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(-) Description

Title :  CRYSTAL STRUCTURE OF MYCOPLASMA ARTHRITIDIS-DERIVED MITOGEN
 
Authors :  L. H. Liu, H. M. Li
Date :  16 Nov 09  (Deposition) - 12 May 10  (Release) - 18 Aug 10  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.80
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Superantigen, Mam, 3D-Domain Swap, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  L. Liu, Z. Li, Y. Guo, S. J. Vanvranken, W. Mourad, H. Li
Crystal Structure Of The Mycoplasma Arthritidis-Derived Mitogen In Apo Form Reveals A 3D Domain-Swapped Dimer.
J. Mol. Biol. V. 399 367 2010
PubMed-ID: 20417218  |  Reference-DOI: 10.1016/J.JMB.2010.04.030

(-) Compounds

Molecule 1 - SUPERANTIGEN
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-6P-1
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: UNP RESIDUES 26-239
    Mutation: YES
    Organism Scientific: MYCOPLASMA ARTHRITIDIS
    Organism Taxid: 2111

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 3)

Asymmetric/Biological Unit (1, 3)
No.NameCountTypeFull Name
1PO43Ligand/IonPHOSPHATE ION

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETYR A:66 , GLN A:129 , TRP A:132BINDING SITE FOR RESIDUE PO4 A 302
2AC2SOFTWAREASP A:205 , HIS B:58 , TYR B:66 , ASP B:115 , LEU B:118 , HOH B:660BINDING SITE FOR RESIDUE PO4 B 301
3AC3SOFTWAREGLU A:175 , LEU B:131 , ASN B:172 , GLU B:175 , HOH B:609BINDING SITE FOR RESIDUE PO4 B 303

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 3KPH)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 3KPH)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3KPH)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3KPH)

(-) Exons   (0, 0)

(no "Exon" information available for 3KPH)

(-) 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:196
 aligned with Q48898_MYCAT | Q48898 from UniProtKB/TrEMBL  Length:238

    Alignment length:196
                                    51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231      
         Q48898_MYCAT    42 QNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELKTTSDFAKAVFE 237
               SCOP domains d3kpha_ A: automated matches                                                                                                                                                                         SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ........hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kph A  17 QNLNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELATTSDFAKAVFE 212
                                    26        36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186       196       206      


Chain B from PDB  Type:PROTEIN  Length:194
 aligned with Q48898_MYCAT | Q48898 from UniProtKB/TrEMBL  Length:238

    Alignment length:194
                                    53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233    
         Q48898_MYCAT    44 LNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELKTTSDFAKAVFE 237
               SCOP domains d3kphb_ B: automated matches                                                                                                                                                                       SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
           Pfam domains (1) MA-Mit-3kphB01 B:19-212                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) MA-Mit-3kphB02 B:19-212                                                                                                                                                                            Pfam domains (2)
         Sec.struct. author ......hhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3kph B  19 LNNVVFTNKELEDIYNLSNKEETKEVLKLFKLKVNQFYRHAFGIVNDYNGLLEYKEIFNMMFLKLSVVFDTQRKEANNVEQIKRNIAILDEIMAKADNDLSYFISQNKNFQELWDKAVKLTKEMKIKLKGQKLDLRDGEVAINKVRELFGSDKNVKELWWFRSLLVKGVYLIKRYYEGDIELATTSDFAKAVFE 212
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178       188       198       208
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: All alpha proteins (14657)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3KPH)

(-) Pfam Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Clan: no clan defined [family: MA-Mit] (3)

(-) Gene Ontology  (0, 0)

Asymmetric/Biological Unit(hide GO term definitions)
    (no "Gene Ontology" information available for 3KPH)

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 Related Entries

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

UniProtKB/TrEMBL
        Q48898_MYCAT | Q48898: 1r5i 2icw 2oje

(-) Related Entries Specified in the PDB File

1r5i CRYSTAL STRUCTURE OF THE MAM-MHC COMPLEX
2icw CRYSTAL STRUCTURE OF A COMPLETE TERNARY COMPLEX BETWEEN TCR, SUPERANTIGEN, AND PEPTIDE-MHC CLASS II MOLECULE