Show PDB file:   
         Plain Text   HTML   (compressed file size)
QuickSearch:   
by PDB,NDB,UniProt,PROSITE Code or Search Term(s)  
(-)Asym./Biol. Unit
(-)Asym./Biol. Unit - sites
collapse expand < >
Image Asym./Biol. Unit
Asym./Biol. Unit  (Jmol Viewer)
Image Asym./Biol. Unit - sites
Asym./Biol. Unit - sites  (Jmol Viewer)

(-) Description

Title :  CRYSTAL STRUCTURE OF HUMAN INTERLEUKIN 6 IN COMPLEX WITH A MODIFIED NUCLEOTIDE APTAMER (SOMAMER SL1025), FORM 2
 
Authors :  D. Davies, T. Edwards, A. Gelinas, T. Jarvis, M. C. Clifton
Date :  05 Nov 13  (Deposition) - 22 Jan 14  (Release) - 01 Jun 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.55
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Selex, Somamer, Cytokine-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  A. D. Gelinas, D. R. Davies, T. E. Edwards, J. C. Rohloff, J. D. Carter, C. Zhang, S. Gupta, Y. Ishikawa, M. Hirota, Y. Nakaishi, T. C. Jarvis, N. Janjic
Crystal Structure Of Interleukin-6 In Complex With A Modified Nucleic Acid Ligand.
J. Biol. Chem. V. 289 8720 2014
PubMed-ID: 24415767  |  Reference-DOI: 10.1074/JBC.M113.532697

(-) Compounds

Molecule 1 - SOMAMER SL1025
    Chains: B, D
    Engineered: YES
    Synthetic: YES
 
Molecule 2 - INTERLEUKIN-6
    Chains: A, C
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: IL6, IFNB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: IL-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/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (7, 34)

Asymmetric/Biological Unit (7, 34)
No.NameCountTypeFull Name
12JU2Mod. Nucleotide2'-DEOXY-5-[(NAPHTHALEN-1-YLMETHYL)CARBAMOYL]URIDINE5'-(DIHYDROGEN PHOSPHATE)
2A2M4Mod. Nucleotide2'-O-METHYLADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
3DUZ16Mod. Nucleotide5-(BENZYLCARBAMOYL)-2'-DEOXYURIDINE 5'-(DIHYDROGENPHOSPHATE)
4NA2Ligand/IonSODIUM ION
5OMC6Mod. NucleotideO2'-METHYLYCYTIDINE-5'-MONOPHOSPHATE
6OMG2Mod. NucleotideO2'-METHYLGUANOSINE-5'-MONOPHOSPHATE
7UPE2Mod. Nucleotide2'-DEOXY-5-[(2-PHENYLETHYL)CARBAMOYL]URIDINE 5'-(DIHYDROGEN PHOSPHATE)

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG B:2 , DA B:4 , DG B:5 , DG B:10 , DG B:11 , DG B:31 , DG B:32BINDING SITE FOR RESIDUE NA B 101
2AC2SOFTWAREDG B:1 , OMG B:6 , UPE B:9 , DG B:10 , DG B:32BINDING SITE FOR RESIDUE NA B 102

(-) SS Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1A:73 -A:83
2C:73 -C:83

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NI9)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NI9)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NI9)

(-) Exons   (0, 0)

(no "Exon" information available for 4NI9)

(-) 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:144
                                                                                                                                                                                
               SCOP domains d4ni9a_ A: Interleukin-6                                                                                                                         SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ......hhhhhhhhhhhhhhhhhhhhhh.........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 4ni9 A  14 PHRQPLTSSERIDKQIRYILDGISALRKETNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM 184
                                    23        33        43|       70        80        90       100       110       120       130|      150       160       170       180    
                                                        43|                                                                  130|                                           
                                                         61                                                                   141                                           


Chain B from PDB  Type:DNA/RNA  Length:32
                                                                
                 4ni9 B   1 GGcAGgxxxGGxAxxaACacGxxAAGxcGxGG  32
                              |  |||10 | |||  20 ||   ||30  
                              3-OMC||  | |||  20-OMC  || |  
                                 6-OMG | |||  | 22-DUZ|| |  
                                  7-DUZ| |||  |  23-DUZ| |  
                                   8-DUZ |||  |      27-DUZ 
                                    9-UPE|||  |       28-OMC
                                      12-2JU  |         30-DUZ
                                        14-DUZ|             
                                         15-DUZ             
                                          16-A2M            


Chain C from PDB  Type:PROTEIN  Length:148
                                                                                                                                                                                    
               SCOP domains d4ni9c_ C: Interleukin-6                                                                                                                             SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhhhhhhhhhhhhhh........hhhhh......hhhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4ni9 C  16 RQPLTSSERIDKQIRYILDGISALRKETNNLNLPKMAEKDGCFQSGFNEETCLVKIITGLLEFEVYLEYLQNRFESSEEQARAVQMSTKVLIQFLQKKAITTPDPTTNASLLTKLQAQNQWLQDMTTHLILRSFKEFLQSSLRALRQM 184
                                    25        35       |61        71        81        91       101       111       121       136       146       156       166       176        
                                                      43|                                                                   130|                                                
                                                       60                                                                    136                                                


Chain D from PDB  Type:DNA/RNA  Length:32
                                                                
                 4ni9 D   1 GGcAGgxxxGGxAxxaACacGxxAAGxcGxGG  32
                              |  |||10 | |||  20 ||   ||30  
                              3-OMC||  | |||  20-OMC  || |  
                                 6-OMG | |||  | 22-DUZ|| |  
                                  7-DUZ| |||  |  23-DUZ| |  
                                   8-DUZ |||  |      27-DUZ 
                                    9-UPE|||  |       28-OMC
                                      12-2JU  |         30-DUZ
                                        14-DUZ|             
                                         15-DUZ             
                                          16-A2M
   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  (1, 2)

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

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NI9)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NI9)

(-) Gene Ontology  (118, 118)

Asymmetric/Biological Unit(hide GO term definitions)

 Visualization

(-) Interactive Views

Asymmetric/Biological Unit
  Complete Structure
    Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
    WebMol | AstexViewer[tm]@PDBe
(Java Applets, require no local installation except for Java; loading may be slow)
    STRAP
(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    RasMol
(require local installation)
    Molscript (VRML)
(requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)
 
  Ligands, Modified Residues, Ions
    2JU  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    A2M  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    DUZ  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    NA  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMC  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    OMG  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    UPE  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 4ni9)
 

(-) Still Images

Jmol
  protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick
[ Asym./Biol. Unit PNG format | Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
  protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick
[ mono PDF format | stereo PDF format ](default orientation, automatically generated)

 Databases and Analysis Tools

(-) Databases

Access by PDB/NDB ID
  4ni9
    Family and Domain Information: ProDom | SYSTERS
    General Structural Information: GlycoscienceDB | MMDB | NDB | OCA | PDB | PDBe | PDBj | PDBsum | PDBWiki | PQS | PROTEOPEDIA
    Orientation in Membranes: OPM
    Protein Surface: SURFACE
    Secondary Structure: DSSP (structure derived) | HSSP (homology derived)
    Structural Genomics: GeneCensus
    Structural Neighbours: CE | VAST
    Structure Classification: CATH | Dali | SCOP
    Validation and Original Data: BMRB Data View | BMRB Restraints Grid | EDS | PROCHECK | RECOORD | WHAT_CHECK
 
Access by UniProt ID/Accession number
  IL6_HUMAN | P05231
    Comparative Protein Structure Models: ModBase
    Genomic Information: Ensembl
    Protein-protein Interaction: DIP
    Sequence, Family and Domain Information: InterPro | Pfam | SMART | UniProtKB/SwissProt
 
Access by Enzyme Classificator   (EC Number)
  (no 'Enzyme Classificator' available)
    General Enzyme Information: BRENDA | EC-PDB | Enzyme | IntEnz
    Pathway: KEGG | MetaCyc
 
Access by Disease Identifier   (MIM ID)
  (no 'MIM ID' available)
    Disease Information: OMIM
 
Access by GenAge ID
  (no 'GenAge ID' available)
    Age Related Information: GenAge

(-) Analysis Tools

Access by PDB/NDB ID
    Domain Information: XDom
    Interatomic Contacts of Structural Units: CSU
    Ligand-protein Contacts: LPC
    Protein Cavities: castP
    Sequence and Secondary Structure: PDBCartoon
    Structure Alignment: STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
    Structure and Sequence Browser: STING
 
Access by UniProt ID/Accession number
  IL6_HUMAN | P05231
    Protein Disorder Prediction: DisEMBL | FoldIndex | GLOBPLOT (for more information see DisProt)

 Related Entries

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

UniProtKB/Swiss-Prot
        IL6_HUMAN | P05231: 1alu 1il6 1n2q 1p9m 2il6 4cni 4j4l 4ni7 4o9h 4zs7 5fuc

(-) Related Entries Specified in the PDB File

4ni7 DIFFERENT CRYSTAL FORM OF SAME COMPLEX