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(-) Description

Title :  CRYSTAL STRUCTURE OF SEK
 
Authors :  S. Gunther, A. K. Varma, B. Moza, E. J. Sundberg
Date :  08 Nov 06  (Deposition) - 26 Jun 07  (Release) - 13 Jul 11  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.56
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Superantigen; T Cell Receptor, Toxin (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  S. Gunther, A. K. Varma, B. Moza, K. J. Kasper, A. W. Wyatt, P. Zhu, A. K. Rahman, Y. Li, R. A. Mariuzza, J. K. Mccormick, E. J. Sundberg
A Novel Loop Domain In Superantigens Extends Their T Cell Receptor Recognition Site
J. Mol. Biol. V. 371 210 2007
PubMed-ID: 17560605  |  Reference-DOI: 10.1016/J.JMB.2007.05.038

(-) Compounds

Molecule 1 - STAPHYLOCOCCAL ENTEROTOXIN K
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: ROSETTA (DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Gene: SEK
    Organism Scientific: STAPHYLOCOCCUS AUREUS SUBSP. AUREUS
    Organism Taxid: 93062
    Strain: COL

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 23)

Asymmetric/Biological Unit (2, 23)
No.NameCountTypeFull Name
1CL13Ligand/IonCHLORIDE ION
2EDO10Ligand/Ion1,2-ETHANEDIOL

(-) Sites  (23, 23)

Asymmetric Unit (23, 23)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREPRO A:189 , GLY B:152 , HIS B:153 , LYS B:154 , HOH B:7028BINDING SITE FOR RESIDUE CL B 5001
02AC2SOFTWARELYS A:156 , ASN A:162BINDING SITE FOR RESIDUE CL A 5002
03AC3SOFTWARELYS B:156 , ASN B:162 , HOH B:7226BINDING SITE FOR RESIDUE CL B 5003
04AC4SOFTWAREGLY A:152 , HIS A:153 , LYS A:154 , PRO B:189 , HOH B:7034BINDING SITE FOR RESIDUE CL A 5004
05AC5SOFTWAREALA B:84 , HOH B:7346BINDING SITE FOR RESIDUE CL B 5005
06AC6SOFTWARESER A:73 , HIS B:142 , TYR B:158BINDING SITE FOR RESIDUE CL B 5006
07AC7SOFTWAREHIS A:142 , TYR A:158 , SER B:73BINDING SITE FOR RESIDUE CL A 5007
08AC8SOFTWAREVAL A:202 , GLU A:203 , HOH A:7315BINDING SITE FOR RESIDUE CL A 5008
09AC9SOFTWAREALA A:84 , HOH A:7264BINDING SITE FOR RESIDUE CL A 5009
10BC1SOFTWAREASN A:94BINDING SITE FOR RESIDUE CL A 5010
11BC2SOFTWAREASP B:185 , HOH B:7115 , HOH B:7251BINDING SITE FOR RESIDUE CL B 5011
12BC3SOFTWAREASN A:11 , HOH A:7332 , TYR B:215 , ALA B:217BINDING SITE FOR RESIDUE CL A 5012
13BC4SOFTWAREVAL B:202 , GLU B:203BINDING SITE FOR RESIDUE CL B 5013
14BC5SOFTWARELEU B:21 , VAL B:24 , PHE B:37 , SER B:38 , ASN B:39BINDING SITE FOR RESIDUE EDO B 7001
15BC6SOFTWARELEU A:21 , VAL A:24 , PHE A:37 , SER A:38 , ASN A:39BINDING SITE FOR RESIDUE EDO A 7002
16BC7SOFTWAREGLU B:135 , ASN B:143 , HOH B:7059 , HOH B:7064 , HOH B:7354BINDING SITE FOR RESIDUE EDO B 7003
17BC8SOFTWARELYS A:16 , SER A:68 , TYR A:69 , ASN A:70 , LYS A:76 , HOH A:7193 , HOH B:7133BINDING SITE FOR RESIDUE EDO A 7004
18BC9SOFTWARELYS B:16 , SER B:68 , TYR B:69 , ASN B:70 , LYS B:76 , HOH B:7017BINDING SITE FOR RESIDUE EDO B 7005
19CC1SOFTWARELEU A:89 , ASP A:90 , GLU A:205 , HOH A:7337 , HOH A:7348BINDING SITE FOR RESIDUE EDO A 7006
20CC2SOFTWAREHIS B:142 , ASN B:143 , GLY B:144 , HOH B:7185 , HOH B:7371BINDING SITE FOR RESIDUE EDO B 7007
21CC3SOFTWAREGLY B:164 , LYS B:165 , ASP B:179 , HOH B:7067BINDING SITE FOR RESIDUE EDO B 7008
22CC4SOFTWAREGLY A:164 , LYS A:165 , TYR A:178 , ASP A:179 , HOH A:7053BINDING SITE FOR RESIDUE EDO A 7009
23CC5SOFTWAREGLU A:135 , ASN A:143 , HOH A:7065 , HOH A:7077 , HOH A:7210 , HOH A:7339BINDING SITE FOR RESIDUE EDO A 7010

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 2NTT)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric/Biological Unit
No.Residues
1Asn A:172 -Asn A:173

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 2NTT)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 2NTT)

(-) Exons   (0, 0)

(no "Exon" information available for 2NTT)

(-) 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:217
 aligned with Q93CC5_STAAU | Q93CC5 from UniProtKB/TrEMBL  Length:242

    Alignment length:217
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       
         Q93CC5_STAAU    24 QGDIGIDNLRNFYTKKDFVDLKDVKDNDTPIANQLQFSNESYDLISESKDFNKFSNFKGKKLDVFGISYNGQCNTKYIYGGVTATNEYLDKSRNIPINIWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEEYGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLDVDISYKE 240
               SCOP domains d2ntta1 A:1-86 automated matches                                                      d2ntta2 A:87-217 automated matches                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeeee........eeeee....eeeee..hhhhhhhhh..eeeeee.eee....eeeee..eee...eeeeeee..eeeee..eeeee.....eeee.eeehhhhhhhhhhhhhhhhh.........hhhhh..........eeeeeeee....eeeee........hhhhhhhhhh...eee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntt A   1 QGDIGIDNLRNFYTKKDFVDLKDVKDNDTPIANQLQFSNESYDLISESKDFNKFSNFKGKKLDVFGISYNGQSNTKYIYGGVTATNEYLDKSRNIPINIWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEEYGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLDVDISYKA 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210       


Chain B from PDB  Type:PROTEIN  Length:217
 aligned with Q93CC5_STAAU | Q93CC5 from UniProtKB/TrEMBL  Length:242

    Alignment length:217
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       
         Q93CC5_STAAU    24 QGDIGIDNLRNFYTKKDFVDLKDVKDNDTPIANQLQFSNESYDLISESKDFNKFSNFKGKKLDVFGISYNGQCNTKYIYGGVTATNEYLDKSRNIPINIWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEEYGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLDVDISYKE 240
               SCOP domains d2nttb1 B:1-86 automated matches                                                      d2nttb2 B:87-217 automated matches                                                                                                  SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) -------Stap_Strp_toxin-2nttB03 B:8-85                                                -------Stap_Strp_tox_C-2nttB01 B:93-214                                                                                          --- Pfam domains (1)
           Pfam domains (2) -------Stap_Strp_toxin-2nttB04 B:8-85                                                -------Stap_Strp_tox_C-2nttB02 B:93-214                                                                                          --- Pfam domains (2)
         Sec.struct. author ..hhhhhhhhhhhhh...eeeeeee........eeeee....eeeee..hhhhhhhhh..eeeeee.eee....eeeee..eee...eeeeeee..eeeee..eeeee.....eeee.eeehhhhhhhhhhhhhhhhh.........hhhhh..........eeeeeeee....eeeee........hhhhhhhhhh...eee...eeeeeeee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2ntt B   1 QGDIGIDNLRNFYTKKDFVDLKDVKDNDTPIANQLQFSNESYDLISESKDFNKFSNFKGKKLDVFGISYNGQSNTKYIYGGVTATNEYLDKSRNIPINIWINGNHKTISTNKVSTNKKFVTAQEIDVKLRKYLQEEYNIYGHNGTKKGEEYGHKSKFYSGFNIGKVTFHLNNNDTFSYDLFYTGDDGLPKSFLKIYEDNKTVESEKFHLDVDISYKA 217
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210
   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, 4)

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 2NTT)

(-) Pfam Domains  (2, 4)

Asymmetric/Biological Unit
(-)
Clan: Ant-toxin_C (48)
(-)
Clan: no clan defined [family: Stap_Strp_toxin] (39)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (Q93CC5_STAAU | Q93CC5)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.
biological process
    GO:0009405    pathogenesis    The set of specific processes that generate the ability of an organism to induce an abnormal, generally detrimental state in another organism.
cellular component
    GO:0005576    extracellular region    The space external to the outermost structure of a cell. For cells without external protective or external encapsulating structures this refers to space outside of the plasma membrane. This term covers the host cell environment outside an intracellular parasite.

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    Asn A:172 - Asn A:173   [ RasMol ]  
 

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        Q93CC5_STAAU | Q93CC5: 3ea6

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2nts