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(-) Description

Title :  CRYSTAL STRUCTURE OF THE MUTANT HUMAN ROR GAMMA LIGAND BINDING DOMAIN WITH COMPOUND A.
 
Authors :  M. Noguchi, A. Nomura, K. Murase, S. Doi, K. Yamaguchi, T. Adachi
Date :  03 Mar 17  (Deposition) - 07 Jun 17  (Release) - 28 Jun 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.60
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B  (1x)
Biol. Unit 2:  C,D  (1x)
Biol. Unit 3:  E,F  (1x)
Biol. Unit 4:  G,H  (1x)
Keywords :  Inhibitor, Ternary Complex, Nuclear Receptor, Transferase-Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Noguchi, A. Nomura, K. Murase, S. Doi, K. Yamaguchi, K. Hirata, M. Shiozaki, S. Hirashima, M. Kotoku, T. Yamaguchi, Y. Katsuda, R. Steensma, X. Li, H. Tao, B. Tse, M. Fenn, R. Babine, E. Bradley, P. Crowe, S. Thacher, T. Adachi, M. Kamada
Ternary Complex Of Human Ror Gamma Ligand-Binding Domain, Inverse Agonist And Smrt Peptide Shows A Unique Mechanism O Corepressor Recruitment
Genes Cells V. 22 535 2017
PubMed-ID: 28493531  |  Reference-DOI: 10.1111/GTC.12494

(-) Compounds

Molecule 1 - UNCHARACTERIZED PROTEIN
    Chains: A, C, E, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Fragment: UNP RESIDUES 248-505
    Gene: RORC
    Mutation: YES
    Organism Common: NORTHERN WHITE-CHEEKED GIBBON
    Organism Scientific: NOMASCUS LEUCOGENYS
    Organism Taxid: 61853
 
Molecule 2 - NUCLEAR RECEPTOR COREPRESSOR 2
    Chains: B, D, F, H
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Fragment: UNP RESIDUES 2346-2367
    Gene: NCOR2, CTG26
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: N-COR2,CTG REPEAT PROTEIN 26,SMAP270,SILENCING MEDIATOR OF RETINOIC ACID AND THYROID HORMONE RECEPTOR,SMRT,T3 RECEPTOR- ASSOCIATING FACTOR,TRAC,THYROID-,RETINOIC-ACID-RECEPTOR-ASSOCIATED COREPRESSOR

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): AB      
Biological Unit 2 (1x):   CD    
Biological Unit 3 (1x):     EF  
Biological Unit 4 (1x):       GH

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
182O4Ligand/Ion(3R,4R)-4-[4-CYCLOPROPYL-5-[3-(2-METHYLPROPYL)CYCLOBUTYL]-1,2,4-TRIAZOL-3-YL]-N-(2,4-DIMETHYLPHENYL)-1-ETHANOYL-PYRROLIDINE-3-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
182O1Ligand/Ion(3R,4R)-4-[4-CYCLOPROPYL-5-[3-(2-METHYLPROPYL)CYCLOBUTYL]-1,2,4-TRIAZOL-3-YL]-N-(2,4-DIMETHYLPHENYL)-1-ETHANOYL-PYRROLIDINE-3-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
182O1Ligand/Ion(3R,4R)-4-[4-CYCLOPROPYL-5-[3-(2-METHYLPROPYL)CYCLOBUTYL]-1,2,4-TRIAZOL-3-YL]-N-(2,4-DIMETHYLPHENYL)-1-ETHANOYL-PYRROLIDINE-3-CARBOXAMIDE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
182O1Ligand/Ion(3R,4R)-4-[4-CYCLOPROPYL-5-[3-(2-METHYLPROPYL)CYCLOBUTYL]-1,2,4-TRIAZOL-3-YL]-N-(2,4-DIMETHYLPHENYL)-1-ETHANOYL-PYRROLIDINE-3-CARBOXAMIDE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
182O1Ligand/Ion(3R,4R)-4-[4-CYCLOPROPYL-5-[3-(2-METHYLPROPYL)CYCLOBUTYL]-1,2,4-TRIAZOL-3-YL]-N-(2,4-DIMETHYLPHENYL)-1-ETHANOYL-PYRROLIDINE-3-CARBOXAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:286 , HIS A:323 , ALA A:327 , VAL A:361 , MET A:365 , ALA A:368 , VAL A:376 , PHE A:377 , PHE A:378 , PHE A:388 , PHE A:401binding site for residue 82O A 9000
2AC2SOFTWAREGLN C:286 , LEU C:287 , HIS C:323 , ALA C:327 , MET C:365 , ALA C:368 , VAL C:376 , PHE C:377 , ILE C:397 , ILE C:400binding site for residue 82O C 9000
3AC3SOFTWAREHIS E:323 , ALA E:327 , MET E:365 , ALA E:368 , VAL E:376 , PHE E:377 , PHE E:378 , HOH E:9104binding site for residue 82O E 9000
4AC4SOFTWAREGLN G:286 , HIS G:323 , ALA G:327 , MET G:365 , ALA G:368 , VAL G:376 , PHE G:377 , PHE G:378 , PHE G:401binding site for residue 82O G 9000

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5X8X)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5X8X)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5X8X)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5X8X)

(-) Exons   (0, 0)

(no "Exon" information available for 5X8X)

(-) 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:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8x A  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain B from PDB  Type:PROTEIN  Length:13
                                              
               SCOP domains ------------- SCOP domains
               CATH domains ------------- CATH domains
               Pfam domains ------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) ------------- SAPs(SNPs)
                    PROSITE ------------- PROSITE
                 Transcript ------------- Transcript
                5x8x B 2347 NMGLEAIIRKALM 2359
                                  2356   


Chain C from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8x C  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain D from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                5x8x D 2346 TNMGLEAIIRKALMG 2360
                                  2355     


Chain E from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                     
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                5x8x E  266 SLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLHPIV  493
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485        


Chain F from PDB  Type:PROTEIN  Length:14
                                               
               SCOP domains -------------- SCOP domains
               CATH domains -------------- CATH domains
               Pfam domains -------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------- SAPs(SNPs)
                    PROSITE -------------- PROSITE
                 Transcript -------------- Transcript
                5x8x F 2346 TNMGLEAIIRKALM 2359
                                  2355    


Chain G from PDB  Type:PROTEIN  Length:224
                                                                                                                                                                                                                                                                 
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhhh..ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhhhhhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                5x8x G  267 LTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPAGKLASLCSQHVERLQIFQHLH  490
                                   276       286       296       306       316       326       336       346       356       366       376       386       396       406       416       426       436       446       456       466       476       486    


Chain H from PDB  Type:PROTEIN  Length:15
                                                
               SCOP domains --------------- SCOP domains
               CATH domains --------------- CATH domains
               Pfam domains --------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------- SAPs(SNPs)
                    PROSITE --------------- PROSITE
                 Transcript --------------- Transcript
                5x8x H 2346 TNMGLEAIIRKALMG 2360
                                  2355
   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 5X8X)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5X8X)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5X8X)

(-) Gene Ontology  (35, 39)

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  NCOR2_HUMAN | Q9Y618
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 Related Entries

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

UniProtKB/Swiss-Prot
        G1RH57_NOMLE | G1RH57: 5x8s 5x8u 5x8w
        NCOR2_HUMAN | Q9Y618: 1kkq 1r2b 1xc5 2gpv 2l5g 2ltp 2odd 2rt5 3r29 3r2a 4a69 4oar 5x8q

(-) Related Entries Specified in the PDB File

5x8q 5x8s 5x8u 5x8w