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(-) Description

Title :  1.75 ANGSTROM CRYSTAL STRUCTURE OF SUPERANTIGEN-LIKE PROTEIN, EXOTOXIN FROM STAPHYLOCOCCUS AUREUS, IN COMPLEX WITH SIALYL-LEWISX.
 
Authors :  G. Minasov, S. Nocadello, L. Shuvalova, E. V. Filippova, A. Halavaty, I. Dubrovska, F. Bagnoli, F. Falugi, M. Bottomley, G. Grandi, W. F. And Center For Structural Genomics Of Infectious Diseases (Csgi
Date :  11 Feb 16  (Deposition) - 24 Feb 16  (Release) - 24 Feb 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.75
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Superantigen-Like Protein, Sialyl-Lewisx, Structural Genomics, Center For Structural Genomics Of Infectious Diseases, Csgid, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  G. Minasov, S. Nocadello, L. Shuvalova, E. V. Filippova, A. Halavaty, I. Dubrovska, F. Bagnoli, F. Falugi, M. Bottomley, G. Grandi, W. F. Anderson, Center For Structural Genomics Of Infectious Diseases (Csgid)
1. 75 Angstrom Crystal Structure Of Superantigen-Like Protein, Exotoxin From Staphylococcus Aureus, In Complex With Sialyl-Lewisx.
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - SUPERANTIGEN-LIKE PROTEIN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Strain: BL21DE3
    Expression System Taxid: 469008
    Gene: SET9, ERS445052_00332, RL02_05830
    Organism Scientific: STAPHYLOCOCCUS AUREUS
    Organism Taxid: 1280

 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  (7, 12)

Asymmetric Unit (7, 12)
No.NameCountTypeFull Name
1FUC2Ligand/IonALPHA-L-FUCOSE
2GAL2Ligand/IonBETA-D-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG2Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5PG42Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7SIA2Ligand/IonO-SIALIC ACID
Biological Unit 1 (6, 6)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3NAG-1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE1Ligand/IonTRIETHYLENE GLYCOL
7SIA1Ligand/IonO-SIALIC ACID
Biological Unit 2 (6, 6)
No.NameCountTypeFull Name
1FUC1Ligand/IonALPHA-L-FUCOSE
2GAL1Ligand/IonBETA-D-GALACTOSE
3NAG1Ligand/IonN-ACETYL-D-GLUCOSAMINE
4NDG1Ligand/Ion2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
5PG41Ligand/IonTETRAETHYLENE GLYCOL
6PGE-1Ligand/IonTRIETHYLENE GLYCOL
7SIA1Ligand/IonO-SIALIC ACID

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:238 , GLN A:240 , HOH A:514 , HOH A:731 , PRO B:203 , ASN B:204 , ARG B:205binding site for residue PGE A 405
2AC2SOFTWAREILE A:202 , ARG A:205 , ILE A:207 , HOH A:566 , HOH A:725 , TRP B:193binding site for residue PG4 A 406
3AC3SOFTWAREHIS B:337 , ARG B:338 , NDG B:401 , FUC B:403 , GAL B:404 , HOH B:519 , HOH B:566 , HOH B:598 , HOH B:649binding site for residue NAG B 402
4AC4SOFTWARETRP A:193 , ARG B:205 , HOH B:626binding site for residue PG4 B 406
5AC5SOFTWARELEU A:290 , ASN A:306 , GLY A:309 , LYS A:325 , TYR A:326 , THR A:327 , GLU A:329 , LYS A:332 , GLN A:335 , HIS A:337 , ARG A:338 , ASP A:341 , HOH A:503 , HOH A:509 , HOH A:528 , HOH A:529 , HOH A:542 , HOH A:547 , HOH A:558 , HOH A:581 , HOH A:603 , HOH A:605 , HOH A:611 , HOH A:623 , HOH A:626 , HOH A:642 , LYS B:260 , GLU B:262 , GLU B:280 , HOH B:502 , HOH B:558binding site for Poly-Saccharide residues NDG A 401 through SIA A 404
6AC6SOFTWARELYS A:238 , GLN A:240 , GLU A:262 , LEU A:290 , ASN A:306 , GLY A:309 , LYS A:325 , TYR A:326 , THR A:327 , GLU A:329 , GLN A:335 , HIS A:337 , ARG A:338 , ASP A:341 , FUC A:402 , HOH A:503 , HOH A:509 , HOH A:510 , HOH A:514 , HOH A:529 , HOH A:547 , HOH A:558 , HOH A:581 , HOH A:603 , HOH A:605 , HOH A:611 , HOH A:623 , HOH A:642 , HOH A:731 , PRO B:203 , ASN B:204 , ARG B:205 , LYS B:260 , GLU B:262 , GLU B:280 , LEU B:290 , ASN B:306 , LYS B:325 , TYR B:326 , THR B:327 , GLU B:329 , LYS B:332 , GLN B:335 , HIS B:337 , ARG B:338 , ASP B:341 , NAG B:402 , HOH B:502 , HOH B:506 , HOH B:516 , HOH B:519 , HOH B:522 , HOH B:532 , HOH B:533 , HOH B:539 , HOH B:561 , HOH B:563 , HOH B:566 , HOH B:576 , HOH B:583 , HOH B:589 , HOH B:598 , HOH B:601 , HOH B:637 , HOH B:649 , HOH B:696 , HOH B:710binding site for Poly-Saccharide residues NDG B 401 through SIA B 405

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5I4D)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Gly A:223 -Pro A:224
2Gly B:223 -Pro B:224

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5I4D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5I4D)

(-) Exons   (0, 0)

(no "Exon" information available for 5I4D)

(-) 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:192
                                                                                                                                                                                                                                
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...hhhhhhhh....eeeeeeeeee........eeee......eeee...hhhhhh....eeeeeeee...........eee..eee.......eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhhh.......eeeeeee....eeeee.....hhhhhh.eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5i4d A 165 TPKYEDLRAYYTKPSFEFEKQFGFMLKPWTTVRFMNVIPNRFIYKIALVGKDEKKYKDGPYDNIDVFIVLEDNKYQLKKYSVGGITKTNSKKVNHKVELSITKKDNQGMISRDVSEYMITKEEISLKELDFKLRKQLIEKHNLYGNMGSGTIVIKMKNGGKYTFELHKKLQEHRMADVIDGTNIDNIEVNIK 356
                                   174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354  


Chain B from PDB  Type:PROTEIN  Length:193
                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhh...eeeeeeeeee........eeee......eeee...hhhhhh....eeeeeeee...........eee..eee.......eeeeeeeeee.....eeeeeeeeee...eeehhhhhhhhhhhhhhhhh.......eeeeeee....eeeee.....hhhhhh.eee...eeeeeeee. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5i4d B 164 MTPKYEDLRAYYTKPSFEFEKQFGFMLKPWTTVRFMNVIPNRFIYKIALVGKDEKKYKDGPYDNIDVFIVLEDNKYQLKKYSVGGITKTNSKKVNHKVELSITKKDNQGMISRDVSEYMITKEEISLKELDFKLRKQLIEKHNLYGNMGSGTIVIKMKNGGKYTFELHKKLQEHRMADVIDGTNIDNIEVNIK 356
                                   173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
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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 5I4D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5I4D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5I4D)

(-) Gene Ontology  (2, 2)

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