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 :  IDENTIFICATION OF A NOVEL ALLOSTERIC BINDING SITE FOR RORGT INHIBITORS
 
Authors :  G. Parthasarathy, S. Soisson
Date :  18 Jun 15  (Deposition) - 16 Dec 15  (Release) - 16 Dec 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.23
Chains :  Asym./Biol. Unit :  A
Keywords :  Allosteric, Inhibitor, Transcription-Transcription Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Scheepstra, S. Leysen, G. C. Van Almen, J. R. Miller, J. Piesvaux, V. Kutilek, H. Van Eenennaam, H. Zhang, K. Barr, S. Nagpal, S. M. Soisson, M. Kornienko, K. Wiley, N. Elsen, S. Sharma, C. C. Correll, B. W. Trotter, M. Van Der Stelt, A. Oubrie, C. Ottmann, G. Parthasarathy, L. Brunsveld
Identification Of An Allosteric Binding Site For Ror Gamma Inhibition.
Nat Commun V. 6 8833 2015
PubMed-ID: 26640126  |  Reference-DOI: 10.1038/NCOMMS9833

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR ROR-GAMMA
    Chains: A
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: LIGAND-BINDING RESIDUES 267-507
    Gene: RORC, NR1F3, RORG, RZRG
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NUCLEAR RECEPTOR RZR-GAMMA,NUCLEAR RECEPTOR SUBFAMILY 1 GROUP F MEMBER 3,RAR-RELATED ORPHAN RECEPTOR C,RETINOID-RELATED ORPHAN RECEPTOR-GAMMA

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 3)

Asymmetric/Biological Unit (2, 3)
No.NameCountTypeFull Name
14Y51Ligand/Ion4-{1-[2-CHLORO-6-(TRIFLUOROMETHYL)BENZOYL]-4-FLUORO-1H-INDAZOL-3-YL}-3-FLUOROBENZOIC ACID
2GOL2Ligand/IonGLYCEROL

(-) Sites  (3, 3)

Asymmetric Unit (3, 3)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:324 , THR A:325 , ILE A:328 , GLN A:329 , LEU A:353 , LYS A:354 , MET A:358 , VAL A:480 , LEU A:483 , GLN A:484 , GLN A:487 , ALA A:496 , ALA A:497 , PHE A:498 , LEU A:501 , LEU A:505 , PHE A:506binding site for residue 4Y5 A 601
2AC2SOFTWARELEU A:324 , LEU A:391binding site for residue GOL A 602
3AC3SOFTWAREGLY A:392 , CYS A:393 , SER A:394 , GLU A:395 , LEU A:396 , LYS A:456 , ARG A:482binding site for residue GOL A 603

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5C4S)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5C4S)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5C4S)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5C4S)

(-) Exons   (0, 0)

(no "Exon" information available for 5C4S)

(-) 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:241
                                                                                                                                                                                                                                                                                 
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5c4s A 267 LTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLHKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFS 507
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486       496       506
   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 5C4S)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5C4S)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5C4S)

(-) Gene Ontology  (37, 37)

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
    4Y5  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
    GOL  [ RasMol | Jena3D ]  +environment [ RasMol | Jena3D ]
 
  Sites
    AC1  [ RasMol ]  +environment [ RasMol ]
    AC2  [ RasMol ]  +environment [ RasMol ]
    AC3  [ RasMol ]  +environment [ RasMol ]
 
  Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 5c4s)
 

(-) 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
  5c4s
    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
  RORG_HUMAN | P51449
    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
  RORG_HUMAN | P51449
    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
        RORG_HUMAN | P51449: 3b0w 3kyt 3l0j 3l0l 4nb6 4nie 4qm0 4s14 4wlb 4wpf 4wqp 4xt9 4ymq 4ypq 4zjr 4zjw 4zom 5aph 5apj 5apk 5ayg 5c4o 5c4t 5c4u 5ejv 5eth 5g42 5g43 5g44 5g45 5g46 5ixk 5iz0 5k38 5k3l 5k3m 5k3n 5k6e 5k74 5lwp 5m96 5nti 5ntk 5ntn 5ntp 5ntq 5ntw 5nu1 5ufo 5ufr 5uhi 5vb3 5vb5 5vb6 5vb7 5x8q

(-) Related Entries Specified in the PDB File

5c4o 5c4t 5c4u