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(-) Description

Title :  CRYSTAL STRUCTURE OF THE ORPHAN NUCLEAR RECEPTOR ROR(GAMMA)T LIGAND-BINDING DOMAIN IN COMPLEX WITH SMALL MOLECULE LIGAND
 
Authors :  Y. L. Ma, L. Q. Yang
Date :  06 Nov 13  (Deposition) - 11 Dec 13  (Release) - 11 Dec 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.01
Chains :  Asym. Unit :  A,B,C,D
Biol. Unit 1:  A,D  (1x)
Biol. Unit 2:  B,C  (1x)
Keywords :  Nuclear Receptor, Ligand Binding Domain, Transcription-Agonist Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  T. Yang, L. Qian, Y. B. Cheng, W. Cai, Y. L. Ma, L. Q. Yang, Q. Q. Wu, L. A. Orband-Miller, L. Zhou, M. Huxdorf, W. Zhang, J. Zhang, J. N. Xiang, S. Leung, Y. Qiu, Z. Zhong, J. D. Elliot, X. C. Lin, Y. H. Wang
Discovery Of Tertiary Amine And Indole Derivatives As Poten Ror-Gamma-T Inverse Agonists
Acs Med. Chem. Lett. 2013
PubMed: search  |  Reference-DOI: 10.1021/ML4003875

(-) Compounds

Molecule 1 - NUCLEAR RECEPTOR ROR-GAMMA
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Taxid: 562
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN, UNP RESIDUES 263-509
    Gene: NR1F3, RORC, 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, RETINOID-RELATED ORPHAN RECEPTOR-GAMMA
 
Molecule 2 - PEPTIDE FROM NUCLEAR RECEPTOR COACTIVATOR 2
    Chains: C, D
    Engineered: YES
    Fragment: UNP RESIDUES 684-697
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric Unit : ABCD
Biological Unit 1 (1x): A  D
Biological Unit 2 (1x):  BC 

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric Unit (2, 4)
No.NameCountTypeFull Name
1DMX2Ligand/Ion3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
2NBH2Ligand/IonN-(4-{[BENZYL(PROPYL)AMINO]METHYL}PHENYL)-2-[4-(ETHYLSULFONYL)PHENYL]ACETAMIDE
Biological Unit 1 (2, 2)
No.NameCountTypeFull Name
1DMX1Ligand/Ion3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
2NBH1Ligand/IonN-(4-{[BENZYL(PROPYL)AMINO]METHYL}PHENYL)-2-[4-(ETHYLSULFONYL)PHENYL]ACETAMIDE
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1DMX1Ligand/Ion3-[BENZYL(DIMETHYL)AMMONIO]PROPANE-1-SULFONATE
2NBH1Ligand/IonN-(4-{[BENZYL(PROPYL)AMINO]METHYL}PHENYL)-2-[4-(ETHYLSULFONYL)PHENYL]ACETAMIDE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:285 , GLN A:286 , LEU A:287 , TRP A:317 , CYS A:320 , HIS A:323 , ARG A:364 , MET A:365 , ARG A:367 , ALA A:368 , PHE A:377 , PHE A:378 , TYR A:502 , HOH A:735BINDING SITE FOR RESIDUE NBH A 601
2AC2SOFTWARETRP A:314 , HIS A:490 , PRO A:491 , ILE A:492 , VAL A:493 , GLU B:333BINDING SITE FOR RESIDUE DMX A 602
3AC3SOFTWARECYS B:285 , GLN B:286 , LEU B:287 , TRP B:317 , CYS B:320 , HIS B:323 , LEU B:324 , ARG B:364 , MET B:365 , ARG B:367 , ALA B:368 , PHE B:377 , PHE B:378 , PHE B:388 , ILE B:400 , TYR B:502 , HOH B:720BINDING SITE FOR RESIDUE NBH B 601
4AC4SOFTWAREGLU A:333 , TRP B:314 , LEU B:489 , HIS B:490 , PRO B:491 , ILE B:492 , VAL B:493BINDING SITE FOR RESIDUE DMX B 602

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4NIE)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 4NIE)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4NIE)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4NIE)

(-) Exons   (0, 0)

(no "Exon" information available for 4NIE)

(-) 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:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhh....hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nie A 264 YASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFST 508
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503     


Chain B from PDB  Type:PROTEIN  Length:245
                                                                                                                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhhhhhhh...ee....eeee..eeehhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4nie B 264 YASLTEIEHLVQSVCKSYRETCQLRLEDLLRQRSNIFSREEVTGYQRKSMWEMWERCAHHLTEAIQYVVEFAKRLSGFMELCQNDQIVLLKAGAMEVVLVRMCRAYNADNRTVFFEGKYGGMELFRALGCSELISSIFDFSHSLSALHFSEDEIALYTALVLINAHRPGLQEKRKVEQLQYNLELAFHHHLCKTHRQSILAKLPPKGKLRSLCSQHVERLQIFQHLHPIVVQAAFPPLYKELFST 508
                                   273       283       293       303       313       323       333       343       353       363       373       383       393       403       413       423       433       443       453       463       473       483       493       503     


Chain C from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4nie C 687 HKILHRLLQ 695


Chain D from PDB  Type:PROTEIN  Length:10
                                          
               SCOP domains ---------- SCOP domains
               CATH domains ---------- CATH domains
               Pfam domains ---------- Pfam domains
         Sec.struct. author .hhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------- SAPs(SNPs)
                    PROSITE ---------- PROSITE
                 Transcript ---------- Transcript
                 4nie D 687 HKILHRLLQD 696
                                   696
   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 4NIE)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4NIE)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4NIE)

(-) Gene Ontology  (81, 98)

Asymmetric Unit(hide GO term definitions)

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  4nie
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  NCOA2_HUMAN | Q15596
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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
        E7EWM1_HUMAN | E7EWM1: 4csj 5aph 5apj
        NCOA2_HUMAN | Q15596: 1gwq 1gwr 1m2z 1mv9 1mvc 1mzn 1p93 1t63 1t65 1uhl 1yok 1zdt 1zdu 1zky 2ao6 2b1v 2b1z 2b23 2fai 2g44 2g5o 2ldc 2p15 2p1t 2p1u 2p1v 2q7j 2q7l 2yjd 2zxz 2zy0 3a9e 3cld 3dzu 3dzy 3e00 3e7c 3e94 3erd 3fug 3gn8 3k22 3k23 3kwy 3kyt 3l0e 3l0j 3l0l 3o1d 3o1e 3oap 3ozj 3pcu 3plz 3q95 3q97 3r5m 3up0 3up3 4csj 4dos 4e2j 4fhh 4fhi 4ia1 4ia2 4ia3 4ia7 4iqr 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4k4j 4k6i 4m8e 4m8h 4nqa 4oc7 4p6w 4p6x 4pld 4ple 4poh 4poj 4pp3 4pp5 4pp6 4ppp 4pps 4pxm 4q0a 4qe6 4qe8 4rfw 4rmc 4rmd 4rme 4ruo 4udc 4udd 4wg0 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 4zo1 4zsh 5aph 5apj 5di7 5did 5die 5dig 5dk9 5dkb 5dke 5dkg 5dks 5dl4 5dlr 5dmc 5dmf 5dp0 5drj 5drm 5dtv 5du5 5due 5dug 5duh 5dvs 5dvv 5dwe 5dwg 5dwi 5dwj 5dx3 5dxb 5dxe 5dxg 5dxk 5dxm 5dxp 5dxq 5dxr 5dy8 5dyb 5dyd 5dz0 5dz1 5dz3 5dzh 5dzi 5e0w 5e0x 5e14 5e15 5e19 5e1c 5ec9 5egv 5ehj 5ei1 5eit 5g3j 5g42 5g43 5g44 5g45 5g46 5g5w 5h1e 5hyr 5i4v 5iaw 5ick 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5l11 5lga 5syz 5tld 5tlf 5tlg 5tll 5tlm 5tlo 5tlp 5tlt 5tlu 5tlv 5tlx 5tly 5tm1 5tm2 5tm3 5tm4 5tm5 5tm6 5tm7 5tm8 5tm9 5tml 5tmm 5tmo 5tmq 5tmr 5tms 5tmt 5tmu 5tmv 5tmw 5tmz 5tn1 5tn3 5tn4 5tn5 5tn6 5tn7 5tn8 5u2d
        RORG_HUMAN | P51449: 3b0w 3kyt 3l0j 3l0l 4nb6 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 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

(no "Related Entries Specified in the PDB File" available for 4NIE)