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(-) Description

Title :  STRUCTURE OF HUMAN HDAC2 IN COMPLEX WITH SAHA (VORINOSTAT)
 
Authors :  R. Fong, P. J. Lupardus
Date :  30 Jul 13  (Deposition) - 21 Aug 13  (Release) - 02 Oct 13  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.85
Chains :  Asym. Unit :  A,B,C
Biol. Unit 1:  A  (1x)
Biol. Unit 2:  B  (1x)
Biol. Unit 3:  C  (1x)
Keywords :  Deacetylase, Histone, Hydrolase-Hydrolase Inhibitor Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google))
 
Reference :  B. E. Lauffer, R. Mintzer, R. Fong, S. Mukund, C. Tam, I. Zilberleyb, B. Flicke, A. Ritscher, G. Fedorowicz, R. Vallero, D. F. Ortwine, J. Gunzner, Z. Modrusan, L. Neumann, C. M. Koth, P. J. Lupardus, J. S. Kaminker, C. E. Heise, P. Steiner
Histone Deacetylase (Hdac) Inhibitor Kinetic Rate Constants Correlate With Cellular Histone Acetylation But Not Transcription And Cell Viability.
J. Biol. Chem. V. 288 26926 2013
PubMed-ID: 23897821  |  Reference-DOI: 10.1074/JBC.M113.490706

(-) Compounds

Molecule 1 - HISTONE DEACETYLASE 2
    ChainsA, B, C
    EC Number3.5.1.98
    EngineeredYES
    Expression SystemSPODOPTERA FRUGIPERDA
    Expression System Taxid7108
    FragmentCORE DOMAIN (UNP RESIDUES 8-376)
    GeneHDAC2
    Organism CommonHUMAN
    Organism ScientificHOMO SAPIENS
    Organism Taxid9606
    SynonymHD2

 Structural Features

(-) Chains, Units

  123
Asymmetric Unit ABC
Biological Unit 1 (1x)A  
Biological Unit 2 (1x) B 
Biological Unit 3 (1x)  C

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (6, 21)

Asymmetric Unit (6, 21)
No.NameCountTypeFull Name
1CA3Ligand/IonCALCIUM ION
2NA3Ligand/IonSODIUM ION
3NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4PG48Ligand/IonTETRAETHYLENE GLYCOL
5SHH3Ligand/IonOCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
6ZN3Ligand/IonZINC ION
Biological Unit 1 (2, 4)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3NHE-1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4PG43Ligand/IonTETRAETHYLENE GLYCOL
5SHH1Ligand/IonOCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
6ZN-1Ligand/IonZINC ION
Biological Unit 2 (3, 5)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3NHE1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4PG43Ligand/IonTETRAETHYLENE GLYCOL
5SHH1Ligand/IonOCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
6ZN-1Ligand/IonZINC ION
Biological Unit 3 (2, 3)
No.NameCountTypeFull Name
1CA-1Ligand/IonCALCIUM ION
2NA-1Ligand/IonSODIUM ION
3NHE-1Ligand/Ion2-[N-CYCLOHEXYLAMINO]ETHANE SULFONIC ACID
4PG42Ligand/IonTETRAETHYLENE GLYCOL
5SHH1Ligand/IonOCTANEDIOIC ACID HYDROXYAMIDE PHENYLAMIDE
6ZN-1Ligand/IonZINC ION

(-) Sites  (21, 21)

Asymmetric Unit (21, 21)
No.NameEvidenceResiduesDescription
01AC1SOFTWAREASP A:181 , HIS A:183 , ASP A:269 , SHH A:407BINDING SITE FOR RESIDUE ZN A 401
02AC2SOFTWAREASP A:179 , ASP A:181 , HIS A:183 , SER A:202 , PHE A:203BINDING SITE FOR RESIDUE CA A 402
03AC3SOFTWAREPHE A:192 , THR A:195 , VAL A:198 , TYR A:227 , HOH A:522 , HOH A:528BINDING SITE FOR RESIDUE NA A 403
04AC4SOFTWARELYS A:71 , ALA A:191BINDING SITE FOR RESIDUE PG4 A 404
05AC5SOFTWAREARG A:311 , GLU A:340 , TYR A:341 , GLY A:343BINDING SITE FOR RESIDUE PG4 A 405
06AC6SOFTWAREASP A:23 , ASN A:26 , TYR A:27 , ASP A:109 , HOH A:802BINDING SITE FOR RESIDUE PG4 A 406
07AC7SOFTWAREPRO A:34 , ASP A:104 , HIS A:145 , HIS A:146 , GLY A:154 , PHE A:155 , ASP A:181 , HIS A:183 , ASP A:269 , TYR A:308 , ZN A:401 , HOH A:606 , HOH A:791BINDING SITE FOR RESIDUE SHH A 407
08AC8SOFTWAREASP B:181 , HIS B:183 , ASP B:269 , SHH B:408BINDING SITE FOR RESIDUE ZN B 401
09AC9SOFTWAREASP B:179 , ASP B:181 , HIS B:183 , SER B:202 , PHE B:203BINDING SITE FOR RESIDUE CA B 402
10BC1SOFTWAREPHE B:192 , THR B:195 , VAL B:198 , TYR B:227 , HOH B:533 , HOH B:549BINDING SITE FOR RESIDUE NA B 403
11BC2SOFTWARETYR A:59 , LYS A:128 , ASP B:21 , ASP B:23 , ARG B:60 , LYS B:63 , GLU B:113BINDING SITE FOR RESIDUE NHE B 404
12BC3SOFTWAREARG B:311 , GLU B:340 , TYR B:341 , GLY B:343 , HOH B:835BINDING SITE FOR RESIDUE PG4 B 405
13BC4SOFTWARELYS B:284 , ASN B:331 , HIS B:349 , GLU C:67 , THR C:70BINDING SITE FOR RESIDUE PG4 B 406
14BC5SOFTWAREARG A:131 , ASP B:23 , ASN B:26 , TYR B:27 , ASP B:109 , GLU B:113BINDING SITE FOR RESIDUE PG4 B 407
15BC6SOFTWAREPRO B:34 , ASP B:104 , HIS B:145 , HIS B:146 , GLY B:154 , ASP B:181 , HIS B:183 , ASP B:269 , TYR B:308 , ZN B:401 , HOH B:671BINDING SITE FOR RESIDUE SHH B 408
16BC7SOFTWAREASP C:181 , HIS C:183 , ASP C:269 , SHH C:406BINDING SITE FOR RESIDUE ZN C 401
17BC8SOFTWAREASP C:179 , ASP C:181 , HIS C:183 , SER C:202 , PHE C:203BINDING SITE FOR RESIDUE CA C 402
18BC9SOFTWAREPHE C:192 , THR C:195 , VAL C:198 , TYR C:227 , HOH C:505 , HOH C:520BINDING SITE FOR RESIDUE NA C 403
19CC1SOFTWAREPRO B:344 , ASP B:345 , ALA C:191 , ARG C:197 , HOH C:540 , HOH C:627BINDING SITE FOR RESIDUE PG4 C 404
20CC2SOFTWAREASN B:354 , LEU C:169 , TYR C:171 , GLN C:173 , ARG C:197BINDING SITE FOR RESIDUE PG4 C 405
21CC3SOFTWAREPRO C:34 , ASP C:104 , HIS C:145 , HIS C:146 , GLY C:154 , ASP C:181 , HIS C:183 , ASP C:269 , TYR C:308 , HIS C:380 , ZN C:401 , HOH C:641 , HOH C:755BINDING SITE FOR RESIDUE SHH C 406

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (6, 6)

Asymmetric Unit
No.Residues
1Phe A:210 -Pro A:211
2Gly A:343 -Pro A:344
3Phe B:210 -Pro B:211
4Gly B:343 -Pro B:344
5Phe C:210 -Pro C:211
6Gly C:343 -Pro C:344

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

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

(-) PROSITE Motifs  (0, 0)

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

(-) Exons   (0, 0)

(no "Exon" information available for 4LXZ)

(-) 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:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....eeee...hhhhh.........hhhhhhhhhhhhhhhhhhh.eee.....hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxz A  12 GKKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLP 379
                                    21        31        41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311       321       331       341       351       361       371        

Chain B from PDB  Type:PROTEIN  Length:367
                                                                                                                                                                                                                                                                                                                                                                                                               
               SCOP domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhh.........hhhhhhhhhhhhhhhhhhhheee.....hhhhhh...hhhhhhhhhhhhhhhh..hhhhhhhh..........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhhh.. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxz B  13 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLP 379
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372       

Chain C from PDB  Type:PROTEIN  Length:368
                                                                                                                                                                                                                                                                                                                                                                                                                
               SCOP domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SCOP domains
               CATH domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeee...hhhhh.........hhhhhhhhhhhhhhhhhhh.eee.....hhhhhh...hhhhhhhhhhh...hhhhhhhhhhhhh.........hhhhhhhhhhhhhhhhhhhhhh....eeee...................hhhhhhhhhhh.....eeeee.....hhhhhhhh.....eeeeeeee...............hhhhh..eeeeee....hhhhhhhhhhhhhhhhhhhhh..eeeee.hhhhh..........hhhhhhhhhhhhhh....eeee.....hhhhhhhhhhhhhhhhh............hhhhhh................hhhhhhhhhhhhhhhhh.... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 4lxz C  13 KKKVCYYYDGDIGNYYYGQGHPMKPHRIRMTHNLLLNYGLYRKMEIYRPHKATAEEMTKYHSDEYIKFLRSIRPDNMSEYSKQMQRFNVGEDCPVFDGLFEFCQLSTGGSVAGAVKLNRQQTDMAVNWAGGLHHAKKSEASGFCYVNDIVLAILELLKYHQRVLYIDIDIHHGDGVEEAFYTTDRVMTVSFHKYGEYFPGTGDLRDIGAGKGKYYAVNFPMRDGIDDESYGQIFKPIISKVMEMYQPSAVVLQCGADSLSGDRLGCFNLTVKGHAKCVEVVKTFNLPLLMLGGGGYTIRNVARCWTYETAVALDCEIPNELPYNDYFEYFGPDFKLHISPSNMTNQNTPEYMEKIKQRLFENLRMLPH 380
                                    22        32        42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312       322       332       342       352       362       372        

   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 4LXZ)

(-) CATH Domains  (0, 0)

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

(-) Pfam Domains  (0, 0)

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

(-) Gene Ontology  (78, 78)

Asymmetric Unit(hide GO term definitions)

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 Related Entries

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

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        HDAC2_HUMAN | Q927693max 4ly1 5iwg 5ix0

(-) Related Entries Specified in the PDB File

4ly1