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(-) Description

Title :  THE PROTAC MZ1 IN COMPLEX WITH THE SECOND BROMODOMAIN OF BRD4 AND PVHL:ELONGINC:ELONGINB
 
Authors :  M. S. Gadd, M. Zengerle, A. Ciulli
Date :  24 Aug 16  (Deposition) - 08 Mar 17  (Release) - 26 Apr 17  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.70
Chains :  Asym. Unit :  A,B,C,D,E,F,G,H
Biol. Unit 1:  A,B,C,D  (1x)
Biol. Unit 2:  E,F,G,H  (1x)
Keywords :  Protac Complex, Targeted Degradation, Chromatin Reader, Ubiquitin Ligase, Bifunctional Ligand, Ligase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Gadd, A. Testa, X. Lucas, K. H. Chan, W. Chen, D. J. Lamont, M. Zengerle, A. Ciulli
Structural Basis Of Protac Cooperative Recognition For Selective Protein Degradation.
Nat. Chem. Biol. V. 13 514 2017
PubMed-ID: 28288108  |  Reference-DOI: 10.1038/NCHEMBIO.2329

(-) Compounds

Molecule 1 - BROMODOMAIN-CONTAINING PROTEIN 4
    Chains: A, E
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PNIC28
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: BRD4, HUNK1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN HUNK1
 
Molecule 2 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 2
    Chains: B, F
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCDFDUET-1
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TCEB2
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ELONGIN 18 KDA SUBUNIT,ELONGIN-B,ELOB,RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT B,SIII P18
 
Molecule 3 - TRANSCRIPTION ELONGATION FACTOR B POLYPEPTIDE 1
    Chains: C, G
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PCDFDUET-1
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: TCEB1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: ELONGIN 15 KDA SUBUNIT,ELONGIN-C,ELOC,RNA POLYMERASE II TRANSCRIPTION FACTOR SIII SUBUNIT C,SIII P15
 
Molecule 4 - VON HIPPEL-LINDAU DISEASE TUMOR SUPPRESSOR
    Chains: D, H
    Engineered: YES
    Expression System: ESCHERICHIA COLI BL21(DE3)
    Expression System Plasmid: PHAT4
    Expression System Taxid: 469008
    Expression System Vector Type: PLASMID
    Gene: VHL
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: PROTEIN G7,PVHL

 Structural Features

(-) Chains, Units

  12345678
Asymmetric Unit : ABCDEFGH
Biological Unit 1 (1x): ABCD    
Biological Unit 2 (1x):     EFGH

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (1, 2)

Asymmetric Unit (1, 2)
No.NameCountTypeFull Name
17592Ligand/Ion(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-CHLOROPHENYL)-4,5,13-TRIMETHYL-3-THIA-1,8,11,12-TETRAZATRICYCLO[8.3.0.0^{2,6}]TRIDECA-2(6),4,7,10,12-PENTAEN-9-YL]ETHANOYLAMINO]ETHOXY]ETHOXY]ETHOXY]ETHANOYLAMINO]-3,3-DIMETHYL-BUTANOYL]-~{N}-[[4-(4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL)PHENYL]METHYL]-4-OXIDANYL-PYRROLIDINE-2-CARBOXAMIDE
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
17591Ligand/Ion(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-CHLOROPHENYL)-4,5,13-TRIMETHYL-3-THIA-1,8,11,12-TETRAZATRICYCLO[8.3.0.0^{2,6}]TRIDECA-2(6),4,7,10,12-PENTAEN-9-YL]ETHANOYLAMINO]ETHOXY]ETHOXY]ETHOXY]ETHANOYLAMINO]-3,3-DIMETHYL-BUTANOYL]-~{N}-[[4-(4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL)PHENYL]METHYL]-4-OXIDANYL-PYRROLIDINE-2-CARBOXAMIDE
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
17591Ligand/Ion(2~{S},4~{R})-1-[(2~{S})-2-[2-[2-[2-[2-[2-[(9~{S})-7-(4-CHLOROPHENYL)-4,5,13-TRIMETHYL-3-THIA-1,8,11,12-TETRAZATRICYCLO[8.3.0.0^{2,6}]TRIDECA-2(6),4,7,10,12-PENTAEN-9-YL]ETHANOYLAMINO]ETHOXY]ETHOXY]ETHOXY]ETHANOYLAMINO]-3,3-DIMETHYL-BUTANOYL]-~{N}-[[4-(4-METHYL-2,3-DIHYDRO-1,3-THIAZOL-5-YL)PHENYL]METHYL]-4-OXIDANYL-PYRROLIDINE-2-CARBOXAMIDE

(-) Sites  (2, 2)

Asymmetric Unit (2, 2)
No.NameEvidenceResiduesDescription
1AC1SOFTWARETRP A:374 , PRO A:375 , ALA A:384 , LEU A:385 , LEU A:387 , ASN A:433 , HIS A:437 , GLU A:438 , VAL A:439 , HOH A:504 , HOH A:507 , TRP D:88 , TYR D:98 , PRO D:99 , ARG D:107 , ILE D:109 , HIS D:110 , SER D:111 , TYR D:112 , HIS D:115 , TRP D:117 , HOH D:404 , HOH D:410 , HOH D:416binding site for residue 759 D 301
2AC2SOFTWARETRP E:374 , PRO E:375 , LEU E:385 , ASN E:433 , HIS E:437 , GLU E:438 , VAL E:439 , HOH E:507 , TRP H:88 , PHE H:91 , TYR H:98 , PRO H:99 , ARG H:107 , ILE H:109 , HIS H:110 , SER H:111 , TYR H:112 , HIS H:115 , TRP H:117 , HOH H:405 , HOH H:407binding site for residue 759 H 301

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5T35)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5T35)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 5T35)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 5T35)

(-) Exons   (0, 0)

(no "Exon" information available for 5T35)

(-) 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:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author hhhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5t35 A 349 KVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD 459
                                   358       368       378       388       398       408       418       428       438       448       458 


Chain B from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh...........eeeeeeeee..ee..............hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5t35 B   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain C from PDB  Type:PROTEIN  Length:87
                                                                                                                       
               SCOP domains --------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeehhhhh.hhhhhhhhh.eee....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------- Transcript
                 5t35 C  16 MMYVKLISSDGHEFIVKREHALTSGTIKAMLSNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    25        35        45 ||     65        75        85        95       105       
                                                          47|                                                      
                                                           58                                                      


Chain D from PDB  Type:PROTEIN  Length:149
                                                                                                                                                                                     
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.....eeeeee.....eee........eeeeeee...eeeeee.......ee................eeeeee....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t35 D  61 PVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIAHQ 209
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200         


Chain E from PDB  Type:PROTEIN  Length:111
                                                                                                                                               
               SCOP domains --------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .hhhhhhhhhhhhhhhhhhhhhhhhhhhh...hhhhhh..hhhhhh....hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------- Transcript
                 5t35 E 349 KVSEQLKCCSGILKEMFAKKHAAYAWPFYKPVDVEALGLHDYCDIIKHPMDMSTIKSKLEAREYRDAQEFGADVRLMFSNCYKYNPPDHEVVAMARKLQDVFEMRFAKMPD 459
                                   358       368       378       388       398       408       418       428       438       448       458 


Chain F from PDB  Type:PROTEIN  Length:104
                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author .eeeeeeee..eeeeeeee...hhhhhhhhhhhhhh.hhh.eeeee..ee.....hhhhhh...........eeeeeeeee..ee..............hhhhh Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------- Transcript
                 5t35 F   1 MDVFLMIRRHKTTIFTDAKESSTVFELKRIVEGILKRPPDEQRLYKDDQLLDDGKTLGECGFTSQTARPQAPATVGLAFRADDTFEALCIEPFSSPPELPDVMK 104
                                    10        20        30        40        50        60        70        80        90       100    


Chain G from PDB  Type:PROTEIN  Length:88
                                                                                                                        
               SCOP domains ---------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eeeee.....eeeeehhhhh.hhhhhhhhh..eee....hhhhhhhhhhhhhhhhhhh...........hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------- Transcript
                 5t35 G  16 MMYVKLISSDGHEFIVKREHALTSGTIKAMLSGNEVNFREIPSHVLSKVCMYFTYKVRYTNSSTEIPEFPIAPEIALELLMAANFLDC 112
                                    25        35        45  ||    64        74        84        94       104        
                                                           48|                                                      
                                                            58                                                      


Chain H from PDB  Type:PROTEIN  Length:147
                                                                                                                                                                                   
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..........eeeeeeee.....eeeeee.....eee........eeeeeee...eeeeee.......ee................eeeeee....hhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhh..hhhhhhhhhhhhhhh Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5t35 H  61 PVLRSVNSREPSQVIFCNRSPRVVLPVWLNFDGEPQPYPTLPPGTGRRIHSYRGHLWLFRDAGTHDGLLVNQTELFVPSLNVDGQPIFANITLPVYTLKERCLQVVRSLVKPENYRRLDIVRSLYEDLEDHPNVQKDLERLTQERIA 207
                                    70        80        90       100       110       120       130       140       150       160       170       180       190       200
   Legend:   → Mismatch (orange background)
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  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 5T35)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5T35)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5T35)

(-) Gene Ontology  (53, 80)

Asymmetric Unit(hide GO term definitions)

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  5t35
    Family and Domain Information: ProDom | SYSTERS
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  BRD4_HUMAN | O60885
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  ELOB_HUMAN | Q15370
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  ELOC_HUMAN | Q15369
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  VHL_HUMAN | P40337
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 Related Entries

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

UniProtKB/Swiss-Prot
        BRD4_HUMAN | O60885: 2i8n 2lsp 2mjv 2n3k 2ncz 2nd0 2nd1 2nnu 2oss 2ouo 2yel 2yem 3mxf 3p5o 3svf 3svg 3u5j 3u5k 3u5l 3uvw 3uvx 3uvy 3uw9 3zyu 4a9l 4bjx 4bw1 4bw2 4bw3 4bw4 4c66 4c67 4cfk 4cfl 4cl9 4clb 4don 4e96 4f3i 4gpj 4hbv 4hbw 4hbx 4hby 4hxk 4hxl 4hxm 4hxn 4hxo 4hxp 4hxr 4hxs 4ioo 4ioq 4ior 4j0r 4j0s 4j3i 4kv1 4kv4 4lr6 4lrg 4lyi 4lys 4lyw 4lzr 4lzs 4men 4meo 4mep 4meq 4mr3 4mr4 4nqm 4nr8 4nuc 4nud 4nue 4o70 4o71 4o72 4o74 4o75 4o76 4o77 4o78 4o7a 4o7b 4o7c 4o7e 4o7f 4ogi 4ogj 4pce 4pci 4ps5 4qb3 4qr3 4qr4 4qr5 4qzs 4uix 4uiy 4uiz 4uyd 4whw 4wiv 4x2i 4xy9 4xya 4yh3 4yh4 4z1q 4z1s 4z93 4zc9 4zw1 5a5s 5a85 5acy 5ad2 5ad3 5bt4 5cfw 5coi 5cp5 5cpe 5cqt 5crm 5crz 5cs8 5ctl 5cy9 5d0c 5d24 5d25 5d26 5d3h 5d3j 5d3l 5d3n 5d3p 5d3r 5d3s 5d3t 5dlx 5dlz 5dw2 5dx4 5e0r 5egu 5ei4 5eis 5f5z 5f60 5f61 5f62 5f63 5fbx 5h21 5hcl 5hls 5hm0 5hq5 5hq6 5hq7 5i80 5i88 5igk 5jwm 5khm 5ku3 5lj1 5lj2 5luu 5u28 5u2c 5u2e 5u2f 5ueo 5uep 5ueq 5uer 5ues 5uet 5ueu 5uev 5uex 5uey 5uez 5uf0 5ula 5uoo 5uvs 5uvt 5uvu 5uvv 5uvw 5uvx 5uvy 5uvz 5wuu
        ELOB_HUMAN | Q15370: 1lm8 1lqb 1vcb 2c9w 2izv 2jz3 2ma9 3dcg 3zkj 3zng 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4n9f 4w9c 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5bo4 5lli 5n4w
        ELOC_HUMAN | Q15369: 1lm8 1lqb 1vcb 2c9w 2izv 2ma9 3dcg 3zkj 3zng 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4n9f 4w9c 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5bo4 5lli 5n4w
        VHL_HUMAN | P40337: 1lm8 1lqb 1vcb 3zrc 3zrf 3ztc 3ztd 3zun 4ajy 4awj 4b95 4b9k 4bks 4bkt 4w9c 4w9d 4w9e 4w9f 4w9g 4w9h 4w9i 4w9j 4w9k 4w9l 4wqo 5lli 5n4w

(-) Related Entries Specified in the PDB File

(no "Related Entries Specified in the PDB File" available for 5T35)