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(-) Description

Title :  GLUCOCORTICOID RECEPTOR DNA BINDING DOMAIN - ICAM1 NF-KB RESPONSE ELEMENT COMPLEX
 
Authors :  W. H. Hudson, E. A. Rye, A. G. Herbst, E. A. Ortlund
Date :  09 Oct 15  (Deposition) - 08 Feb 17  (Release) - 08 Feb 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.40
Chains :  Asym./Biol. Unit :  A,B,C,D
Keywords :  Dna Binding Proteins, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. H. Hudson, E. A. Rye, J. C. Nwachukwu, I. M. De Vera, A. G. Herbst, D. J. Kojetin, K. W. Nettles, E. A. Ortlund
Cryptic Glucocorticoid Receptor Binding Sites Pervade Genomic Nf-Kb Response Elements
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - DNA (5'-D(*GP*CP*TP*CP*CP*GP*GP*AP*AP*TP*TP*TP*CP*CP*AP*A)- 3')
    Chains: C
    Engineered: YES
    Fragment: UNP RESIDUES 391-480
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 2 - DNA (5'-D(*TP*TP*GP*GP*AP*AP*AP*TP*TP*CP*CP*GP*GP*AP*GP*C)- 3')
    Chains: D
    Engineered: YES
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES
 
Molecule 3 - GLUCOCORTICOID RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Strain: BL21 (DE3) PLYSS
    Expression System Taxid: 469008
    Gene: NR3C1, GRL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GR,NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABCD

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 4)

Asymmetric/Biological Unit (1, 4)
No.NameCountTypeFull Name
1ZN4Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:421 , CYS A:424 , CYS A:438 , CYS A:441binding site for residue ZN A 601
2AC2SOFTWARECYS A:457 , CYS A:463 , CYS A:473 , CYS A:476 , HOH A:706binding site for residue ZN A 602
3AC3SOFTWARECYS B:457 , CYS B:463 , CYS B:473 , CYS B:476binding site for residue ZN B 601
4AC4SOFTWARECYS B:421 , CYS B:424 , CYS B:438 , CYS B:441binding site for residue ZN B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5E6D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5E6D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5E6D)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5E6D)

(-) Exons   (0, 0)

(no "Exon" information available for 5E6D)

(-) 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:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeehhhhhhhhhhhhhh.....................hhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5e6d A 418 PKLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 490
                                   427       437       447       457       467       477       487   


Chain B from PDB  Type:PROTEIN  Length:72
                                                                                                        
               SCOP domains ------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ...........eee..eee..hhhhhh...........................hhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------ Transcript
                 5e6d B 419 KLCLVCSDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 490
                                   428       438       448       458       468       478       488  


Chain C from PDB  Type:DNA  Length:16
                                                
                 5e6d C   1 GCTCCGGAATTTCCAA  16
                                    10      


Chain D from PDB  Type:DNA  Length:16
                                                
                 5e6d D   1 TTGGAAATTCCGGAGC  16
                                    10
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  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 5E6D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5E6D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5E6D)

(-) Gene Ontology  (37, 37)

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
        GCR_HUMAN | P04150: 1m2z 1nhz 1p93 3bqd 3cld 3e7c 3h52 3k22 3k23 4csj 4hn5 4hn6 4lsj 4mdd 4p6w 4p6x 4udc 4udd 5cbx 5cby 5cbz 5cc1 5e69 5e6a 5e6b 5e6c 5emc 5emp 5emq 5g3j 5g5w

(-) Related Entries Specified in the PDB File

5e69 5e6a 5e6b 5e6c