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(-) Description

Title :  1.7 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF PUTATIVE NUCLEOSIDE DIPHOSPHATE KINASE FROM TOXOPLASMA GONDII WITH TYROSINE OF TAG BOUND TO ACTIVE SITE
 
Authors :  G. Minasov, J. Ruan, H. Ngo, L. Shuvalova, I. Dubrovska, K. Flores, W. F. Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  09 Jun 15  (Deposition) - 24 Jun 15  (Release) - 24 Jun 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1:  A,B,C,E,F,G  (1x)
Biol. Unit 2:  D,H,I,J,K,L  (1x)
Keywords :  Structural Genomics, Niaid, National Institute Of Allergy And Infectious Diseases, Center For Structural Genomics Of Infectious Diseases, Csgid, 2-Layer Sandwich, Putative Nucleoside Diphosphate Kinase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, J. Ruan, H. Ngo, L. Shuvalova, I. Dubrovska, K. Flores, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 7 Angstrom Resolution Crystal Structure Of Putative Nucleoside Diphosphate Kinase From Toxoplasma Gondii With Tyrosine Of Tag Bound To Active Site.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEOSIDE DIPHOSPHATE KINASE
    Chains: A, B, C, D, E, F, G, H, I, J, K, L
    EC Number: 2.7.4.6
    Engineered: YES
    Expression System: ESCHERICHIA COLI 'BL21-GOLD(DE3)PLYSS AG'
    Expression System Plasmid: PMCSG28
    Expression System Strain: BL21(DE3)/PMAGIC
    Expression System Taxid: 866768
    Gene: TGME49_295350
    Organism Scientific: TOXOPLASMA GONDII ME49
    Organism Taxid: 508771

 Structural Features

(-) Chains, Units

  123456789101112
Asymmetric Unit : ABCDEFGHIJKL
Biological Unit 1 (1x): ABC EFG     
Biological Unit 2 (1x):    D   HIJKL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 7)

Asymmetric Unit (2, 7)
No.NameCountTypeFull Name
1BCT6Ligand/IonBICARBONATE ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 1 (1, 4)
No.NameCountTypeFull Name
1BCT4Ligand/IonBICARBONATE ION
2PEG-1Ligand/IonDI(HYDROXYETHYL)ETHER
Biological Unit 2 (2, 3)
No.NameCountTypeFull Name
1BCT2Ligand/IonBICARBONATE ION
2PEG1Ligand/IonDI(HYDROXYETHYL)ETHER

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:14 , THR A:96 , ARG A:107 , ASN A:117 , VAL A:119 , HIS A:120 , HOH A:363binding site for residue BCT A 201
2AC2SOFTWAREGLN B:6 , ARG B:8 , HOH B:304binding site for residue BCT B 201
3AC3SOFTWAREGLN C:6 , ARG C:8 , GLU C:143 , HOH C:307binding site for residue BCT C 201
4AC4SOFTWARELYS D:14 , THR D:96 , ASN D:117 , HIS D:120 , HOH D:338 , HOH D:423binding site for residue BCT D 201
5AC5SOFTWARELYS D:14 , TYR D:54 , LEU D:66binding site for residue PEG D 202
6AC6SOFTWAREHOH B:459 , GLN C:148 , ARG E:20 , HOH E:285 , GLN F:148 , HOH F:306 , HOH F:326 , HOH F:335binding site for residue BCT F 201
7AC7SOFTWARELYS I:14 , THR I:96 , ASN I:117 , HIS I:120 , HOH I:305 , HOH I:325binding site for residue BCT I 201

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5BXI)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5BXI)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5BXI)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5BXI)

(-) Exons   (0, 0)

(no "Exon" information available for 5BXI)

(-) 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:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi A   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYE 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  


Chain B from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi B   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQ 155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152   


Chain C from PDB  Type:PROTEIN  Length:143
                                                                                                                                                                               
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhh..hhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi C   4 KQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYAGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQ 155
                                    13        23        33        43        53 ||     72        82        92       102       112       122       132       142       152   
                                                                              55|                                                                                          
                                                                               65                                                                                          


Chain D from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi D   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQGENLY 160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152        


Chain E from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi E   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQ 155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152   


Chain F from PDB  Type:PROTEIN  Length:153
                                                                                                                                                                                         
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi F   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQ 155
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152   


Chain G from PDB  Type:PROTEIN  Length:158
                                                                                                                                                                                              
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh....... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi G   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQGENLY 160
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152        


Chain H from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhh.eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi H   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYE 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  


Chain I from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi I   4 KQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQ 155
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153  


Chain J from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..........hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi J   4 KQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYEQ 155
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143       153  


Chain K from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi K   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYE 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152  


Chain L from PDB  Type:PROTEIN  Length:152
                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eeeeeehhhhhhh.hhhhhhhhhhhhh.eeeeeeee..hhhhhhhhhhhhh...hhhhhhhhhh...eeeeeee..hhhhhhhhhhh..hhhhh...hhhhhhh.hhhhh.eee..hhhhhhhhhhhhhhhhhh......hhhhhh. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5bxi L   3 AKQQERTYIMVKPDGVQRGLVSEVIRRFEQRGYKLVALKMKSPDATLLEEHYADLKGKPFFPGLISYMTSGPVVCMVWEGTDVVKQGRRMLGETRPLESNPGTLRGDFCIDVGRNIVHGSDSVESANKEISLWFTPEEICEWTSAQHKWVYE 154
                                    12        22        32        42        52        62        72        82        92       102       112       122       132       142       152
   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  (0, 0)

(no "SCOP Domain" information available for 5BXI)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5BXI)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5BXI)

(-) Gene Ontology  (10, 10)

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  5bxi
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  B9Q287_TOXGV | B9Q287
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 Related Entries

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

UniProtKB/TrEMBL
        B9Q287_TOXGV | B9Q287: 4o0n

(-) Related Entries Specified in the PDB File

4o0n 2.4 ANGSTROM RESOLUTION CRYSTAL STRUCTURE OF THE SAME PROTEIN IN COMPLEX WITH SULFATE IONS. RELATED ID: CSGID-IDP92074 RELATED DB: TARGETTRACK