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(-) Description

Title :  A-DNA DECAMER GCGTA(T23)TACGC WITH INCORPORATED 2'-METHOXY-3'-METHYLENEPHOSPHATE-THYMIDINE
 
Authors :  M. Egli, V. Tereshko, M. Teplova, G. Minasov, A. Joachimiak, R. Sanishvili, C. M. Weeks, R. Miller, M. A. Maier, H. An, P. Dan Cook, M. Manoharan
Date :  27 Dec 99  (Deposition) - 04 Apr 00  (Release) - 24 Feb 09  (Revision)
Method :  X-RAY DIFFRACTION
Resolution :  0.83
Chains :  Asym./Biol. Unit :  A,B
Keywords :  Modified A-Decamer At 0. 83 A Resolution, Deoxyribonucleic Acid, Dna (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )
 
Reference :  M. Egli, V. Tereshko, M. Teplova, G. Minasov, A. Joachimiak, R. Sanishvili, C. M. Weeks, R. Miller, M. A. Maier, H. An, P. Dan Cook, M. Manoharan
X-Ray Crystallographic Analysis Of The Hydration Of A- And B-Form Dna At Atomic Resolution.
Biopolymers V. 48 234 1998 (for further references see the PDB file header)

(-) Compounds

Molecule 1 - 5'-D(*GP*CP*GP*TP*AP*(T23)P*AP*CP*GP*C)-3'
    Chains: A, B
    Engineered: YES
    Synthetic: YES

 Structural Features

(-) Chains, Units

  12
Asymmetric/Biological Unit : AB

Summary Information (see also Sequences/Alignments below)

(-) Ligands, Modified Residues, Ions  (3, 6)

Asymmetric/Biological Unit (3, 6)
No.NameCountTypeFull Name
1MG2Ligand/IonMAGNESIUM ION
2SPM2Ligand/IonSPERMINE
3T232Mod. Nucleotide2'-O-METHYL-3'-METHYL-3'-DEOXY-ARABINOFURANOSYL-THYMINE-5'-PHOSPHATE

(-) Sites  (4, 4)

Asymmetric Unit (4, 4)
No.NameEvidenceResiduesDescription
1AC1SOFTWAREDG A:9 , HOH A:329 , HOH A:341 , HOH A:358 , HOH A:502 , DG B:13 , DT B:14 , DC B:18 , DG B:19 , HOH B:470 , HOH B:1222BINDING SITE FOR RESIDUE SPM B 221
2AC2SOFTWAREHOH A:336 , HOH A:442 , DG B:11 , DC B:18 , DG B:19 , DC B:20 , HOH B:362 , HOH B:367 , HOH B:449BINDING SITE FOR RESIDUE SPM B 222
3AC3SOFTWAREHOH A:302 , HOH A:305 , HOH A:306 , HOH A:307 , HOH B:303 , HOH B:304BINDING SITE FOR RESIDUE MG A 301
4AC4SOFTWAREHOH B:1302 , HOH B:1303 , HOH B:1304 , HOH B:1305 , HOH B:1306 , HOH B:1307BINDING SITE FOR RESIDUE MG B 1301

(-) SS Bonds  (0, 0)

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

(-) Cis Peptide Bonds  (0, 0)

(no "Cis Peptide Bond" information available for 1DPL)

 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 1DPL)

(-) Sequences/Alignments

Asymmetric/Biological Unit
   Reformat: Number of residues per line =  ('0' or empty: single-line sequence representation)
  Number of residues per labelling interval =   
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Chain A from PDB  Type:DNA/RNA  Length:10
                                         
                  1dpl A  1 GCGTAtACGC 10
                                 |  10
                                 6-T23


Chain B from PDB  Type:DNA/RNA  Length:10
                                         
                  1dpl B 11 GCGTAtACGC 20
                                 |  20
                                16-T23
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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 1DPL)

(-) CATH Domains  (0, 0)

(no "CATH Domain" information available for 1DPL)

(-) Pfam Domains  (0, 0)

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(-) Gene Ontology  (0, 0)

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