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(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN IL-1BETA IN COMPLEX WITH THE THERAPEUTIC ANTIBODY BINDING FRAGMENT OF CANAKINUMAB
 
Authors :  M. Blech, S. Hoerer
Date :  19 Jul 12  (Deposition) - 19 Dec 12  (Release) - 17 Jul 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.03
Chains :  Asym./Biol. Unit :  A,H,L
Keywords :  Immunglobulin Fold, Interleukin-1Beta Binding, Immune System (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  M. Blech, D. Peter, P. Fischer, M. M. Bauer, M. Hafner, M. Zeeb, H. Nar
One Traget-Two Different Binding Modes: Structural Insights Into Gevokizumab And Canakinumab Interactions To Interleukin-1Beta
J. Mol. Biol. V. 425 94 2013
PubMed-ID: 23041424  |  Reference-DOI: 10.1016/J.JMB.2012.09.021

(-) Compounds

Molecule 1 - INTERLEUKIN-1 BETA
    ChainsA
    EngineeredYES
    FragmentHUMAN INTERLEUKIN-1BETA
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-1 BETA, CATABOLIN
    SyntheticYES
 
Molecule 2 - HEAVY CHAIN OF ANTIBODY BINDING FRAGMENT OF CANAKINUMAB
    ChainsH
    EngineeredYES
    FragmentHEAVY CHAIN OF ANTIBODY BINDING FRAGMENT OF CANAKINUMAB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES
 
Molecule 3 - LIGHT CHAIN OF ANTIBODY BINDING FRAGMENT OF CANAKINUMAB
    ChainsL
    EngineeredYES
    FragmentLIGHT CHAIN OF ANTIBODY BINDING FRAGMENT OF CANAKINUMAB
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SyntheticYES

 Structural Features

(-) Chains, Units

  123
Asymmetric/Biological Unit AHL

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (0, 0)

(no "Ligand,Modified Residues,Ions" information available for 4G6J)

(-) Sites  (0, 0)

(no "Site" information available for 4G6J)

(-) SS Bonds  (4, 4)

Asymmetric/Biological Unit
No.Residues
1H:22 -H:96
2H:145 -H:201
3L:23 -L:88
4L:134 -L:194

(-) Cis Peptide Bonds  (6, 6)

Asymmetric/Biological Unit
No.Residues
1Tyr A:90 -Pro A:91
2Phe H:151 -Pro H:152
3Glu H:153 -Pro H:154
4Ser L:7 -Pro L:8
5Leu L:94 -Pro L:95
6Tyr L:140 -Pro L:141

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4G6J)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4G6J)

(-) Exons   (0, 0)

(no "Exon" information available for 4G6J)

(-) 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:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee....eeeeee..eeeee..hhhhhhhh..eeeee........eeeeeee.....eeeeeeee..eeeeeeee...........hhh.eeeeee....eeeee......eee......ee.eee..........eeeee.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6j A   4 RSLNCTLRDSQQKSLVMSGPYELKALHLQGQDMEQQVVFSMSFVQGEESNDKIPVALGLKEKNLYLSCVLKDDKPTLQLESVDPKNYPKKKMEKRFVFNKIEINNKLEFESAQFPNWYISTSQAENMPVFLGGTKGGQDITDFTMQFVS 152
                                    13        23        33        43        53        63        73        83        93       103       113       123       133       143         

Chain H from PDB  Type:PROTEIN  Length:218
                                                                                                                                                                                                                                                          
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee..eee.....eeeeeeee..hhhhh.eeeeee......eeeeee......eee.......eeeeee....eeeeee...hhhhheeeeeeee.....eeee...eeeee........eeeee..hhh.ee..eeeeeeeeeee.....eeee.hhh.....ee...ee.....eeeeeeeeee.hhh.....eeeeeehhhheeeeee... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6j H   1 QVQLVESGGGVVQPGRSLRLSCAASGFTFSVYGMNWVRQAPAKGLEWVAIIWYDGDNQYYADSVKGRFTISRDNSKNTLYLQMNGLRAEDTAVYYCARDLRTGPFDYWGQGTLVTVSSASTKGPSVFPLAPSSKSTSGGTAALGCLVKDYFPEPVTVSWNSGALTSGVHTFPAVLQSSGLYSLSSVVTVPSSSLGTQTYICNVNHKPSNTKVDKRVAP 218
                                    10        20        30        40        50        60        70        80        90       100       110       120       130       140       150       160       170       180       190       200       210        

Chain L from PDB  Type:PROTEIN  Length:212
                                                                                                                                                                                                                                                    
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee..eeee.....eeeeeee.......eeeeee......eeeee...ee.......eeeeee..eeeeee...hhhhh.eeeeee......ee...eeeee.......eeeee..hhhhhhh.eeeeeeeeeee.....eeeeee..ee....eeeee.........eeeeeeeeeehhhhhhh.eeeeeee.......eeeeee.. Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4g6j L   1 EIVLTQSPDFQSVTPKEKVTITCRASQSIGSSLHWYQQKPDQSPKLLIKYASQSFSGVPSRFSGSGSGTDFTLTINSLEAEDAAAYYCHQSSSLPFTFGPGTKVDIKRTVAAPSVFIFPPSDEQLKSGTASVVCLLNNFYPREAKVQWKVDNALQSGNSQESVTEQDSKDSTYSLSSTLTLSKADYEKHKVYACEVTHQGLSSPVTKSFNRG 212
                                    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  (0, 0)

(no "SCOP Domain" information available for 4G6J)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4G6J)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4G6J)

(-) Gene Ontology  (146, 146)

Asymmetric/Biological Unit(hide GO term definitions)

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  Sites
(no "Sites" information available for 4g6j)
 
  Cis Peptide Bonds
    Glu H:153 - Pro H:154   [ RasMol ]  
    Leu L:94 - Pro L:95   [ RasMol ]  
    Phe H:151 - Pro H:152   [ RasMol ]  
    Ser L:7 - Pro L:8   [ RasMol ]  
    Tyr A:90 - Pro A:91   [ RasMol ]  
    Tyr L:140 - Pro L:141   [ RasMol ]  
 

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 Related Entries

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

UniProtKB/Swiss-Prot
        IL1B_HUMAN | P015841hib 1i1b 1iob 1itb 1l2h 1s0l 1t4q 1too 1tp0 1twe 1twm 21bi 2i1b 2kh2 2nvh 31bi 3ltq 3o4o 3pok 41bi 4dep 4g6m 4gaf 4gai 4i1b 5bvp 5i1b 5mvz 6i1b 7i1b 9ilb

(-) Related Entries Specified in the PDB File

4g5z ANTIBODY BINDING FRAGMENT IN ITS UNBOUND STATE