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(-) Description

Title :  HDAC1:MTA1 IN COMPLEX WITH INOSITOL-6-PHOSPHATE AND A NOVEL PEPTIDE INHIBITOR BASED ON HISTONE H4
 
Authors :  C. J. Millard, N. S. Robertson, P. J. Watson, A. G. Jameson, J. W. R. Schwa
Date :  23 Feb 16  (Deposition) - 11 May 16  (Release) - 11 May 16  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  3.30
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A,B,C  (2x)
Keywords :  Transcription Repression Inositol Phosphate Corepressor Histone Deacetylase Hdac1 Hdac3 Histones, Transcription, Metastasis Associated Protein, Ip6 (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  P. J. Watson, C. J. Millard, A. M. Riley, N. S. Robertson, L. C. Wright, H. Y. Godage, S. M. Cowley, A. G. Jamieson, B. V. Potter, J. W. Schwabe
Insights Into The Activation Mechanism Of Class I Hdac Complexes By Inositol Phosphates.
Nat Commun V. 7 11262 2016
PubMed-ID: 27109927  |  Reference-DOI: 10.1038/NCOMMS11262

(-) Compounds

Molecule 1 - METASTASIS-ASSOCIATED PROTEIN MTA1
    Chains: A
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Cell Line: HEK293F
    Expression System Plasmid: PCDNA3
    Expression System Taxid: 9606
    Gene: MTA1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
 
Molecule 2 - HISTONE DEACETYLASE 1
    Chains: B
    EC Number: 3.5.1.98
    Engineered: YES
    Expression System: HOMO SAPIENS
    Expression System Plasmid: PCDNA3
    Expression System Strain: HEK293F
    Expression System Taxid: 9606
    Gene: HDAC1, RPD3L1
    Organism Common: HUMAN
    Organism Scientific: HOMO SAPIENS
    Organism Taxid: 9606
    Synonym: HDAC1
 
Molecule 3 - GLY-ALA-6A0-ARG-HIS
    Chains: C
    Engineered: YES
    Expression System: SYNTHETIC CONSTRUCT
    Expression System Taxid: 32630
    Organism Scientific: SYNTHETIC CONSTRUCT
    Organism Taxid: 32630

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit : ABC
Biological Unit 1 (2x): ABC

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (4, 5)

Asymmetric Unit (4, 5)
No.NameCountTypeFull Name
16A01Mod. Amino Acid(2S)-2-AMINO-8-(HYDROXYAMINO)-8-OXOOCTANOIC ACID
2I6P1Ligand/IonINOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
3K2Ligand/IonPOTASSIUM ION
4ZN1Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
16A02Mod. Amino Acid(2S)-2-AMINO-8-(HYDROXYAMINO)-8-OXOOCTANOIC ACID
2I6P2Ligand/IonINOSITOL 1,2,3,4,5,6-HEXAKISPHOSPHATE
3K-1Ligand/IonPOTASSIUM ION
4ZN-1Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWARELYS A:305 , TYR A:327 , TYR A:328 , LYS A:331 , GLY B:27 , LYS B:31 , ARG B:270 , ILE B:305binding site for residue I6P A 401
2AC2SOFTWAREASP B:176 , HIS B:178 , ASP B:264 , 6A0 C:16binding site for residue ZN B 401
3AC3SOFTWAREASP B:174 , ASP B:176 , HIS B:178 , SER B:197 , PHE B:198binding site for residue K B 402
4AC4SOFTWAREPHE B:187 , THR B:190 , VAL B:193 , TYR B:222binding site for residue K B 403

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (1, 1)

Asymmetric Unit
No.Residues
1Phe B:205 -Pro B:206

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 5ICN)

(-) 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:168
                                                                                                                                                                                                        
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author .........................hhhh.eeeee......hhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh.hhhhhhhhh....hhhhhhhhhhhhh......... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 5icn A 165 GEIRVGNRYQADITDLLKEGEEDGRDQSRLETQVWEAHNPLTDKQIDQFLVVARSVGTFARALDSLHMSAAAASRDITLFHAMDTLHKNIYDISKAISALVPQGGPVLCRDEMEEWSASEANLFEEALEKYGKDFTDIQQDFLPWKSLTSIIEYYYMWKTTDRYVQQK 340
                                   174       184       194       204       214       224   ||  242       252       262       272       282       292       302       312       322       332        
                                                                                         228|                                                                                                       
                                                                                          237                                                                                                       


Chain B from PDB  Type:PROTEIN  Length:369
                                                                                                                                                                                                                                                                                                                                                                                                                 
               SCOP domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee.hhhhhh..........hhhhhhhhhhhhhh.hhhhheeeee...hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee................hhhhhhhhhhhhhhh...eeee.....hhhhhhhhhhhhhhhhh............hhhhh.................hhhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 5icn B   8 RRKVCYYYDGDVGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKANAEEMTKYHSDDYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVASAVKLNKQQTDIAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNYPLRDGIDDESYEAIFKPVMSKVMEMFQPSAVVLQCGSDSLSGDRLGCFNLTIKGHAKCVEFVKSFNLPMLMLGGGGYTIRNVARCWTYETAVALDTEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTNEYLEKIKQRLFENLRMLPHA 376
                                    17        27        37        47        57        67        77        87        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         


Chain C from PDB  Type:PROTEIN  Length:5
                                     
               SCOP domains ----- SCOP domains
               CATH domains ----- CATH domains
               Pfam domains ----- Pfam domains
         Sec.struct. author ..... Sec.struct. author
                 SAPs(SNPs) ----- SAPs(SNPs)
                    PROSITE ----- PROSITE
                 Transcript ----- Transcript
                 5icn C  14 GAxRH  18
                              |  
                             16-6A0
   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 5ICN)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (89, 102)

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  MTA1_HUMAN | Q13330
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 Related Entries

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

UniProtKB/Swiss-Prot
        HDAC1_HUMAN | Q13547: 1tyi 4bkx
        MTA1_HUMAN | Q13330: 4bkx 4pby 4pbz 4pc0 5fxy

(-) Related Entries Specified in the PDB File

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