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(-) Description

Title :  THE CRYSTAL STRUCTURE OF STX2 AND A DISACCHARIDE LIGAND
 
Authors :  J. Yin, M. N. G. James, J. M. Jacobson, P. I. Kitov, D. R. Bundle, G. Mulvey G. Armstrong
Date :  04 Aug 13  (Deposition) - 20 Nov 13  (Release) - 19 Feb 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B,C,D,E,F
Keywords :  Rrna N-Glycosylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  J. M. Jacobson, J. Yin, P. I. Kitov, G. Mulvey, T. P. Griener, M. N. James G. Armstrong, D. R. Bundle
The Crystal Structure Of Shiga Toxin Type 2 With Bound Disaccharide Guides The Design Of A Heterobifunctional Toxi Inhibitor.
J. Biol. Chem. V. 289 885 2014
PubMed-ID: 24225957  |  Reference-DOI: 10.1074/JBC.M113.518886

(-) Compounds

Molecule 1 - SHIGA TOXIN 2 A-SUBUNIT
    Chains: A
    EC Number: 3.2.2.22
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: STX2 SUBUNIT A (UNP ENTRIES 230-319)
    Gene: ECS1205, STX 2 A-SUBUNIT, STX2 A-SUBUNIT, STX2A, Z1464
    Organism Taxid: 83334
    Synonym: SHIGA TOXIN 2 SUBUNIT A, SHIGA-LIKE TOXIN II A SUBUNIT ENCODED BY BACTERIOPHAGE BP-933W
 
Molecule 2 - SHIGA TOXIN 2 B SUBUNIT
    Chains: B, C, D, E, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: STX2 SUBUNIT B (UNP ENTRIES 20-89)
    Gene: STX2B, STX2DB, STX2VB, STXB2, STXII, VTX2B
    Organism Scientific: ESCHERICHIA COLI
    Organism Taxid: 562
    Synonym: SHIGA TOXIN 2 SUBUNIT B, SHIGA TOXIN 2, SUBUNIT B, SHIGA TOXIN 2V SUBUNIT A, SHIGA TOXIN 2V SUBUNIT B, STX2B, STX2B PROTEIN, STX2D B SUBUNIT, VEROCYTOTOXIN 2 SUBUNIT B, VEROCYTOTOXIN 2 VARIANT B SUBUNIT

 Structural Features

(-) Chains, Units

  123456
Asymmetric/Biological Unit : ABCDEF

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 7)

Asymmetric/Biological Unit (3, 7)
No.NameCountTypeFull Name
11PS3Ligand/Ion3-PYRIDINIUM-1-YLPROPANE-1-SULFONATE
2A2G2Ligand/IonN-ACETYL-2-DEOXY-2-AMINO-GALACTOSE
3MBG2Ligand/IonMETHYL-BETA-GALACTOSE

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREHOH A:593 , ASN B:14 , ASP B:16 , THR B:18 , TRP B:29 , HOH B:208BINDING SITE FOR RESIDUE 1PS B 101
2AC2SOFTWAREASN C:14 , ASP C:16 , THR C:18 , TRP C:29 , HOH C:216 , HOH C:251 , HOH C:255 , SER D:58BINDING SITE FOR RESIDUE 1PS C 101
3AC3SOFTWARESER C:58 , ASN D:14 , ASP D:16 , THR D:18 , TRP D:29 , HOH D:209 , HOH D:250 , HOH D:252BINDING SITE FOR RESIDUE 1PS D 101
4AC4SOFTWARELYS F:12 , ASN F:14 , THR F:20 , GLU F:27 , TRP F:29 , GLY F:59 , MBG F:102 , HOH F:210 , HOH F:231 , HOH F:253BINDING SITE FOR RESIDUE A2G F 101
5AC5SOFTWAREASP F:16 , THR F:18 , TRP F:29 , GLY F:59 , A2G F:101BINDING SITE FOR RESIDUE MBG F 102
6AC6SOFTWAREGLU B:15 , SER F:53 , SER F:54 , GLY F:61 , A2G F:104 , HOH F:235 , HOH F:256BINDING SITE FOR RESIDUE MBG F 103
7AC7SOFTWAREHOH A:401 , HOH A:547 , HOH A:628 , GLU B:15 , TRP F:29 , THR F:30 , SER F:31 , ARG F:32 , PHE F:62 , ALA F:63 , MBG F:103BINDING SITE FOR RESIDUE A2G F 104

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:241 -A:260
2B:3 -B:56
3C:3 -C:56
4D:3 -D:56
5E:3 -E:56
6F:3 -F:56

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4M1U)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4M1U)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4M1U)

(-) Exons   (0, 0)

(no "Exon" information available for 4M1U)

(-) 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:281
                                                                                                                                                                                                                                                                                                                         
               SCOP domains d4m1ua_ A: Shiga toxin, A-chain                                                                                                                                                                                                                                                           SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee..hhhhhhhhhhhhhhhheeeeeeeee..eeeeee.......eeeeeee...........eeeeee.....eeeeee....eeee.hhhh.......eeee.....hhhhhhhhhh......eehhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....ee.hhhhhhhhhhhhhhhhhhhhh.....eee..eee.hhhhhhhhh.ee.............eeee..eeeehhhhhhhh...hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4m1u A   1 REFTIDFSTQQSYVSSLNSIRTEISTPLEHISQGTTSVSVINHTPPGSYFAVDIRGLDVYQARFDHLRLIIEQNNLYVAGFVNTATNTFYRFSDFTHISVPGVTTVSMTTDSSYTTLQRVAALERSGMQISRHSLVSSYLALMEFSGNTMTRDASRAVLRFVTVTAEALRFRQIQREFRQALSETAPVYTMTPGDVDLTLNWGRISNVLPEYRGEDGVRVGRISFNNISAILGTVAVILNCHECQITGDRPVIKINNTLWESNTAAAFLNRKSQFLYTTGK 297
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240 ||    266       276       286       296 
                                                                                                                                                                                                                                                                           242|                                      
                                                                                                                                                                                                                                                                            259                                      


Chain B from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m1ub_ B: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4m1u B   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain C from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m1uc_ C: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeeeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4m1u C   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain D from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m1ud_ D: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4m1u D   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain E from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m1ue_ E: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee...........eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4m1u E   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70


Chain F from PDB  Type:PROTEIN  Length:70
                                                                                                      
               SCOP domains d4m1uf_ F: Verotoxin-1/shiga-toxin, B-pentamer                         SCOP domains
               CATH domains ---------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeee.eeeeee.....eeeee..eeeee...hhhhhhhhhhhhh.eeeee.......ee..eeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------- Transcript
                 4m1u F   1 ADCAKGKIEFSKYNEDDTFTVKVDGKEYWTSRWNLQPLLQSAQLTGMTVTIKSSTCESGSGFAEVQFNND  70
                                    10        20        30        40        50        60        70
   Legend:   → Mismatch (orange background)
  - → Gap (green background, '-', border residues have a numbering label)
    → Modified Residue (blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
  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  (2, 6)

Asymmetric/Biological Unit
(-)
Class: All beta proteins (24004)
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4M1U)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4M1U)

(-) Gene Ontology  (5, 5)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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(-) Related Entries Specified in the PDB File

1bos 1r4p