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(-) Description

Title :  CRYSTAL STRUCTURE OF A LOW OCCUPANCY FRAGMENT CANDIDATE (N-(4-METHYL-1,3-THIAZOL-2-YL)PROPANAMIDE) BOUND ADJACENT TO THE UBIQUITIN BINDING POCKET OF THE HDAC6 ZINC-FINGER DOMAIN
 
Authors :  R. J. Harding, W. Tempel, P. Collins, N. Pearce, J. Brandao-Neto, A. Dou M. Ravichandran, M. Schapira, C. Bountra, A. M. Edwards, F. Von Delft V. Santhakumar, C. M. Arrowsmith, Structural Genomics Consortium
Date :  14 Jun 16  (Deposition) - 27 Jul 16  (Release) - 27 Jul 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.05
Chains :  Asym./Biol. Unit :  A
Keywords :  Histone Deacetylase, Hdac, Hdac6, Fragment Screening, Structural Genomics Consortium, Sgc, Diamond I04-1 Xchem, Pandda, Hydrolase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  R. J. Harding, W. Tempel, P. Collins, N. Pearce, J. Brandao-Neto, A. Douangamath, M. Ravichandran, M. Schapira, C. Bountra, A. M. Edwards, F. Von Delft, V. Santhakumar, C. M. Arrowsmith, Structural Genomics Consortium (Sgc)
Crystal Structure Of A Low Occupancy Fragment Candidate (N-(4-Methyl-1, 3-Thiazol-2-Yl)Propanamide) Bound Adjacent T The Ubiquitin Binding Pocket Of The Hdac6 Zinc-Finger Domai
To Be Published
PubMed: search

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 6
    Chains: A
    EC Number: 3.5.1.98
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PET28-LIC
    Expression System Strain: BL21 (DE3) CODON PLUS
    Expression System Taxid: 469008
    Gene: HDAC6, KIAA0901, JM21
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HD6

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (5, 43)

Asymmetric/Biological Unit (5, 43)
No.NameCountTypeFull Name
16T41Ligand/Ion~{N}-(4-METHYL-1,3-THIAZOL-2-YL)ETHANAMIDE
2FMT2Ligand/IonFORMIC ACID
3NA1Ligand/IonSODIUM ION
4UNX36Ligand/IonUNKNOWN ATOM OR ION
5ZN3Ligand/IonZINC ION

(-) Sites  (7, 7)

Asymmetric Unit (7, 7)
No.NameEvidenceResiduesDescription
1AC1SOFTWARECYS A:1145 , CYS A:1148 , HIS A:1164 , HIS A:1170binding site for residue ZN A 1301
2AC2SOFTWARECYS A:1133 , CYS A:1136 , CYS A:1153 , HIS A:1160binding site for residue ZN A 1302
3AC3SOFTWARECYS A:1113 , HIS A:1115 , CYS A:1183 , CYS A:1186binding site for residue ZN A 1303
4AC4SOFTWARETRP A:1143 , GLY A:1154 , ARG A:1155 , LEU A:1162 , TYR A:1184 , HOH A:1409 , HOH A:1417binding site for residue FMT A 1304
5AC5SOFTWARETRP A:1143 , TRP A:1182 , TYR A:1189 , 6T4 A:1306 , HOH A:1445binding site for residue FMT A 1305
6AC6SOFTWAREGLU A:1141 , ASN A:1142 , TRP A:1143 , SER A:1175 , ASP A:1178 , TYR A:1189 , ASN A:1200 , FMT A:1305binding site for residue 6T4 A 1306
7AC7SOFTWARETYR A:1156 , ILE A:1157 , HOH A:1449 , HOH A:1469 , HOH A:1470binding site for residue NA A 1343

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 5B8D)

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 5B8D)

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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(-) PROSITE Motifs  (0, 0)

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(-) Exons   (0, 0)

(no "Exon" information available for 5B8D)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
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Chain A from PDB  Type:PROTEIN  Length:100
                                                                                                                                     
               SCOP domains ---------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ---------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ---------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ......hhhhh......................eeee.....eee.....hhhhhhhhhhh..eeee.....eee....ee..hhhhhhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ---------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ---------------------------------------------------------------------------------------------------- Transcript
                5b8d A 1109 PLPWCPHLVAVCPIPAAGLDVTQPCGDCGTIQENWVCLSCYQVYCGRYINGHMLQHHGNSGHPLVLSYIDLSAWCYYCQAYVHHQALLDVKNIAHQNKFG 1208
                                  1118      1128      1138      1148      1158      1168      1178      1188      1198      1208
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  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 5B8D)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 5B8D)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 5B8D)

(-) Gene Ontology  (90, 90)

Asymmetric/Biological Unit(hide GO term definitions)

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 Related Entries

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        HDAC6_HUMAN | Q9UBN7: 3c5k 3gv4 3phd 5edu 5kh3 5kh7 5kh9

(-) Related Entries Specified in the PDB File

5kh3 5kh7 5kh9