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(-) Description

Title :  INTERLEUKIN-23 COMPLEX WITH AN ANTAGONISTIC ALPHABODY, CRYSTAL FORM 2
 
Authors :  J. Desmet, K. Verstraete, Y. Bloch, E. Lorent, Y. Wen, B. Devreese, K. Vandenbroucke, S. Loverix, T. Hettmann, S. Deroo, K. Somers, P. Hen I. Lasters, S. Savvides
Date :  29 Nov 16  (Deposition) - 11 Jan 17  (Release) - 01 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.40
Chains :  Asym./Biol. Unit :  A,B,C
Keywords :  Single-Chain Antiparallel Triple-Helix Coiled-Coil, Immunoglobulin- Like, 4-Alpha Helical Bundle, Antagonist, N-Linked Glycosylation, Cytokine-Antagonist Complex, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Desmet, K. Verstraete, Y. Bloch, E. Lorent, Y. Wen, B. Devreese, K. Vandenbroucke, S. Loverix, T. Hettmann, S. Deroo, K. Somers, P. Henderikx, I. Lasters, S. Savvides
Structural Basis Of Il-23 Antagonism By An Alphabody Protei
Nature Communications V. 5 5237 2014
PubMed-ID: 25354530  |  Reference-DOI: 10.1038/NCOMMS6237

(-) Compounds

Molecule 1 - INTERLEUKIN-12 SUBUNIT BETA
    ChainsA
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    GeneIL12B, NKSF2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-12B,CYTOTOXIC LYMPHOCYTE MATURATION FACTOR 40 KDA SUBUNIT,CLMF P40,IL-12 SUBUNIT P40,NK CELL STIMULATORY FACTOR CHAIN 2,NKSF2
 
Molecule 2 - INTERLEUKIN-23 SUBUNIT ALPHA
    ChainsB
    EngineeredYES
    Expression SystemHOMO SAPIENS
    Expression System Cell LineHEK293T
    Expression System CommonHUMAN
    Expression System PlasmidPHLSEC
    Expression System Taxid9606
    Expression System Vector TypePLASMID
    GeneIL23A, SGRF, UNQ2498/PRO5798
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-23-A,INTERLEUKIN-23 SUBUNIT P19,IL-23P19
 
Molecule 3 - ALPHABODY MA12
    ChainsC
    EngineeredYES
    Expression SystemESCHERICHIA COLI BL21(DE3)
    Expression System PlasmidPET16B
    Expression System Taxid469008
    Expression System VariantPLYSS
    Expression System Vector TypePLASMID
    Organism ScientificSYNTHETIC CONSTRUCT
    Organism Taxid32630

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 5)

Asymmetric/Biological Unit (3, 5)
No.NameCountTypeFull Name
1BMA1Ligand/IonBETA-D-MANNOSE
2MAN2Ligand/IonALPHA-D-MANNOSE
3NAG2Ligand/IonN-ACETYL-D-GLUCOSAMINE

(-) Sites  (1, 1)

Asymmetric Unit (1, 1)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:24 , GLU A:34 , HIS A:105 , TYR A:220 , ASN A:222binding site for Poly-Saccharide residues NAG A 500 through MAN A 504 bound to ASN A 222

(-) SS Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1A:50 -A:90
2A:131 -A:142
3A:170 -A:193
4A:199 -B:73
5A:300 -A:327
6B:77 -B:89

(-) Cis Peptide Bonds  (3, 3)

Asymmetric/Biological Unit
No.Residues
1Glu A:122 -Pro A:123
2Thr A:264 -Pro A:265
3Glu B:112 -Pro B:113

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5MJ4)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5MJ4)

(-) Exons   (0, 0)

(no "Exon" information available for 5MJ4)

(-) 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:289
                                                                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeee..eeeeeee.......eeeeee........eeeee.......ee..eeeeee.hhhhheeeeeee..eeeeeeeeeeeeee..ee.................eee......eeeeeeee.....eeeeeeeee.....eeeee...eeee...eeeeeeeee............eeeeeeeee..eeeeeeeeehhhhhh.....eeeeee....eeeee.............eeeeeee..eeeee...eee........eeeeeee..........eee... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5mj4 A  23 IWELKKDVYVVELDWYPDAPGEMVVLTCDTPEEDGITWTLDQSSEVLGSGKTLTIQVKEFGDAGQYTCHKGGEVLSHSLLLLHKKEDGIWSTDILKDQKEPKNKTFLRCEAKNYSGRFTCWWLTTISTDLTFSVKSSRGSSDPQGVTCGAATLSAEREYEYSVECQEDSACPAAEESLPIEVMVDAVHKLKYENYTSSFFIRDIIKPDPPKNLQLKPLKVEVSWEYPDTWSTPHSYFSLTFCVQVQKDRVFTDKTSATVICRKNASISVRAQDRYYSSSWSEWASVPCS 328
                                    32        42        52        62        72        82        92       102       112       122       132       142       152       162       172      |188       198       208       218       228       238       252       262       272     ||289       299       309       319         
                                                                                                                                                                                      179|                                                          247|                       278|                                          
                                                                                                                                                                                       186                                                           252                        286                                          

Chain B from PDB  Type:PROTEIN  Length:162
                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh............hhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5mj4 B  27 SPAWTQCQQLSQKLCTLAWSAHPLVGHMDLREEGDEETTNDVPHIQCGDGCDPQGLRDNSQFCLQRIHQGLIFYEKLLGSDIFTGEPSLLPDSPVGQLHASLLGLSQLLQPEGHHWETQQIPSLSPSQPWQRLLLRFKILRSLQAFVAVAARVFAHGAATLS 188
                                    36        46        56        66        76        86        96       106       116       126       136       146       156       166       176       186  

Chain C from PDB  Type:PROTEIN  Length:81
                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------- Transcript
                 5mj4 C   2 MSIQEIQKEIAQIQAVIAGIQKYIYTMSIEEIQKQIAAIQCQIAAIQKQIYAMSIEEIQKQIAAIQEQILAIYKQIMAMVT 118
                                    11        21      ||49        59        69  ||    97       107       117 
                                                     28|                       72|                           
                                                      47                        91                           

   Legend:   → Mismatch (orange background)
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    → 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  (0, 0)

(no "SCOP Domain" information available for 5MJ4)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5MJ4)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5MJ4)

(-) Gene Ontology  (77, 108)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL12B_HUMAN | P294601f42 1f45 3d85 3d87 3duh 3hmx 3qwr 4grw 5mj3
        IL23A_HUMAN | Q9NPF73d85 3d87 3duh 3qwr 4grw 5mj3

(-) Related Entries Specified in the PDB File

5mj3 SAME COMPLEX BUT IN CRYSTALLIZED IN DIFFERENT SPACE GROUP