee....hhhhh...........eeeeeeee..eeeee.......eeeee..eeeeeeeeeeeehhhhhhhhhh..ee.hhhhhhhhhhh...eeeeee.........eeeeee.eeeeeeee....eeeeeeee...ee..eeeeeeeeee.....eeeeeeeeee.......eeeeeeeee....eeeeeeeeee.hhhh..-...eeee..eeeee........eeeeeeeeeee....eeeeeeeee..------...........eeeeeeeeee....eeeeeeeeeeeeeeee.------....eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bs0 B   5 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEAKSST-----GPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMD-MNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQ------LILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQT------TEMLRQSHSQINAVVSYSKNFHHH 436
                                    14        24        34        44        54        64      |  -  |     84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    | |314       324       334       344       354   |     -|      374       384       394       404 |     414       424       434  
                                                                                             71    77                                                                                                                                                                                                                                     309 |                                            358    365                                      406    413                       
                                                                                                                                                                                                                                                                                                                                            311                                                                                                                             


Chain B from PDB  Type:PROTEIN  Length:414
 aligned with Q51971_PSEPU | Q51971 from UniProtKB/TrEMBL  Length:453

    Alignment length:432
                                                                                                                                                                                                                                                                                                                                                                                                                                                                      453   
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444        |-  
         Q51971_PSEPU    25 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEPKSSTRSNNRAPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMDSMNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQQALDSELILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQTPSYLAGTEMLRQSHSQINAVVSYSKNF---   -
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains 3bs0B00 B:5-436 Outer membrane protein transport protein (OMPP1/Fad     L/TodX)                                                                                                                                                                                                                                                                                                                                                                  CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .....hhhhhhh.........hhhhhh.hhhhhhhh...eeeeeeeeeeeeeeeee.....eeee..-----...eeeeeeeeeee..eeeeeeeeeeeeeeee....hhhhh...........eeeeeeee..eeeee.......eeeee..eeeeeeeeeeeehhhhhhhhhh..ee.hhhhhhhhhhh...eeeeee.........eeeeee.eeeeeeee....eeeeeeee...ee..eeeeeeeeee.....eeeeeeeeee.......eeeeeeeee....eeeeeeeeee.hhhh..-...eeee..eeeee........eeeeeeeeeee....eeeeeeeee..------...........eeeeeeeeee....eeeeeeeeeeeeeeee.------....eeeeeeeeeeeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 3bs0 B   5 DLEGYGAISRAMGGTSSSYYTGNAALISNPATLSFAPDGNQFELGLDVVTTDIKVHDSHGAEAKSST-----GPYVGPQLSYVAQLDDWRFGAGLFVSSGLGTEYGSKSFLSQTENGIQTSFDNSSRLIVLRAPIGFSYQATSKLTFGASVDLVWTSLNLELLLPSSQVGALTAQGNLSGGLVPSLAGFVGTGGAAHFSLSRNSTAGGAVDAVGWGGRLGLTYKLTDNTVLGAMYNFKTSVGDLEGKATLSAISGDGAVLPLDGDIRVKNFEMPASLTLGLAHQFNERWVVAADIKRAYWGDVMD-MNVAFISQLGGIDVALPHRYQDITVASIGTAYKYNNDLTLRAGYSYAQ------LILPVIPAYLKRHVTFGGEYDFDKDSRINLAISFGLRERVQT------TEMLRQSHSQINAVVSYSKNFHHH 436
                                    14        24        34        44        54        64      |  -  |     84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304    | |314       324       334       344       354   |     -|      374       384       394       404 |     414       424       434  
                                                                                             71    77                                                                                                                                                                                                                                     309 |                                            358    365                                      406    413                       
                                                                                                                                                                                                                                                                                                                                            311
   Legend:   → Mismatch (orange background)
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  extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '|'

 Classification and Annotation

(-) SCOP Domains  (0, 0)

(no "SCOP Domain" information available for 3BS0)

(-) CATH Domains  (1, 2)

Asymmetric Unit
(-)
Class: Mainly Beta (13760)

(-) Pfam Domains  (0, 0)

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  Q51971_PSEPU | Q51971
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 Related Entries

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

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        Q51971_PSEPU | Q51971: 3brz
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(-) Related Entries Specified in the PDB File

3bry 3brz