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(-) Description

Title :  CRYSTAL STRUCTURE OF S39D HDAC8 IN COMPLEX WITH A LARGAZOLE ANALOGUE.
 
Authors :  C. Decroos, D. W. Christianson
Date :  22 Oct 14  (Deposition) - 08 Apr 15  (Release) - 22 Apr 15  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.18
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Metalloenzyme, Hydrolase, Histone Deacetylase, Enzyme Inhibitor Complex, Largazole Analogue, Thiol Inhibitor, Arginase/Deacetylase Fold, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  C. Decroos, D. J. Clausen, B. E. Haines, O. Wiest, R. M. Williams, D. W. Christianson
Variable Active Site Loop Conformations Accommodate The Binding Of Macrocyclic Largazole Analogues To Hdac8.
Biochemistry V. 54 2126 2015
PubMed-ID: 25793284  |  Reference-DOI: 10.1021/ACS.BIOCHEM.5B00010

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 8
    ChainsA, B
    EC Number3.5.1.98
    EngineeredYES
    Expression SystemESCHERICHIA COLI
    Expression System PlasmidPHD2-XA-HIS
    Expression System StrainBL21(DE3)
    Expression System Taxid469008
    Expression System Vector TypePLASMID
    FragmentS39D HDAC8
    GeneHDAC8, HDACL1, CDA07
    MutationYES
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHD8

 Structural Features

(-) Chains, Units

  12
Asymmetric Unit AB
Biological Unit 1 (1x)A 
Biological Unit 2 (1x) B

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 10)

Asymmetric Unit (5, 10)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IMD1Ligand/IonIMIDAZOLE
3K4Ligand/IonPOTASSIUM ION
4L8G2Ligand/Ion(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,20,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
5ZN2Ligand/IonZINC ION
Biological Unit 1 (3, 3)
No.NameCountTypeFull Name
1GOL1Ligand/IonGLYCEROL
2IMD1Ligand/IonIMIDAZOLE
3K-1Ligand/IonPOTASSIUM ION
4L8G1Ligand/Ion(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,20,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
5ZN-1Ligand/IonZINC ION
Biological Unit 2 (1, 1)
No.NameCountTypeFull Name
1GOL-1Ligand/IonGLYCEROL
2IMD-1Ligand/IonIMIDAZOLE
3K-1Ligand/IonPOTASSIUM ION
4L8G1Ligand/Ion(5R,8S,11S)-5-METHYL-8-(PROPAN-2-YL)-11-[(1E)-4-SULFANYLBUT-1-EN-1-YL]-3-THIA-7,10,14,20,21-PENTAAZATRICYCLO[14.3.1.1~2,5~]HENICOSA-1(20),2(21),16,18-TETRAENE-6,9,13-TRIONE
5ZN-1Ligand/IonZINC ION

(-) Sites  (10, 10)

Asymmetric Unit (10, 10)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:178 , HIS A:180 , ASP A:267 , L8G A:404BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200BINDING SITE FOR RESIDUE K A 402
03AC3SOFTWAREPHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:501 , HOH A:503BINDING SITE FOR RESIDUE K A 403
04AC4SOFTWARETYR A:100 , HIS A:143 , PHE A:152 , HIS A:180 , PHE A:208 , TYR A:306 , ZN A:401 , IMD A:405 , HOH A:671 , HOH A:672 , HOH A:673 , LYS B:33 , PRO B:273 , TYR B:306BINDING SITE FOR RESIDUE L8G A 404
05AC5SOFTWAREPRO A:273 , L8G A:404 , MET B:274 , L8G B:404BINDING SITE FOR RESIDUE IMD A 405
06AC6SOFTWARELYS A:289 , TYR A:317 , GLY A:320 , LYS A:325 , HOH A:607BINDING SITE FOR RESIDUE GOL A 406
07AC7SOFTWAREASP B:178 , HIS B:180 , ASP B:267 , L8G B:404BINDING SITE FOR RESIDUE ZN B 401
08AC8SOFTWAREASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200BINDING SITE FOR RESIDUE K B 402
09AC9SOFTWAREPHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:501 , HOH B:503BINDING SITE FOR RESIDUE K B 403
10BC1SOFTWARELYS A:33 , PRO A:273 , TYR A:306 , IMD A:405 , LYS B:33 , HIS B:143 , PHE B:152 , HIS B:180 , PHE B:208 , ASP B:267 , TYR B:306 , ZN B:401 , HOH B:574 , HOH B:634BINDING SITE FOR RESIDUE L8G B 404

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 4RN1)

(-) Cis Peptide Bonds  (4, 4)

Asymmetric Unit
No.Residues
1Phe A:208 -Pro A:209
2Gly A:341 -Pro A:342
3Phe B:208 -Pro B:209
4Gly B:341 -Pro B:342

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 4RN1)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 4RN1)

(-) Exons   (0, 0)

(no "Exon" information available for 4RN1)

(-) 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:361
                                                                                                                                                                                                                                                                                                                                                                                                         
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhh................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rn1 A  14 LVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEGDDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVI 378
                                    23        33        43        53        63        73        83   ||   97       107       117       127       137       147       157       167       177       187       197       207       217       227       237       247       257       267       277       287       297       307       317       327       337       347       357       367       377 
                                                                                                    87|                                                                                                                                                                                                                                                                                              
                                                                                                     92                                                                                                                                                                                                                                                                                              

Chain B from PDB  Type:PROTEIN  Length:359
                                                                                                                                                                                                                                                                                                                                                                                                       
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eee.hhhhhhhhh......hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhh.................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4rn1 B  13 SLVPVYIYSPEYVSMCDSLAKIPKRADMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQDHPDSIEYGLGCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    22        32        42        52        62        72        82 ||     96  ||   108       118       128       138       148       158       168       178       188       198       208       218       228       238       248       258       268       278       288       298       308       318       328       338       348       358       368         
                                                                                                  84|        99|                                                                                                                                                                                                                                                                                   
                                                                                                   89        102                                                                                                                                                                                                                                                                                   

   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 4RN1)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 4RN1)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 4RN1)

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

UniProtKB/Swiss-Prot
        HDAC8_HUMAN | Q9BY411t64 1t67 1t69 1vkg 1w22 2v5w 2v5x 3ew8 3ewf 3ezp 3ezt 3f06 3f07 3f0r 3mz3 3mz4 3mz6 3mz7 3rqd 3sff 3sfh 4qa0 4qa1 4qa2 4qa3 4qa4 4qa5 4qa6 4qa7 4rn0 4rn2 5bwz 5d1b 5d1c 5d1d 5dc5 5dc6 5dc7 5dc8 5fcw 5ths 5tht 5thu 5thv

(-) Related Entries Specified in the PDB File

4rn0 4rn2