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(-) Description

Title :  CRYSTAL STRUCTURE OF G305A 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 :  1.87
Chains :  Asym. Unit :  A,B
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Keywords :  Zinc Histone Deactylase, 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, 34)

Asymmetric Unit (4, 34)
No.NameCountTypeFull Name
1B3N2Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2EDO26Ligand/Ion1,2-ETHANEDIOL
3K4Ligand/IonPOTASSIUM ION
4ZN2Ligand/IonZINC ION
Biological Unit 1 (2, 15)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2EDO14Ligand/Ion1,2-ETHANEDIOL
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION
Biological Unit 2 (2, 13)
No.NameCountTypeFull Name
1B3N1Ligand/Ion4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2EDO12Ligand/Ion1,2-ETHANEDIOL
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (34, 34)

Asymmetric Unit (34, 34)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:178 , HIS A:180 , ASP A:267 , B3N 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:519 , HOH A:630binding site for residue K A 403
04AC4SOFTWAREHIS A:142 , HIS A:143 , PHE A:152 , ASP A:178 , HIS A:180 , ASP A:267 , GLY A:304 , TYR A:306 , ZN A:401 , EDO A:416 , HOH A:543 , ILE B:34 , PHE B:152 , PRO B:273 , TYR B:306 , B3N B:404binding site for residue B3N A 404
05AC5SOFTWAREPRO A:281 , VAL A:282 , TYR A:317 , LEU A:346 , GLU A:347 , ILE A:348 , HOH A:505 , HOH A:551binding site for residue EDO A 405
06AC6SOFTWAREALA A:188 , HOH A:528binding site for residue EDO A 406
07AC7SOFTWAREVAL A:61 , SER A:63 , HIS A:360 , GLN A:363 , HOH A:641binding site for residue EDO A 407
08AC8SOFTWARELYS A:132 , LEU A:292 , GLN A:295 , LEU A:296 , EDO A:412binding site for residue EDO A 408
09AC9SOFTWAREALA A:68 , PHE A:70 , HIS A:71 , HOH A:504 , HOH A:516binding site for residue EDO A 409
10AD1SOFTWARELYS A:374 , HIS A:375 , VAL A:376binding site for residue EDO A 410
11AD2SOFTWARETYR A:317 , THR A:326 , LEU A:327 , SER A:329 , GLU A:347 , HOH A:551 , HOH A:568binding site for residue EDO A 411
12AD3SOFTWAREGLN A:293 , VAL A:321 , ILE A:322 , EDO A:408 , HOH A:512binding site for residue EDO A 412
13AD4SOFTWAREPHE A:208 , PRO A:209 , GLY A:210 , HOH A:518binding site for residue EDO A 413
14AD5SOFTWAREGLN A:236 , ASP A:237 , THR A:280 , PRO A:350 , HOH A:502 , HOH A:525 , HOH A:586binding site for residue EDO A 414
15AD6SOFTWARETYR A:18 , ALA A:38 , VAL A:41 , HIS A:42 , SER A:138 , EDO A:418 , HOH A:511binding site for residue EDO A 415
16AD7SOFTWARETRP A:141 , HIS A:142 , GLY A:151 , CYS A:153 , GLY A:304 , TYR A:306 , B3N A:404 , HOH A:642binding site for residue EDO A 416
17AD8SOFTWARETRP A:141 , PHE A:152 , TYR A:154 , LEU A:155binding site for residue EDO A 417
18AD9SOFTWAREARG A:37 , ALA A:38 , TRP A:137 , SER A:138 , TRP A:315 , EDO A:415 , HOH A:501binding site for residue EDO A 418
19AE1SOFTWAREASP B:178 , HIS B:180 , ASP B:267 , B3N B:404binding site for residue ZN B 401
20AE2SOFTWAREASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200binding site for residue K B 402
21AE3SOFTWAREPHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:534 , HOH B:631binding site for residue K B 403
22AE4SOFTWARELYS A:33 , ILE A:34 , PRO A:273 , TYR A:306 , B3N A:404 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , ASP B:267 , GLY B:304 , TYR B:306 , ZN B:401 , HOH B:551 , HOH B:638binding site for residue B3N B 404
23AE5SOFTWAREALA B:188 , HOH B:509 , HOH B:559binding site for residue EDO B 405
24AE6SOFTWAREPRO B:230 , ILE B:231 , GLN B:232 , ASN B:357 , ARG B:361 , ILE B:362 , ILE B:365 , EDO B:407 , HOH B:511binding site for residue EDO B 406
25AE7SOFTWAREPHE B:203 , ASP B:213 , ARG B:361 , EDO B:406binding site for residue EDO B 407
26AE8SOFTWAREPHE B:207 , PHE B:208 , PRO B:209 , GLY B:210 , EDO B:415 , HOH B:503 , HOH B:627binding site for residue EDO B 408
27AE9SOFTWAREPRO B:281 , VAL B:282 , TYR B:317 , LEU B:346 , GLU B:347 , ILE B:348 , HOH B:524 , HOH B:588binding site for residue EDO B 409
28AF1SOFTWARECYS A:275 , ARG A:353 , LYS B:202 , SER B:204 , ASP B:233 , HOH B:518binding site for residue EDO B 410
29AF2SOFTWAREGLU B:65 , ALA B:68binding site for residue EDO B 411
30AF3SOFTWAREVAL B:214 , SER B:215 , TYR B:368 , ASN B:372binding site for residue EDO B 412
31AF4SOFTWARETYR B:111 , TRP B:141 , PHE B:152 , CYS B:153 , TYR B:154 , LEU B:155binding site for residue EDO B 413
32AF5SOFTWAREVAL B:133 , LEU B:292 , GLN B:295 , LEU B:296binding site for residue EDO B 414
33AF6SOFTWARESER B:150 , PHE B:208 , PRO B:209 , EDO B:408 , HOH B:510 , HOH B:578binding site for residue EDO B 415
34AF7SOFTWARETHR B:326binding site for residue EDO B 416

(-) SS Bonds  (0, 0)

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

(-) 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 5THV)

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5THV)

(-) 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:349
                                                                                                                                                                                                                                                                                                                                                                                             
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhhhh....hhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhh.hhhhhh...hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhhh...........hhhhhh................hhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5thv A  15 VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQDSIEYGLTEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGAYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHV 376
                                    24        34        44        54        64        74        84|     |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         
                                                                                                84|    98|                                                                                                                                                                                                                                                                               
                                                                                                 92    105                                                                                                                                                                                                                                                                               


Chain B from PDB  Type:PROTEIN  Length:347
                                                                                                                                                                                                                                                                                                                                                                                           
               SCOP domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..eee.hhhhhhhhh......hhhhhhhhhhhhh.hhhhheee.....hhhhhh...hhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh...eeeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5thv B  15 VPVYIYSPEYVSMCDSLAKIPKRASMVHSLIEAYALHKQMRIVKPKVASMEEMATFHTDAYLQHLQKVSQEYGLTEGIFDYAAAIGGATITAAQCLIDGMCKVAINWSGGWHHAKKDEASGFCYLNDAVLGILRLRRKFERILYVDLDLHHGDGVEDAFSFTSKVMTVSLHKFSPGFFPGTGDVSDVGLGKGRYYSVNVPIQDGIQDEKYYQICESVLKEVYQAFNPKAVVLQLGADTIAGDPMCSFNMTPVGIGKCLKYILQWQLATLILGGGAYNLANTARCWTYLTGVILGKTLSSEIPDHEFFTAYGPDYVLEITPSCRPDRNEPHRIQQILNYIKGNLKHVV 377
                                    24        34        44        54        64        74        84|| ||  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       
                                                                                                 85| ||                                                                                                                                                                                                                                                                                
                                                                                                  96 ||                                                                                                                                                                                                                                                                                
                                                                                                    98|                                                                                                                                                                                                                                                                                
                                                                                                    105
   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 5THV)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (26, 26)

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 Related Entries

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UniProtKB/Swiss-Prot
        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 5thu

(-) Related Entries Specified in the PDB File

5ths 5tht 5thu