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(-) Description

Title :  THE 1.7A CRYSTAL STRUCTURE OF ACTIBIND A T2 RIBONUCLEASES AS ANTITUMORIGENIC AGENTS
 
Authors :  O. Almog, A. Gonzalez
Date :  07 Aug 11  (Deposition) - 22 Aug 12  (Release) - 22 Aug 12  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  1.80
Chains :  Asym./Biol. Unit :  A
Keywords :  Hydrolase, Ribonuclease (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. De Leeuw, A. Gonzalez, A. Lanir, L. Roiz, P. Smirnoff, B. Schwartz, O. Shoseyov, O. Almog
The 1. 8 A Crystal Structure Of Actibind Suggests A Mode Of Action For T2 Ribonucleases As Antitumorigenic Agents.
J. Med. Chem. V. 55 1013 2012
PubMed-ID: 22216760  |  Reference-DOI: 10.1021/JM1015507

(-) Compounds

Molecule 1 - ACTIBIND
    Chains: A
    Organism Scientific: ASPERGILLUS NIGER
    Organism Taxid: 5061

 Structural Features

(-) Chains, Units

  1
Asymmetric/Biological Unit : A

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 8)

Asymmetric/Biological Unit (3, 8)
No.NameCountTypeFull Name
1EDO3Ligand/Ion1,2-ETHANEDIOL
2NAG3Ligand/IonN-ACETYL-D-GLUCOSAMINE
3PO42Ligand/IonPHOSPHATE ION

(-) Sites  (8, 8)

Asymmetric Unit (8, 8)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREASN A:97 , SER A:100 , ALA A:104 , GLN A:156 , NAG A:302 , HOH A:439 , HOH A:440 , HOH A:490 , HOH A:538 , HOH A:610 , HOH A:617BINDING SITE FOR RESIDUE NAG A 301
2AC2SOFTWAREGLN A:156 , NAG A:301 , HOH A:440 , HOH A:462 , HOH A:476 , HOH A:648BINDING SITE FOR RESIDUE NAG A 302
3AC3SOFTWAREGLN A:37 , GLN A:105 , ASN A:106 , TYR A:154 , HOH A:596BINDING SITE FOR RESIDUE NAG A 303
4AC4SOFTWAREHIS A:74 , TRP A:77 , HIS A:133 , GLU A:134 , LYS A:137 , HIS A:138 , HOH A:410 , HOH A:506 , HOH A:578 , HOH A:612BINDING SITE FOR RESIDUE PO4 A 304
5AC5SOFTWAREGLU A:109 , LEU A:110 , TYR A:113 , GLN A:164 , LYS A:171 , TYR A:259 , HOH A:444 , HOH A:580BINDING SITE FOR RESIDUE PO4 A 305
6AC6SOFTWAREASP A:65 , GLY A:66 , LYS A:115 , GLU A:116 , HOH A:619 , HOH A:621BINDING SITE FOR RESIDUE EDO A 306
7AC7SOFTWARESER A:43 , CYS A:45 , ASP A:60 , ASP A:62 , PRO A:63 , HOH A:459 , HOH A:651BINDING SITE FOR RESIDUE EDO A 307
8AC8SOFTWARETHR A:24 , ILE A:25 , ASP A:161 , HOH A:402BINDING SITE FOR RESIDUE EDO A 308

(-) SS Bonds  (5, 5)

Asymmetric/Biological Unit
No.Residues
1A:28 -A:45
2A:36 -A:81
3A:44 -A:149
4A:89 -A:141
5A:214 -A:248

(-) Cis Peptide Bonds  (2, 2)

Asymmetric/Biological Unit
No.Residues
1Ser A:48 -Pro A:49
2Asp A:62 -Pro A:63

 Sequence-Structure Mapping

(-) SAPs(SNPs)/Variants  (0, 0)

(no "SAP(SNP)/Variant" information available for 3TBJ)

(-) PROSITE Motifs  (0, 0)

(no "PROSITE Motif" information available for 3TBJ)

(-) Exons   (0, 0)

(no "Exon" information available for 3TBJ)

(-) 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:237
 aligned with Q45U61_ASPNG | Q45U61 from UniProtKB/TrEMBL  Length:270

    Alignment length:237
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253       
         Q45U61_ASPNG    24 TIDTCSSDSPLSCQTDNEASCCFNSPGGSLLQTQFWDYDPSDGPSGSWTIHGLWPDNCDGTYQEYCDESREYSNITSILEAQNRTELLSYMKEYWPDYEGADEDESFWEHEWNKHGTCINTIEPSCYTDYYAQEEVGDFFQQVVDLFKTLDSYTALSDAGITPSEDATYKLSDIEDALAAIHDGYPPYVGCEDGALSQLYYYFNVKGSAIGGTYVASERLEDSNCKDSGIKYPPKYS 260
               SCOP domains d3tbja_ A: automated matches                                                                                                                                                                                                                  SCOP domains
               CATH domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............................eeeeeee.............eeeeeeee..........hhhhh..hhhhhhhhh.hhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhh.hhhhhhhh...........hhhhhhhhhhh.......eeeee..eeeeeeeeeeee......eeee..................... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 3tbj A  24 TIDTCSSDSPLSCQTDNEASCCFNSPGGSLLQTQFWDYDPSDGPSDSWTIHGLWPDNCDGTYQEYCDESREYSNITSILEAQNRTELLSYMKEYWPDYEGADEDESFWEHEWNKHGTCINTIEPSCYTDYYAQEEVGDFFQQVVDLFKTLDSYTALSDAGITPSEDATYKLSDIEDALAAIHDGYPPYVGCEDGALSQLYYYFNVKGSAIGGTYVASERLEDSNCKDSGIKYPPKYS 260
                                    33        43        53        63        73        83        93       103       113       123       133       143       153       163       173       183       193       203       213       223       233       243       253
   Legend:   → Mismatch (orange background)
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  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, 1)

Asymmetric/Biological Unit
(-)
Class: Alpha and beta proteins (a+b) (23004)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 3TBJ)

(-) Pfam Domains  (0, 0)

(no "Pfam Domain" information available for 3TBJ)

(-) Gene Ontology  (3, 3)

Asymmetric/Biological Unit(hide GO term definitions)
Chain A   (Q45U61_ASPNG | Q45U61)
molecular function
    GO:0003723    RNA binding    Interacting selectively and non-covalently with an RNA molecule or a portion thereof.
    GO:0033897    ribonuclease T2 activity    Catalysis of the two-stage endonucleolytic cleavage to nucleoside 3'-phosphates and 3'-phosphooligonucleotides with 2',3'-cyclic phosphate intermediates.
biological process
    GO:0090502    RNA phosphodiester bond hydrolysis, endonucleolytic    The chemical reactions and pathways involving the hydrolysis of internal 3',5'-phosphodiester bonds in one or two strands of ribonucleotides.

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 Related Entries

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UniProtKB/TrEMBL
        Q45U61_ASPNG | Q45U61: 3d3z

(-) Related Entries Specified in the PDB File

3d3z