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(-) Description

Title :  CRYSTAL STRUCTURE OF RETINOIC ACID RECEPTOR-RELATED ORPHAN RECEPTOR (ROR) GAMMA LIGAND BINDING DOMAIN COMPLEX WITH ML209
 
Authors :  P. Huang, F. Rastinejad, J. Lu
Date :  19 May 16  (Deposition) - 31 May 17  (Release) - 31 May 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.67
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Biol. Unit 4:  D  (1x)
Keywords :  Double Helix, Protein Binding (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. Huang, F. Rastinejad
Crystal Structure Of Retinoic Acid Receptor-Related Orphan Receptor (Ror) Gamma Ligand Binding Domain Complex With Ml209
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR ROR-GAMMA
    Chains: A, B, C, D
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28
    Expression System Strain: BL21-CODONPLUS(DE3)-RIL
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN
    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

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A   
Biological Unit 2 (1x):  B  
Biological Unit 3 (1x):   C 
Biological Unit 4 (1x):    D

Summary Information (see also Sequences/Alignments below)

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

Asymmetric Unit (1, 4)
No.NameCountTypeFull Name
16Q64Ligand/Ion(3S)-3-(2H-1,3-BENZODIOXOL-5-YL)-1-[(3R,5S)-3,5-DIMETHYLPIPERIDIN-1-YL]-3-(2-HYDROXY-4,6-DIMETHOXYPHENYL)PROPAN-1-ONE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
16Q61Ligand/Ion(3S)-3-(2H-1,3-BENZODIOXOL-5-YL)-1-[(3R,5S)-3,5-DIMETHYLPIPERIDIN-1-YL]-3-(2-HYDROXY-4,6-DIMETHOXYPHENYL)PROPAN-1-ONE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
16Q61Ligand/Ion(3S)-3-(2H-1,3-BENZODIOXOL-5-YL)-1-[(3R,5S)-3,5-DIMETHYLPIPERIDIN-1-YL]-3-(2-HYDROXY-4,6-DIMETHOXYPHENYL)PROPAN-1-ONE
Biological Unit 3 (1, 1)
No.NameCountTypeFull Name
16Q61Ligand/Ion(3S)-3-(2H-1,3-BENZODIOXOL-5-YL)-1-[(3R,5S)-3,5-DIMETHYLPIPERIDIN-1-YL]-3-(2-HYDROXY-4,6-DIMETHOXYPHENYL)PROPAN-1-ONE
Biological Unit 4 (1, 1)
No.NameCountTypeFull Name
16Q61Ligand/Ion(3S)-3-(2H-1,3-BENZODIOXOL-5-YL)-1-[(3R,5S)-3,5-DIMETHYLPIPERIDIN-1-YL]-3-(2-HYDROXY-4,6-DIMETHOXYPHENYL)PROPAN-1-ONE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREGLN A:286 , HIS A:323 , ALA A:327 , LEU A:362 , MET A:365 , PHE A:388 , ILE A:400 , HIS A:479binding site for residue 6Q6 A 600
2AC2SOFTWAREGLN B:286 , HIS B:323 , LEU B:324 , LEU B:362 , MET B:365 , VAL B:376 , PHE B:378 , PHE B:388 , ILE B:400 , HIS B:479binding site for residue 6Q6 B 600
3AC3SOFTWAREGLN C:286 , HIS C:323 , ALA C:327 , LEU C:362 , MET C:365 , PHE C:388 , ILE C:400 , HIS C:479binding site for residue 6Q6 C 600
4AC4SOFTWAREGLN D:286 , HIS D:323 , LEU D:324 , LEU D:362 , MET D:365 , PHE D:378 , PHE D:388 , HIS D:479binding site for residue 6Q6 D 600

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5K3N)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5K3N)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5K3N)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5K3N)

(-) Exons   (0, 0)

(no "Exon" information available for 5K3N)

(-) 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..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k3n A 265 ASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPI 492
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484        


Chain B from PDB  Type:PROTEIN  Length:226
                                                                                                                                                                                                                                                                  
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhh..hhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhh.......... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5k3n B 265 ASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLH 490
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484      


Chain C from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhh...ee....eeee..eee....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....hhhhhh...hhhhhhhhhhhhhhhh....... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k3n C 265 ASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPI 492
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484        


Chain D from PDB  Type:PROTEIN  Length:228
                                                                                                                                                                                                                                                                    
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhh...ee....eeee..eee.hhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhh......hhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5k3n D 265 ASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPI 492
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484
   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 5K3N)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5K3N)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5K3N)

(-) Gene Ontology  (37, 37)

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  RORG_HUMAN | P51449
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 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 5c4s 5c4t 5c4u 5ejv 5eth 5g42 5g43 5g44 5g45 5g46 5ixk 5iz0 5k38 5k3l 5k3m 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

5k38 5k3l 5k3m