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(-) Description

Title :  CRYSTAL STRUCTURE OF AN HDAC HOMOLOG COMPLEXED WITH TRICHOSTATIN A
 
Authors :  M. S. Finnin, J. R. Donigian, N. P. Pavletich
Date :  28 Jul 99  (Deposition) - 15 Sep 99  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  2.00
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Alpha/Beta Fold, Hydroxamic Acid, Charge-Relay System, Penta-Coordinated Zinc, Lyase (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. S. Finnin, J. R. Donigian, A. Cohen, V. M. Richon, R. A. Rifkind, P. A. Marks, R. Breslow, N. P. Pavletich
Structures Of A Histone Deacetylase Homologue Bound To The Tsa And Saha Inhibitors.
Nature V. 401 188 1999
PubMed-ID: 10490031  |  Reference-DOI: 10.1038/43710
(for further references see the PDB file header)

(-) Compounds

Molecule 1 - HDLP (HISTONE DEACETYLASE-LIKE PROTEIN)
    Chains: A, B
    Engineered: YES
    Expression System: ESCHERICHIA COLI
    Expression System Plasmid: PGEX-4T3
    Expression System Taxid: 562
    Mutation: YES
    Organism Scientific: AQUIFEX AEOLICUS
    Organism Taxid: 63363

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (2, 4)

Asymmetric/Biological Unit (2, 4)
No.NameCountTypeFull Name
1TSN2Ligand/IonTRICHOSTATIN A
2ZN2Ligand/IonZINC ION

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASP A:168 , HIS A:170 , ASP A:258 , TSN A:502BINDING SITE FOR RESIDUE ZN A 501
2AC2SOFTWAREASP B:168 , HIS B:170 , ASP B:258 , TSN B:504BINDING SITE FOR RESIDUE ZN B 503
3AC3SOFTWAREASN A:20 , PRO A:22 , HIS A:131 , HIS A:132 , PHE A:141 , ASP A:168 , HIS A:170 , ASP A:258 , LEU A:265 , TYR A:297 , ZN A:501 , HOH A:707 , GLU B:195 , PHE B:200BINDING SITE FOR RESIDUE TSN A 502
4AC4SOFTWAREGLU A:195 , PHE A:200 , ASN B:20 , PRO B:22 , HIS B:131 , HIS B:132 , PHE B:141 , ASP B:168 , HIS B:170 , ASP B:258 , LEU B:265 , TYR B:297 , ZN B:503BINDING SITE FOR RESIDUE TSN B 504

(-) SS Bonds  (0, 0)

(no "SS Bond" information available for 1C3R)

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Phe A:198 -Pro A:199
2Phe B:198 -Pro B:199

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 1C3R)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 1C3R)

(-) Exons   (0, 0)

(no "Exon" information available for 1C3R)

(-) Sequences/Alignments

Asymmetric/Biological 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:372
 aligned with O67135_AQUAE | O67135 from UniProtKB/TrEMBL  Length:375

    Alignment length:372
                                    11        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  
         O67135_AQUAE     2 KKVKLIGTLDYGKYRYPKNHPLKIPRVSLLLRFLDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERCQCVPKGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINDPAVGIEYLRKKGFKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGGGGYHPYALARAWTLIWCELSGREVPEKLNNKAKELLKSIDFEEFDDEVDRSYMLETLKDPWRGGEVRKEVKDTLEKAKA 373
               SCOP domains d1c3ra_ A: HDAC homologue                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1c3rA00 A:2-373  [code=3.40.800.20, no name defined]                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhhh.....hhhhh.hhhhhhhhhhhh...hhh.eee....hhhhhh...hhhhhhhhhhhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhh..eeee...................hhhhhhhhhhhhh....eeeee.....hhhhhhhh.....eeeeeeee.................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhh.....eeeee................hhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...........hhhhhh...........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c3r A   2 KKVKLIGTLDYGKYRYPKNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERSQSVPKGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGGGGYHPYALARAWTLIWCELSGREVPEKLNNKAKELLKSIDFEEFDDEVDRSYMLETLKDPWRGGEVRKEVKDTLEKAKA 373
                                    11        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:372
 aligned with O67135_AQUAE | O67135 from UniProtKB/TrEMBL  Length:375

    Alignment length:372
                                    11        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  
         O67135_AQUAE     2 KKVKLIGTLDYGKYRYPKNHPLKIPRVSLLLRFLDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERCQCVPKGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINDPAVGIEYLRKKGFKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGGGGYHPYALARAWTLIWCELSGREVPEKLNNKAKELLKSIDFEEFDDEVDRSYMLETLKDPWRGGEVRKEVKDTLEKAKA 373
               SCOP domains d1c3rb_ B: HDAC homologue                                                                                                                                                                                                                                                                                                                                                            SCOP domains
               CATH domains 1c3rB00 B:2-373  [code=3.40.800.20, no name defined]                                                                                                                                                                                                                                                                                                                                 CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Pfam domains
         Sec.struct. author ..eeeeehhhhhhh.....hhhhh.hhhhhhhhhhhh...hhh.eee....hhhhhh...hhhhhhhhhhhhhhh....hhhhhhh............hhhhhhhhhhhhhhhhhhhh..eeee...................hhhhhhhhhhhhh....eeeee.....hhhhhhhh.....eeeeeeee.................hhhhh..eeeeee....hhhhhhhhhhhhhhhhhh.....eeeee................hhhhhhhhhhhhhhhhh..eee.....hhhhhhhhhhhhhhhhhh.......hhhhhhhhhh...........hhhhhh...........hhhhhhhhhhhh. Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 1c3r B   2 KKVKLIGTLDYGKYRYPKNHPLKIPRVSLLLRFKDAMNLIDEKELIKSRPATKEELLLFHTEDYINTLMEAERSQSVPKGAREKYNIGGYENPVSYAMFTGSSLATGSTVQAIEEFLKGNVAFNPAGGMHHAFKSRANGFCYINNPAVGIEYLRKKGFKRILYIDLDAHHCDGVQEAFYDTDQVFVLSLHQSPEYAFPFEKGFLEEIGEGKGKGYNLNIPLPKGLNDNEFLFALEKSLEIVKEVFEPEVYLLQLGTDPLLEDYLSKFNLSNVAFLKAFNIVREVFGEGVYLGGGGYHPYALARAWTLIWCELSGREVPEKLNNKAKELLKSIDFEEFDDEVDRSYMLETLKDPWRGGEVRKEVKDTLEKAKA 373
                                    11        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
   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  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a/b) (23833)

(-) CATH Domains  (1, 2)

Asymmetric/Biological Unit
(-)
Class: Alpha Beta (26913)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 1C3R)

(-) Gene Ontology  (1, 1)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A,B   (O67135_AQUAE | O67135)
molecular function
    GO:0046872    metal ion binding    Interacting selectively and non-covalently with any metal ion.

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 Related Entries

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        O67135_AQUAE | O67135: 1c3p 1c3s

(-) Related Entries Specified in the PDB File

1c3p 1c3s