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(-) Description

Title :  CRYSTAL STRUCTURE OF G304A HDAC8 IN COMPLEX WITH M344
 
Authors :  N. J. Porter, D. W. Christianson
Date :  30 Sep 16  (Deposition) - 21 Dec 16  (Release) - 21 Dec 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.95
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zinc Histone Deacetylase, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  N. J. Porter, N. H. Christianson, C. Decroos, D. W. Christianson
Structural And Functional Influence Of The Glycine-Rich Loo G302Gggy On The Catalytic Tyrosine Of Histone Deacetylase 8
Biochemistry V. 55 6718 2016
PubMed: search  |  Reference-DOI: 10.1021/ACS.BIOCHEM.6B01014

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 8
    Chains: A, B
    EC Number: 3.5.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET20B
    Expression System Strain: BL21 (DE3)
    Expression System Taxid: 562
    Gene: HDAC8, HDACL1, CDA07
    Mutation: YES
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD8

 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  (4, 9)

Asymmetric Unit (4, 9)
No.NameCountTypeFull Name
1B3N2Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2GGG1Ligand/IonGLYCYLGLYCYLGLYCINE
3K4Ligand/IonPOTASSIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (1, 1)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2GGG-1Ligand/IonGLYCYLGLYCYLGLYCINE
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 2)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2GGG1Ligand/IonGLYCYLGLYCYLGLYCINE
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (9, 9)

Asymmetric Unit (9, 9)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:178 , HIS A:180 , ASP A:267 , ALA A:304 , B3N A:404binding site for residue ZN A 401
2AC2SOFTWAREASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200binding site for residue K A 402
3AC3SOFTWAREPHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:529 , HOH A:630binding site for residue K A 403
4AC4SOFTWAREHIS A:142 , HIS A:143 , GLY A:151 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , ALA A:304 , TYR A:306 , ZN A:401 , HOH A:622 , PHE B:152 , PRO B:273 , MET B:274 , TYR B:306 , B3N B:404binding site for residue B3N A 404
5AC5SOFTWAREASP B:178 , HIS B:180 , ASP B:267 , ALA B:304 , B3N B:404binding site for residue ZN B 401
6AC6SOFTWAREASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200binding site for residue K B 402
7AC7SOFTWAREPHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:526 , HOH B:611binding site for residue K B 403
8AC8SOFTWAREPHE A:152 , PRO A:273 , MET A:274 , TYR A:306 , B3N A:404 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , ASP B:267 , ALA B:304 , TYR B:306 , ZN B:401 , HOH B:590binding site for residue B3N B 404
9AC9SOFTWAREGLU B:335 , PHE B:336 , THR B:338binding site for residue GGG B 405

(-) SS Bonds  (0, 0)

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

(-) 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 5THU)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5THU)

(-) 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:358
                                                                                                                                                                                                                                                                                                                                                                                                      
               SCOP domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhhh...hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhh..................hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhhh....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5thu A  14 LVPVYIYSPEYVSMCDSKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSDHPDSIEYGLGYDCPATEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGAGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVVI 378
                                    23      ||35        45        55        65        75       |90       100       110       120       130       140       150       160       170       180       190       200       210       220       230       240       250       260       270       280       290       300       310       320       330       340       350       360       370        
                                           30|                                                83|                                                                                                                                                                                                                                                                                                 
                                            33                                                 89                                                                                                                                                                                                                                                                                                 


Chain B from PDB  Type:PROTEIN  Length:344
                                                                                                                                                                                                                                                                                                                                                                                        
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eee.hhhhhhhhh..hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5thu B  14 LVPVYIYSPEYVSMCDSPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEYGLTEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGAGYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    23      ||37        47        57        67        77       |97||     113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       263       273       283       293       303       313       323       333       343       353       363       373    
                                           30|                                                85| ||                                                                                                                                                                                                                                                                                
                                            35                                                 96 ||                                                                                                                                                                                                                                                                                
                                                                                                 98|                                                                                                                                                                                                                                                                                
                                                                                                 105
   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 5THU)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

Asymmetric Unit(hide GO term definitions)

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  3.5.1.98
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        HDAC8_HUMAN | Q9BY41: 1t64 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 4rn1 4rn2 5bwz 5d1b 5d1c 5d1d 5dc5 5dc6 5dc7 5dc8 5fcw 5ths 5tht 5thv

(-) Related Entries Specified in the PDB File

5ths 5tht 5thv