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(-) Description

Title :  S425G GLUCOCORTICOID RECEPTOR DNA BINDING DOMAIN - (+)GRE COMPLEX
 
Authors :  W. H. Hudson, E. A. Weikum, E. A. Ortlund
Date :  01 Jul 15  (Deposition) - 23 Dec 15  (Release) - 16 Mar 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.30
Chains :  Asym. Unit :  A,B,C,D,W,X,Y,Z
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  W,X,Y,Z  (1x)
Keywords :  Dna Binding Protein, Dna Binding Protein-Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  W. H. Hudson, B. R. Kossmann, I. M. De Vera, S. W. Chuo, E. R. Weikum, G. N. Eick, J. W. Thornton, I. N. Ivanov, D. J. Kojetin, E. A. Ortlund
Distal Substitutions Drive Divergent Dna Specificity Among Paralogous Transcription Factors Through Subdivision Of Conformational Space.
Proc. Natl. Acad. Sci. Usa V. 113 326 2016
PubMed-ID: 26715749  |  Reference-DOI: 10.1073/PNAS.1518960113

(-) Compounds

Molecule 1 - GLUCOCORTICOID RECEPTOR
    Chains: A, B, W, X
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Gene: NR3C1, GRL
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: GR,NUCLEAR RECEPTOR SUBFAMILY 3 GROUP C MEMBER 1
 
Molecule 2 - DNA (5'- D(*CP*CP*AP*GP*AP*AP*CP*AP*GP*AP*GP*TP*GP*TP*TP*CP*TP*G)-3')
    Chains: C, Z
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES
 
Molecule 3 - DNA (5'- D(*TP*CP*AP*GP*AP*AP*CP*AP*CP*TP*CP*TP*GP*TP*TP*CP*TP*G)-3')
    Chains: D, Y
    Engineered: YES
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDWXYZ
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     WXYZ

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 8)

Asymmetric Unit (1, 8)
No.NameCountTypeFull Name
1ZN8Ligand/IonZINC ION
Biological Unit 1 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION
Biological Unit 2 (0, 0)
No.NameCountTypeFull Name
1ZN-1Ligand/IonZINC ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
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:476binding site for residue ZN A 602
3AC3SOFTWARECYS B:421 , CYS B:424 , CYS B:438 , CYS B:441binding site for residue ZN B 601
4AC4SOFTWARECYS B:457 , CYS B:463 , CYS B:473 , CYS B:476binding site for residue ZN B 602
5AC5SOFTWARECYS W:421 , CYS W:424 , CYS W:438 , CYS W:441binding site for residue ZN W 601
6AC6SOFTWARECYS W:457 , CYS W:463 , CYS W:473 , CYS W:476binding site for residue ZN W 602
7AC7SOFTWARECYS X:421 , CYS X:424 , CYS X:438 , CYS X:441binding site for residue ZN X 601
8AC8SOFTWARECYS X:457 , CYS X:463 , CYS X:473 , CYS X:476binding site for residue ZN X 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5CC1)

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Gln X:452 -His X:453

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5CC1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5CC1)

(-) Exons   (0, 0)

(no "Exon" information available for 5CC1)

(-) 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:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..eeehhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 5cc1 A 417 PPKLCLVCGDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEAR 491
                                   426       436       446       456       466       476       486     


Chain B from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeehhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5cc1 B 418 PKLCLVCGDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 490
                                   427       437       447       457       467       477       487   


Chain C from PDB  Type:DNA  Length:18
                                                  
                 5cc1 C   1 CCAGAACAGAGTGTTCTG  18
                                    10        


Chain D from PDB  Type:DNA  Length:18
                                                  
                 5cc1 D   1 TCAGAACACTCTGTTCTG  18
                                    10        


Chain W from PDB  Type:PROTEIN  Length:75
                                                                                                           
               SCOP domains --------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .............eee..eeehhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------- Transcript
                 5cc1 W 417 PPKLCLVCGDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEAR 491
                                   426       436       446       456       466       476       486     


Chain X from PDB  Type:PROTEIN  Length:73
                                                                                                         
               SCOP domains ------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eee..eeehhhhhhhhhhhhhhh...............hhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------- Transcript
                 5cc1 X 418 PKLCLVCGDEASGCHYGVLTCGSCKVFFKRAVEGQHNYLCAGRNDCIIDKIRRKNCPACRYRKCLQAGMNLEA 490
                                   427       437       447       457       467       477       487   


Chain Y from PDB  Type:DNA  Length:18
                                                  
                 5cc1 Y   1 TCAGAACACTCTGTTCTG  18
                                    10        


Chain Z from PDB  Type:DNA  Length:18
                                                  
                 5cc1 Z   1 CCAGAACAGAGTGTTCTG  18
                                    10
   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 5CC1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5CC1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5CC1)

(-) Gene Ontology  (37, 37)

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        GCR_HUMAN | P04150: 1m2z 1nhz 1p93 3bqd 3cld 3e7c 3h52 3k22 3k23 4csj 4hn5 4hn6 4lsj 4mdd 4p6w 4p6x 4udc 4udd 5cbx 5cby 5cbz 5e69 5e6a 5e6b 5e6c 5e6d 5emc 5emp 5emq 5g3j 5g5w

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