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(-) Description

Title :  CRYSTAL STRUCTURE OF HERA-LBD (Y537S) IN COMPLEX WITH BENZOPHENONE-2
 
Authors :  V. Delfosse, M. Grimaldi, W. Bourguet
Date :  28 Aug 13  (Deposition) - 03 Sep 14  (Release) - 17 Dec 14  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.15
Chains :  Asym./Biol. Unit :  A,B,F,G
Keywords :  Ligand-Binding Domain Of Nuclear Hormone Receptor, Hormone Receptor (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  V. Delfosse, M. Grimaldi, V. Cavailles, P. Balaguer, W. Bourguet
Structural And Functional Profiling Of Environmental Ligand For Estrogen Receptors.
Environ. Health Perspect. V. 122 1306 2014
PubMed-ID: 25260197  |  Reference-DOI: 10.1289/EHP.1408453

(-) Compounds

Molecule 1 - ESTROGEN RECEPTOR
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET32A
    Expression System Strain: BL21(DE3)
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Fragment: LIGAND BINDING DOMAIN (UNP RESIDUES 302-552)
    Gene: ESR, ESR1, NR3A1
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ER, ER-ALPHA, ESTRADIOL RECEPTOR, NUCLEAR RECEPTOR SUBFAMILY 3 GROUP A MEMBER 1
 
Molecule 2 - NUCLEAR RECEPTOR COACTIVATOR 1
    Chains: F, G
    Engineered: YES
    Fragment: COACTIVATOR PEPTIDE SRC-1 (UNP RESIDUES 686-698)
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: NCOA-1, CLASS E BASIC HELIX-LOOP-HELIX PROTEIN 74, BHLHE74, PROTEIN HIN-2, RIP160, RENAL CARCINOMA ANTIGEN NY-REN-52, STEROID RECEPTOR COACTIVATOR 1, SRC-1
    Synthetic: YES

 Structural Features

(-) Chains, Units

  1234
Asymmetric/Biological Unit : ABFG

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 12)

Asymmetric/Biological Unit (3, 12)
No.NameCountTypeFull Name
127M2Ligand/IonBIS(2,4-DIHYDROXYPHENYL)METHANONE
2CSO6Mod. Amino AcidS-HYDROXYCYSTEINE
3GOL4Ligand/IonGLYCEROL

(-) Sites  (6, 6)

Asymmetric Unit (6, 6)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELEU A:346 , LEU A:349 , ALA A:350 , GLU A:353 , MET A:388 , LEU A:391 , ILE A:424 , HIS A:524 , LEU A:525BINDING SITE FOR RESIDUE 27M A 601
2AC2SOFTWAREGLU A:323 , TRP A:393 , GLY A:442 , HOH A:749BINDING SITE FOR RESIDUE GOL A 602
3AC3SOFTWAREASN A:439 , GLN A:441 , GLU A:444 , ALA A:493 , LEU A:495BINDING SITE FOR RESIDUE GOL A 603
4AC4SOFTWARELEU B:346 , LEU B:349 , ALA B:350 , GLU B:353 , LEU B:391 , ILE B:424 , HIS B:524 , LEU B:525BINDING SITE FOR RESIDUE 27M B 601
5AC5SOFTWAREASN B:407 , LEU B:408 , LEU B:409 , GLN B:414BINDING SITE FOR RESIDUE GOL B 602
6AC6SOFTWAREGLN B:441 , GLU B:444 , ALA B:493 , ARG B:503BINDING SITE FOR RESIDUE GOL B 603

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

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

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4MGC)

(-) 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:238
                                                                                                                                                                                                                                                                              
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhh.............hhhhhhhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeee.hhhhhh.hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.......hhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mgc A 306 LALSLTADQMVSALLDAEPPILYSEYDPTRFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEcAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFKSLEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKcKNVVPLSDLLLEMLDAHRL 549
                                   315       325       335|      346       356       366       376    |  386       396       406       416|      426       436       446       456    || 471       481       491       501       511       521       531       541        
                                                       335|                                         381-CSO                             417-CSO                                     461|                                                            530-CSO               
                                                        337                                                                                                                          467                                                                                  


Chain B from PDB  Type:PROTEIN  Length:237
                                                                                                                                                                                                                                                                             
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhhhhhhhhh...............hhhhhhhhhhhhhhhhhhhhhhhhh........hhhhhhhhhhhhhhhhhhhhhhhhhh....eeeee..eeeehhhhh...hhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4mgc B 305 SLALSLTADQMVSALLDAEPPILYSEYDPTRPFSEASMMGLLTNLADRELVHMINWAKRVPGFVDLTLHDQVHLLEcAWLEILMIGLVWRSMEHPGKLLFAPNLLLDRNQGKcVEGMVEIFDMLLATSSRFRMMNLQGEEFVCLKSIILLNSGVYTFEEKDHIHRVLDKITDTLIHLMAKAGLTLQQQHQRLAQLLLILSHIRHMSNKGMEHLYSMKcKNVVPLSDLLLEMLDAHRL 549
                                   314       324       334       344       354       364       374      |384       394       404       414  |    424       434       444       454      |472       482       492       502       512       522       532       542       
                                                                                                      381-CSO                             417-CSO                                     461|                                                         530-CSO               
                                                                                                                                                                                       470                                                                               


Chain F 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
                 4mgc F 688 KILHRLLQE 696


Chain G from PDB  Type:PROTEIN  Length:9
                                         
               SCOP domains --------- SCOP domains
               CATH domains --------- CATH domains
               Pfam domains --------- Pfam domains
         Sec.struct. author .hhhhhh.. Sec.struct. author
                 SAPs(SNPs) --------- SAPs(SNPs)
                    PROSITE --------- PROSITE
                 Transcript --------- Transcript
                 4mgc G 688 KILHRLLQE 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 4MGC)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (139, 156)

Asymmetric/Biological Unit(hide GO term definitions)

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  NCOA1_HUMAN | Q15788
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 Related Entries

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

UniProtKB/Swiss-Prot
        ESR1_HUMAN | P03372: 1a52 1akf 1ere 1err 1g50 1gwq 1gwr 1hcp 1hcq 1l2i 1pcg 1qkt 1qku 1r5k 1sj0 1uom 1x7e 1x7r 1xp1 1xp6 1xp9 1xpc 1xqc 1yim 1yin 1zky 2ayr 2b1v 2b1z 2b23 2bj4 2fai 2g44 2g5o 2i0j 2iog 2iok 2jf9 2jfa 2llo 2llq 2ocf 2ouz 2p15 2pog 2q6j 2q70 2qa6 2qa8 2qab 2qe4 2qgt 2qgw 2qh6 2qr9 2qse 2qxm 2qxs 2qzo 2r6w 2r6y 2yat 2yja 3cbm 3cbo 3cbp 3dt3 3erd 3ert 3hlv 3hm1 3l03 3os8 3os9 3osa 3q95 3q97 3uu7 3uua 3uuc 3uud 4aa6 4dma 4iu7 4iui 4iv2 4iv4 4ivw 4ivy 4iw6 4iw8 4iwc 4iwf 4jc3 4jdd 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgd 4o6f 4pp6 4ppp 4pps 4pxm 4q13 4q50 4tuz 4tv1 4xi3 4zn7 4zn9 4znh 4zns 4znt 4znu 4znv 4znw 5aau 5aav 5acc 5ak2 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 5egv 5ehj 5ei1 5eit 5fqp 5fqr 5fqs 5fqt 5fqv 5hyr 5jmm 5kcc 5kcd 5kce 5kcf 5kct 5kcu 5kcw 5kd9 5kr9 5kra 5krc 5krf 5krh 5kri 5krj 5krk 5krl 5krm 5kro 5n10 5t0x 5t92 5t97 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 5tn9 5tnb 5u2b 5u2d
        NCOA1_HUMAN | Q15788: 1fm6 1fm9 1k4w 1k74 1k7l 1kv6 1n4h 1nq7 1nrl 1p8d 1pzl 1rdt 1tfc 1u3r 1u3s 1x76 1x78 1x7b 1x7j 1xiu 1xv9 1xvp 1yy4 1yye 1zaf 2a3i 2c52 2fvj 2gtk 2hbh 2hc4 2hcd 2hfp 2npa 2nv7 2p54 2prg 3bej 3bqd 3ctb 3cwd 3dct 3dcu 3dr1 3et1 3et3 3fei 3fej 3fur 3fxv 3g8i 3g9e 3gyt 3gyu 3h0a 3hc5 3hc6 3hvl 3ipq 3ips 3ipu 3kmr 3lmp 3okh 3oki 3olf 3oll 3ols 3omk 3omm 3omo 3omp 3omq 3oof 3ook 3p88 3p89 3qt0 3rut 3ruu 3rvf 3s9s 3t03 3uu7 3uua 3uud 3v9y 3vn2 4dk7 4dk8 4dm6 4dm8 4dqm 4f9m 4fgy 4g1d 4g1y 4g1z 4g20 4g21 4g2h 4hee 4j5w 4j5x 4jyg 4jyh 4jyi 4mg5 4mg6 4mg7 4mg8 4mg9 4mga 4mgb 4mgd 4ruj 4rup 4tuz 4tv1 4uda 4udb 4y29 5a86 5avi 5avl 5azt 5dsh 5dv3 5dv6 5dv8 5dvc 5dwl 5e7v 5hjs 5ji0 5jmm 5l7e 5l7g 5l7h 5nma 5x8u 5x8w

(-) Related Entries Specified in the PDB File

3uu7 CRYSTAL STRUCTURE OF HERA-LBD (Y537S) IN COMPLEX WITH BISPHENOL-A
3uua CRYSTAL STRUCTURE OF HERA-LBD (Y537S) IN COMPLEX WITH BISPHENOL-AF
3uuc CRYSTAL STRUCTURE OF HERA-LBD (WT) IN COMPLEX WITH BISPHENOL-C
3uud CRYSTAL STRUCTURE OF HERA-LBD (Y537S) IN COMPLEX WITH ESTRADIOL
4mg5
4mg6
4mg7
4mg8
4mg9
4mga
4mgb
4mgd