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(-) Description

Title :  MODULAR EVOLUTION AND DESIGN OF THE PROTEIN BINDING INTERFACE
 
Authors :  H. K. Cheong, H. J. Kim
Date :  07 Feb 13  (Deposition) - 12 Feb 14  (Release) - 07 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,C  (1x)
Biol. Unit 2:  B,D  (1x)
Keywords :  Lrr, Il-6 Binding, Interleukin 6, Extracellular Matrix, Protein Binding-Cytokine Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  J. Lee, H. J. Kim, C. Yang, J. Choi, H. Kyeong, J. Yuk, K. Park, Y. J. Kim, W. Heu, S. Lee, D. Kim, E. K. Jo, H. K. Cheong, H. S. Kim
Modular Evolution And Design Of The Protein Binding Interface
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - INTERNALIN B,REPEAT MODULES,VARIABLE LYMPHOCYTE RECEPTOR B
    ChainsA, B
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    FragmentUNP RESIDUES 43-100,UNP RESIDUES 141-232
    GeneVLRB
    Organism CommonINSHORE HAGFISH
    Organism ScientificLISTERIA MONOCYTOGENES, SYNTHETIC CONSTRUCT, EPTATRETUS BURGERI
    Organism Taxid1639, 32630, 7764
    Other DetailsCHIMERA OF RESIDUES 43-100 FROM INTERNALIN B, REPEAT MODULES, RESIDUES 141-232 FROM VARIABLE LYMPHOCYTE RECEPTOR B, AND 8 HIS TAGS
 
Molecule 2 - INTERLEUKIN-6
    ChainsC, D
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System Taxid562
    GeneIL6, IFNB2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymIL-6,B-CELL STIMULATORY FACTOR 2,BSF-2,CTL DIFFERENTIATION FACTOR,CDF,HYBRIDOMA GROWTH FACTOR,INTERFERON BETA-2,IFN-BETA-2

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit ABCD
Biological Unit 1 (1x)A C 
Biological Unit 2 (1x) B D

Summary Information (see also Sequences/Alignments below)

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

(no "Ligand,Modified Residues,Ions" information available for 4J4L)

(-) Sites  (0, 0)

(no "Site" information available for 4J4L)

(-) SS Bonds  (7, 7)

Asymmetric Unit
No.Residues
1A:254 -A:287
2A:256 -A:299
3B:254 -B:287
4C:44 -C:50
5C:73 -C:83
6D:44 -D:50
7D:73 -D:83

(-) Cis Peptide Bonds  (2, 2)

Asymmetric Unit
No.Residues
1Cys A:256 -Pro A:257
2Cys B:256 -Pro B:257

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4J4L)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4J4L)

(-) Exons   (0, 0)

(no "Exon" information available for 4J4L)

(-) Sequences/Alignments

Asymmetric 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:258
                                                                                                                                                                                                                                                                                                  
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhh.hhhhhhhhhhhhh........hhhhhhhh.eeee.........hhhhh....eeeeee.....hhhhh......eeeeee..................eeee....................eee.....................eee.....................eee.....................eee............hhhhhhhhhhh.......................hhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4j4l A  43 PIKQIFPDDAFAETIKANLKKKSVTDAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLTLEPNQLQSLPNGVFDKLTNLKELQLWANQLQSLPDGVFDKLTNLTYLNLAFNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPKGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIICP 300
                                    52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292        

Chain B from PDB  Type:PROTEIN  Length:251
                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhh.hhhhhhhhhhhhh..hhhhhhh..eeee.........hhhhh....eeeeee.....hhhhhhh....eeeeee..................eeee....................eee.....................eee.....................eee.....................eee............hhhhhhhhhhhh..ee......hhhhh.......hhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4l B  43 PIKQIFPDDAFAETIKANLKAVTQNELNSIDQIIANNSDIKSVQGIQYLPNVRYLALGGNKLHDISALKELTNLTYLTLEPNQLQSLPNGVFDKLTNLKELQLWANQLQSLPDGVFDKLTNLTYLNLAFNQLQSLPKGVFDKLTNLTELDLSYNQLQSLPKGVFDKLTQLKDLRLYQNQLKSVPDGVFDRLTSLQYIWLHDNPWDCTCPGIRYLSEWINKHSGVVRNSAGSVAPDSAKCSGSGKPVRSIIC 299
                                    52        62|       78        88        98       108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298 
                                              62|                                                                                                                                                                                                                                      
                                               69                                                                                                                                                                                                                                      

Chain C from PDB  Type:PROTEIN  Length:155
                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..........hhhhh......hhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4l C  17 GSLTSSERIDKQIRYILDGISALRKETCNKSNMCENLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNTTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM 184
                                    26        36        46    ||  65        75        85        95       105       115       125      |139       149       159       169       179     
                                                             51|                                                                    132|                                               
                                                              61                                                                     137                                               

Chain D from PDB  Type:PROTEIN  Length:166
                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhh............hhhhh.....hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4j4l D  19 LTSSERIDKQIRYILDGISALRKETCNKSNMCESSKEALAENNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAKNLDAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM 184
                                    28        38        48        58        68        78        88        98       108       118       128       138       148       158       168       178      

   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 4J4L)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4J4L)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4J4L)

(-) Gene Ontology  (120, 120)

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  Cis Peptide Bonds
    Cys A:256 - Pro A:257   [ RasMol ]  
    Cys B:256 - Pro B:257   [ RasMol ]  
 
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 Related Entries

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

UniProtKB/Swiss-Prot
        IL6_HUMAN | P052311alu 1il6 1n2q 1p9m 2il6 4cni 4ni7 4ni9 4o9h 4zs7 5fuc
        Q4G1L3_EPTBU | Q4G1L33rfs
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        Q4G1L3_EPTBU | Q4G1L32o6s 3a79 4uip

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 4J4L)