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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
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: IL12B, NKSF2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-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
    Chains: B
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293T
    Expression System Common: HUMAN
    Expression System Plasmid: PHLSEC
    Expression System Taxid: 9606
    Expression System Vector Type: PLASMID
    Gene: IL23A, SGRF, UNQ2498/PRO5798
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-23-A,INTERLEUKIN-23 SUBUNIT P19,IL-23P19
 
Molecule 3 - ALPHABODY MA12
    Chains: C
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PET16B
    Expression System Taxid: 469008
    Expression System Variant: PLYSS
    Expression System Vector Type: PLASMID
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 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)
  - → 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  (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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  5mj4
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  IL12B_HUMAN | P29460
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  IL23A_HUMAN | Q9NPF7
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 Related Entries

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

UniProtKB/Swiss-Prot
        IL12B_HUMAN | P29460: 1f42 1f45 3d85 3d87 3duh 3hmx 3qwr 4grw 5mj3
        IL23A_HUMAN | Q9NPF7: 3d85 3d87 3duh 3qwr 4grw 5mj3

(-) Related Entries Specified in the PDB File

5mj3 SAME COMPLEX BUT IN CRYSTALLIZED IN DIFFERENT SPACE GROUP