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(-) Description

Title :  CRYSTAL STRUCTURE OF THE GSPB SIGLEC DOMAIN WITH SIALYL T ANTIGEN BOUND
 
Authors :  L. V. Loukachevitch, K. P. Fialkowski, Z. Wawrzak, T. M. Iverson
Date :  17 Mar 16  (Deposition) - 13 Apr 16  (Release) - 13 Apr 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.25
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Bacterial Adhesin, Lectin, Immunoglobulin Fold, Serine-Rich Repeat, Sugar Binding Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. M. Pyburn, B. A. Bensing, Y. Q. Xiong, B. J. Melancon, T. M. Tomasiak, N. J. Ward, V. Yankovskaya, K. M. Oliver, G. Cecchini, G. A. Sulikowski M. J. Tyska, P. M. Sullam, T. M. Iverson
A Structural Model For Binding Of The Serine-Rich Repeat Adhesin Gspb To Host Carbohydrate Receptors.
Plos Pathog. V. 7 02112 2011
PubMed-ID: 21765814  |  Reference-DOI: 10.1371/JOURNAL.PPAT.1002112
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - PLATELET BINDING PROTEIN GSPB
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PBG101
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: BINDING REGION, SIGLEC DOMAIN
    Gene: GSPB
    Organism Scientific: STREPTOCOCCUS GORDONII
    Organism Taxid: 1302
    Synonym: SERINE-RICH ADHESIN FOR PLATELETS,SERINE-RICH REPEAT PROTEIN GSPB

 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  (4, 8)

Asymmetric Unit (4, 8)
No.NameCountTypeFull Name
1A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3MG2Ligand/IonMAGNESIUM ION
4SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (3, 3)
No.NameCountTypeFull Name
1A2G1Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3MG-1Ligand/IonMAGNESIUM ION
4SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:399 , GLU A:401 , ASP A:427 , ASN A:428 , ASP A:490binding site for residue MG A 601
2AC2SOFTWAREASP B:399 , GLU B:401 , ASP B:427 , ASN B:428 , ASP B:490binding site for residue MG B 601
3AC3SOFTWARETYR A:443 , ARG A:449 , ILE A:479 , ASP A:481 , TYR A:482 , THR A:483 , ARG A:484 , TYR A:485 , GLY A:503 , ALA A:506 , VAL A:507 , HOH A:707 , HOH A:714 , HOH A:721 , HOH A:733 , HOH A:738 , HOH A:745 , HOH A:758 , HOH A:759 , HOH A:765 , HOH A:770 , HOH A:790 , HOH A:807 , HOH A:813 , HOH A:817 , HOH A:818 , HOH A:820 , HOH A:834 , HOH A:840 , HOH A:857 , HOH A:870 , GLN B:460 , GLY B:462 , ASN B:463 , HOH B:826 , HOH B:858binding site for Poly-Saccharide residues SIA A 602 through A2G A 604
4AC4SOFTWARETYR A:443 , ARG A:449 , GLY A:462 , ASN A:463 , ILE A:479 , ASP A:481 , TYR A:482 , THR A:483 , ARG A:484 , TYR A:485 , GLY A:503 , ALA A:506 , VAL A:507 , HOH A:707 , HOH A:714 , HOH A:721 , HOH A:733 , HOH A:738 , HOH A:745 , HOH A:758 , HOH A:759 , HOH A:765 , HOH A:770 , HOH A:790 , HOH A:807 , HOH A:813 , HOH A:817 , HOH A:818 , HOH A:820 , HOH A:825 , HOH A:834 , HOH A:840 , HOH A:846 , HOH A:857 , HOH A:870 , LEU B:442 , TYR B:443 , ARG B:449 , GLN B:460 , GLY B:462 , ASN B:463 , ASP B:481 , TYR B:482 , THR B:483 , ARG B:484 , TYR B:485 , GLY B:503 , ALA B:506 , HOH B:720 , HOH B:722 , HOH B:728 , HOH B:748 , HOH B:768 , HOH B:777 , HOH B:790 , HOH B:794 , HOH B:798 , HOH B:809 , HOH B:813 , HOH B:823 , HOH B:826 , HOH B:839 , HOH B:847 , HOH B:858binding site for Poly-Saccharide residues SIA B 602 through A2G B 604

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5IUC)

(-) 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:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...eeeee...eeeeeeeee......hhhhheee..............eeeeeee..eeeeeeeee.......eeeeeeee..........hhhhhhhhhhh......eeeeeee Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iuc A 399 DTERPVVNVPSEITVYRGESFEYFATVTDNSNAFDLAKTVVRWLYSNQPGRGTEWLQYSVTQVGNQLKVRIFGNVPIDTTIGDYTRYVVATDAAGNVNATQTEMGNAAVDKTSVNGQFKLIIR 521
                                   408       418       428       438       448       458       468       478       488       498       508       518   


Chain B from PDB  Type:PROTEIN  Length:123
                                                                                                                                                           
               SCOP domains --------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .....eee...eeee....eeeeeeeee......hhhhheee..............eeeeeee..eeeeeeeee.......eeeeeeee..........hhhhhhhhhhh......eeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------- Transcript
                 5iuc B 399 DTERPVVNVPSEITVYRGESFEYFATVTDNSNAFDLAKTVVRWLYSNQPGRGTEWLQYSVTQVGNQLKVRIFGNVPIDTTIGDYTRYVVATDAAGNVNATQTEMGNAAVDKTSVNGQFKLIIR 521
                                   408       418       428       438       448       458       468       478       488       498       508       518
   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 5IUC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (3, 3)

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        GSPB_STRGN | Q939N5: 3qc5 3qc6

(-) Related Entries Specified in the PDB File

3qc5 3qc6