data_1Y8V
# 
_entry.id   1Y8V 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.376 
_audit_conform.dict_location   http://mmcif.pdb.org/dictionaries/ascii/mmcif_pdbx.dic 
# 
loop_
_database_2.database_id 
_database_2.database_code 
_database_2.pdbx_database_accession 
_database_2.pdbx_DOI 
PDB   1Y8V         pdb_00001y8v 10.2210/pdb1y8v/pdb 
NDB   AD0042       ?            ?                   
RCSB  RCSB031262   ?            ?                   
WWPDB D_1000031262 ?            ?                   
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 1Y7F 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-[hydroxy(methyleneamino)oxy]ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y84 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(imidazolyl)ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y86 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(fluoro)ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y8L 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-[2-(trifluoro)ethyl] Thymidine (T*)
;
unspecified 
PDB 1Y9F 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-allyl Thymidine (T*)
;
unspecified 
PDB 1Y9S 
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propargyl Thymidine (T*)
;
unspecified 
PDB 1WV5 
;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL  THYMINE IN PLACE OF T6, MG-FORM
;
unspecified 
PDB 1WV6 
;X-RAY STRUCTURE OF THE A-DECAMER GCGTATACGC WITH A SINGLE 2'-O-BUTYL  THYMINE IN PLACE OF T6, SR-FORM
;
unspecified 
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        1Y8V 
_pdbx_database_status.recvd_initial_deposition_date   2004-12-13 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    RCSB 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.SG_entry                        . 
_pdbx_database_status.pdb_format_compatible           Y 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.status_code_cs                  ? 
_pdbx_database_status.status_code_nmr_data            ? 
_pdbx_database_status.methods_development_category    ? 
# 
loop_
_audit_author.name 
_audit_author.pdbx_ordinal 
'Egli, M.'      1  
'Minasov, G.'   2  
'Tereshko, V.'  3  
'Pallan, P.S.'  4  
'Teplova, M.'   5  
'Inamati, G.B.' 6  
'Lesnik, E.A.'  7  
'Owens, S.R.'   8  
'Ross, B.S.'    9  
'Prakash, T.P.' 10 
'Manoharan, M.' 11 
# 
_citation.id                        primary 
_citation.title                     
;Probing the Influence of Stereoelectronic Effects on the Biophysical Properties of Oligonucleotides: Comprehensive Analysis of the RNA Affinity, Nuclease Resistance, and Crystal Structure of Ten 2'-O-Ribonucleic Acid Modifications.
;
_citation.journal_abbrev            Biochemistry 
_citation.journal_volume            44 
_citation.page_first                9045 
_citation.page_last                 9057 
_citation.year                      2005 
_citation.journal_id_ASTM           BICHAW 
_citation.country                   US 
_citation.journal_id_ISSN           0006-2960 
_citation.journal_id_CSD            0033 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   15966728 
_citation.pdbx_database_id_DOI      10.1021/bi050574m 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Egli, M.'      1  ? 
primary 'Minasov, G.'   2  ? 
primary 'Tereshko, V.'  3  ? 
primary 'Pallan, P.S.'  4  ? 
primary 'Teplova, M.'   5  ? 
primary 'Inamati, G.B.' 6  ? 
primary 'Lesnik, E.A.'  7  ? 
primary 'Owens, S.R.'   8  ? 
primary 'Ross, B.S.'    9  ? 
primary 'Prakash, T.P.' 10 ? 
primary 'Manoharan, M.' 11 ? 
# 
_cell.entry_id           1Y8V 
_cell.length_a           24.831 
_cell.length_b           45.314 
_cell.length_c           45.682 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        90.00 
_cell.Z_PDB              8 
_cell.pdbx_unique_axis   ? 
# 
_symmetry.entry_id                         1Y8V 
_symmetry.space_group_name_H-M             'P 21 21 21' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                19 
_symmetry.space_group_name_Hall            ? 
# 
loop_
_entity.id 
_entity.type 
_entity.src_method 
_entity.pdbx_description 
_entity.formula_weight 
_entity.pdbx_number_of_molecules 
_entity.pdbx_ec 
_entity.pdbx_mutation 
_entity.pdbx_fragment 
_entity.details 
1 polymer syn "5'-D(*GP*CP*GP*TP*AP*(P2T)P*AP*CP*GP*C)-3'" 3103.085 2   ? ? ? ? 
2 water   nat water                                        18.015   119 ? ? ? ? 
# 
_entity_poly.entity_id                      1 
_entity_poly.type                           polydeoxyribonucleotide 
_entity_poly.nstd_linkage                   no 
_entity_poly.nstd_monomer                   yes 
_entity_poly.pdbx_seq_one_letter_code       '(DG)(DC)(DG)(DT)(DA)(P2T)(DA)(DC)(DG)(DC)' 
_entity_poly.pdbx_seq_one_letter_code_can   GCGTATACGC 
_entity_poly.pdbx_strand_id                 A,B 
_entity_poly.pdbx_target_identifier         ? 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1  DG  n 
1 2  DC  n 
1 3  DG  n 
1 4  DT  n 
1 5  DA  n 
1 6  P2T n 
1 7  DA  n 
1 8  DC  n 
1 9  DG  n 
1 10 DC  n 
# 
_struct_ref.id                         1 
_struct_ref.entity_id                  1 
_struct_ref.db_name                    PDB 
_struct_ref.db_code                    1Y8V 
_struct_ref.pdbx_db_accession          1Y8V 
_struct_ref.pdbx_db_isoform            ? 
_struct_ref.pdbx_seq_one_letter_code   ? 
_struct_ref.pdbx_align_begin           ? 
# 
loop_
_struct_ref_seq.align_id 
_struct_ref_seq.ref_id 
_struct_ref_seq.pdbx_PDB_id_code 
_struct_ref_seq.pdbx_strand_id 
_struct_ref_seq.seq_align_beg 
_struct_ref_seq.pdbx_seq_align_beg_ins_code 
_struct_ref_seq.seq_align_end 
_struct_ref_seq.pdbx_seq_align_end_ins_code 
_struct_ref_seq.pdbx_db_accession 
_struct_ref_seq.db_align_beg 
_struct_ref_seq.pdbx_db_align_beg_ins_code 
_struct_ref_seq.db_align_end 
_struct_ref_seq.pdbx_db_align_end_ins_code 
_struct_ref_seq.pdbx_auth_seq_align_beg 
_struct_ref_seq.pdbx_auth_seq_align_end 
1 1 1Y8V A 1 ? 10 ? 1Y8V 1  ? 10 ? 1  10 
2 1 1Y8V B 1 ? 10 ? 1Y8V 11 ? 20 ? 11 20 
# 
loop_
_chem_comp.id 
_chem_comp.type 
_chem_comp.mon_nstd_flag 
_chem_comp.name 
_chem_comp.pdbx_synonyms 
_chem_comp.formula 
_chem_comp.formula_weight 
DA  'DNA linking' y "2'-DEOXYADENOSINE-5'-MONOPHOSPHATE"    ? 'C10 H14 N5 O6 P' 331.222 
DC  'DNA linking' y "2'-DEOXYCYTIDINE-5'-MONOPHOSPHATE"     ? 'C9 H14 N3 O7 P'  307.197 
DG  'DNA linking' y "2'-DEOXYGUANOSINE-5'-MONOPHOSPHATE"    ? 'C10 H14 N5 O7 P' 347.221 
DT  'DNA linking' y "THYMIDINE-5'-MONOPHOSPHATE"            ? 'C10 H15 N2 O8 P' 322.208 
HOH non-polymer   . WATER                                   ? 'H2 O'            18.015  
P2T 'RNA linking' n 
;2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE
;
? 'C13 H21 N2 O9 P' 380.288 
# 
_exptl.entry_id          1Y8V 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      2.07 
_exptl_crystal.density_percent_sol   40.60 
_exptl_crystal.description           ? 
_exptl_crystal.F_000                 ? 
_exptl_crystal.preparation           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, HANGING DROP' 
_exptl_crystal_grow.temp            295 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              6.0 
_exptl_crystal_grow.pdbx_details    
'10%MPD, 40mM Na-Cacodilate, 12 mM Spermine, 80mM KCL, pH 6.0, VAPOR DIFFUSION, HANGING DROP, temperature 295K' 
_exptl_crystal_grow.pdbx_pH_range   . 
# 
loop_
_exptl_crystal_grow_comp.crystal_id 
_exptl_crystal_grow_comp.id 
_exptl_crystal_grow_comp.sol_id 
_exptl_crystal_grow_comp.name 
_exptl_crystal_grow_comp.volume 
_exptl_crystal_grow_comp.conc 
_exptl_crystal_grow_comp.details 
1 1 1 MPD           ? ? ? 
1 2 1 Na-Cacodilate ? ? ? 
1 3 1 Spermine      ? ? ? 
1 4 1 KCL           ? ? ? 
1 5 1 H2O           ? ? ? 
1 6 2 MPD           ? ? ? 
1 7 2 Na-Cacodilate ? ? ? 
1 8 2 KCL           ? ? ? 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           110 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               'IMAGE PLATE' 
_diffrn_detector.type                   'RIGAKU RAXIS IIC' 
_diffrn_detector.pdbx_collection_date   1998-06-10 
_diffrn_detector.details                Mirrors 
# 
_diffrn_radiation.diffrn_id                        1 
_diffrn_radiation.wavelength_id                    1 
_diffrn_radiation.pdbx_monochromatic_or_laue_m_l   M 
_diffrn_radiation.monochromator                    No 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.5418 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      'ROTATING ANODE' 
_diffrn_source.type                        'RIGAKU RU200' 
_diffrn_source.pdbx_synchrotron_site       ? 
_diffrn_source.pdbx_synchrotron_beamline   ? 
_diffrn_source.pdbx_wavelength             1.5418 
_diffrn_source.pdbx_wavelength_list        ? 
# 
_reflns.entry_id                     1Y8V 
_reflns.observed_criterion_sigma_F   ? 
_reflns.observed_criterion_sigma_I   -3.0 
_reflns.d_resolution_high            1.50 
_reflns.d_resolution_low             50.0 
_reflns.number_all                   8698 
_reflns.number_obs                   8698 
_reflns.percent_possible_obs         99.4 
_reflns.pdbx_Rmerge_I_obs            0.053 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        40.0 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              8.3 
_reflns.R_free_details               ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             1.50 
_reflns_shell.d_res_low              1.55 
_reflns_shell.percent_possible_all   97.4 
_reflns_shell.Rmerge_I_obs           0.407 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    3.4 
_reflns_shell.pdbx_redundancy        4.0 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      820 
_reflns_shell.number_measured_all    ? 
_reflns_shell.number_measured_obs    ? 
_reflns_shell.number_unique_obs      ? 
_reflns_shell.pdbx_chi_squared       ? 
_reflns_shell.pdbx_diffrn_id         ? 
_reflns_shell.pdbx_ordinal           1 
# 
_refine.entry_id                                 1Y8V 
_refine.ls_d_res_high                            1.50 
_refine.ls_d_res_low                             20.0 
_refine.pdbx_ls_sigma_F                          0.0 
_refine.pdbx_ls_sigma_I                          ? 
_refine.ls_number_reflns_all                     8451 
_refine.ls_number_reflns_obs                     8451 
_refine.ls_number_reflns_R_free                  895 
_refine.ls_percent_reflns_obs                    97.1 
_refine.ls_R_factor_all                          ? 
_refine.ls_R_factor_obs                          ? 
_refine.ls_R_factor_R_work                       0.1794 
_refine.ls_R_factor_R_free                       0.2164 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.ls_percent_reflns_R_free                 ? 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_starting_model                      410D 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.pdbx_R_Free_selection_details            Random 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_stereochemistry_target_values       ? 
_refine.solvent_model_details                    ? 
_refine.solvent_model_param_bsol                 ? 
_refine.solvent_model_param_ksol                 ? 
_refine.occupancy_max                            ? 
_refine.occupancy_min                            ? 
_refine.pdbx_isotropic_thermal_model             Isotropic 
_refine.B_iso_mean                               21.4 
_refine.aniso_B[1][1]                            0.962 
_refine.aniso_B[1][2]                            0.000 
_refine.aniso_B[1][3]                            0.000 
_refine.aniso_B[2][2]                            -2.985 
_refine.aniso_B[2][3]                            0.000 
_refine.aniso_B[3][3]                            2.023 
_refine.details                                  'Conjugate gradient refinement using maximum likelihood target for amplitudes' 
_refine.correlation_coeff_Fo_to_Fc               ? 
_refine.correlation_coeff_Fo_to_Fc_free          ? 
_refine.pdbx_solvent_vdw_probe_radii             ? 
_refine.pdbx_solvent_ion_probe_radii             ? 
_refine.pdbx_solvent_shrinkage_radii             ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_refine.overall_SU_B                             ? 
_refine.overall_SU_ML                            ? 
_refine.pdbx_overall_ESU_R                       ? 
_refine.pdbx_overall_ESU_R_Free                  ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_wR_factor_R_free                      ? 
_refine.ls_wR_factor_R_work                      ? 
_refine.overall_FOM_free_R_set                   ? 
_refine.overall_FOM_work_R_set                   ? 
_refine.pdbx_refine_id                           'X-RAY DIFFRACTION' 
_refine.pdbx_diffrn_id                           1 
_refine.pdbx_TLS_residual_ADP_flag               ? 
_refine.pdbx_overall_phase_error                 ? 
_refine.pdbx_overall_SU_R_free_Cruickshank_DPI   ? 
_refine.pdbx_overall_SU_R_Blow_DPI               ? 
_refine.pdbx_overall_SU_R_free_Blow_DPI          ? 
# 
_refine_hist.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_hist.cycle_id                         LAST 
_refine_hist.pdbx_number_atoms_protein        0 
_refine_hist.pdbx_number_atoms_nucleic_acid   412 
_refine_hist.pdbx_number_atoms_ligand         0 
_refine_hist.number_atoms_solvent             128 
_refine_hist.number_atoms_total               540 
_refine_hist.d_res_high                       1.50 
_refine_hist.d_res_low                        20.0 
# 
loop_
_refine_ls_restr.type 
_refine_ls_restr.dev_ideal 
_refine_ls_restr.dev_ideal_target 
_refine_ls_restr.weight 
_refine_ls_restr.number 
_refine_ls_restr.pdbx_refine_id 
_refine_ls_restr.pdbx_restraint_function 
c_bond_d    0.009 ? ? ? 'X-RAY DIFFRACTION' ? 
c_angle_deg 1.30  ? ? ? 'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   ? 
_refine_ls_shell.d_res_high                       1.50 
_refine_ls_shell.d_res_low                        1.53 
_refine_ls_shell.number_reflns_R_work             ? 
_refine_ls_shell.R_factor_R_work                  0.3009 
_refine_ls_shell.percent_reflns_obs               93.2 
_refine_ls_shell.R_factor_R_free                  0.2957 
_refine_ls_shell.R_factor_R_free_error            ? 
_refine_ls_shell.percent_reflns_R_free            ? 
_refine_ls_shell.number_reflns_R_free             52 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
# 
_struct.entry_id                  1Y8V 
_struct.title                     
;Crystal structure of the A-DNA GCGTAT*CGC with a 2'-O-propyl Thymidine (T*)
;
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        1Y8V 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            
;A-DNA, O2'-modification, decamer, DNA
;
# 
loop_
_struct_asym.id 
_struct_asym.pdbx_blank_PDB_chainid_flag 
_struct_asym.pdbx_modified 
_struct_asym.entity_id 
_struct_asym.details 
A N N 1 ? 
B N N 1 ? 
C N N 2 ? 
D N N 2 ? 
# 
_struct_biol.id                    1 
_struct_biol.details               'Chains A and B form duplex' 
_struct_biol.pdbx_parent_biol_id   ? 
# 
loop_
_struct_conn.id 
_struct_conn.conn_type_id 
_struct_conn.pdbx_leaving_atom_flag 
_struct_conn.pdbx_PDB_id 
_struct_conn.ptnr1_label_asym_id 
_struct_conn.ptnr1_label_comp_id 
_struct_conn.ptnr1_label_seq_id 
_struct_conn.ptnr1_label_atom_id 
_struct_conn.pdbx_ptnr1_label_alt_id 
_struct_conn.pdbx_ptnr1_PDB_ins_code 
_struct_conn.pdbx_ptnr1_standard_comp_id 
_struct_conn.ptnr1_symmetry 
_struct_conn.ptnr2_label_asym_id 
_struct_conn.ptnr2_label_comp_id 
_struct_conn.ptnr2_label_seq_id 
_struct_conn.ptnr2_label_atom_id 
_struct_conn.pdbx_ptnr2_label_alt_id 
_struct_conn.pdbx_ptnr2_PDB_ins_code 
_struct_conn.ptnr1_auth_asym_id 
_struct_conn.ptnr1_auth_comp_id 
_struct_conn.ptnr1_auth_seq_id 
_struct_conn.ptnr2_auth_asym_id 
_struct_conn.ptnr2_auth_comp_id 
_struct_conn.ptnr2_auth_seq_id 
_struct_conn.ptnr2_symmetry 
_struct_conn.pdbx_ptnr3_label_atom_id 
_struct_conn.pdbx_ptnr3_label_seq_id 
_struct_conn.pdbx_ptnr3_label_comp_id 
_struct_conn.pdbx_ptnr3_label_asym_id 
_struct_conn.pdbx_ptnr3_label_alt_id 
_struct_conn.pdbx_ptnr3_PDB_ins_code 
_struct_conn.details 
_struct_conn.pdbx_dist_value 
_struct_conn.pdbx_value_order 
_struct_conn.pdbx_role 
covale1  covale both ? A DA  5  "O3'" ? ? ? 1_555 A P2T 6  P  ? ? A DA  5  A P2T 6  1_555 ? ? ? ? ? ? ?            1.610 ? ? 
covale2  covale both ? A P2T 6  "O3'" ? ? ? 1_555 A DA  7  P  ? ? A P2T 6  A DA  7  1_555 ? ? ? ? ? ? ?            1.609 ? ? 
covale3  covale both ? B DA  5  "O3'" ? ? ? 1_555 B P2T 6  P  ? ? B DA  15 B P2T 16 1_555 ? ? ? ? ? ? ?            1.596 ? ? 
covale4  covale both ? B P2T 6  "O3'" ? ? ? 1_555 B DA  7  P  ? ? B P2T 16 B DA  17 1_555 ? ? ? ? ? ? ?            1.609 ? ? 
hydrog1  hydrog ?    ? A DG  1  N1    ? ? ? 1_555 B DC  10 N3 ? ? A DG  1  B DC  20 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog2  hydrog ?    ? A DG  1  N2    ? ? ? 1_555 B DC  10 O2 ? ? A DG  1  B DC  20 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ?    ? A DG  1  O6    ? ? ? 1_555 B DC  10 N4 ? ? A DG  1  B DC  20 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ?    ? A DC  2  N3    ? ? ? 1_555 B DG  9  N1 ? ? A DC  2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog5  hydrog ?    ? A DC  2  N4    ? ? ? 1_555 B DG  9  O6 ? ? A DC  2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog6  hydrog ?    ? A DC  2  O2    ? ? ? 1_555 B DG  9  N2 ? ? A DC  2  B DG  19 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ?    ? A DG  3  N1    ? ? ? 1_555 B DC  8  N3 ? ? A DG  3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ?    ? A DG  3  N2    ? ? ? 1_555 B DC  8  O2 ? ? A DG  3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ?    ? A DG  3  O6    ? ? ? 1_555 B DC  8  N4 ? ? A DG  3  B DC  18 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ?    ? A DT  4  N3    ? ? ? 1_555 B DA  7  N1 ? ? A DT  4  B DA  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog11 hydrog ?    ? A DT  4  O4    ? ? ? 1_555 B DA  7  N6 ? ? A DT  4  B DA  17 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog12 hydrog ?    ? A DA  5  N1    ? ? ? 1_555 B P2T 6  N3 ? ? A DA  5  B P2T 16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog13 hydrog ?    ? A DA  5  N6    ? ? ? 1_555 B P2T 6  O4 ? ? A DA  5  B P2T 16 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog14 hydrog ?    ? A P2T 6  N3    ? ? ? 1_555 B DA  5  N1 ? ? A P2T 6  B DA  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog15 hydrog ?    ? A P2T 6  O4    ? ? ? 1_555 B DA  5  N6 ? ? A P2T 6  B DA  15 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog16 hydrog ?    ? A DA  7  N1    ? ? ? 1_555 B DT  4  N3 ? ? A DA  7  B DT  14 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog17 hydrog ?    ? A DA  7  N6    ? ? ? 1_555 B DT  4  O4 ? ? A DA  7  B DT  14 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog18 hydrog ?    ? A DC  8  N3    ? ? ? 1_555 B DG  3  N1 ? ? A DC  8  B DG  13 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog19 hydrog ?    ? A DC  8  N4    ? ? ? 1_555 B DG  3  O6 ? ? A DC  8  B DG  13 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog20 hydrog ?    ? A DC  8  O2    ? ? ? 1_555 B DG  3  N2 ? ? A DC  8  B DG  13 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog21 hydrog ?    ? A DG  9  N1    ? ? ? 1_555 B DC  2  N3 ? ? A DG  9  B DC  12 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog22 hydrog ?    ? A DG  9  N2    ? ? ? 1_555 B DC  2  O2 ? ? A DG  9  B DC  12 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog23 hydrog ?    ? A DG  9  O6    ? ? ? 1_555 B DC  2  N4 ? ? A DG  9  B DC  12 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog24 hydrog ?    ? A DC  10 N3    ? ? ? 1_555 B DG  1  N1 ? ? A DC  10 B DG  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog25 hydrog ?    ? A DC  10 N4    ? ? ? 1_555 B DG  1  O6 ? ? A DC  10 B DG  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog26 hydrog ?    ? A DC  10 O2    ? ? ? 1_555 B DG  1  N2 ? ? A DC  10 B DG  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
hydrog ? ? 
# 
_database_PDB_matrix.entry_id          1Y8V 
_database_PDB_matrix.origx[1][1]       1.000000 
_database_PDB_matrix.origx[1][2]       0.000000 
_database_PDB_matrix.origx[1][3]       0.000000 
_database_PDB_matrix.origx[2][1]       0.000000 
_database_PDB_matrix.origx[2][2]       1.000000 
_database_PDB_matrix.origx[2][3]       0.000000 
_database_PDB_matrix.origx[3][1]       0.000000 
_database_PDB_matrix.origx[3][2]       0.000000 
_database_PDB_matrix.origx[3][3]       1.000000 
_database_PDB_matrix.origx_vector[1]   0.00000 
_database_PDB_matrix.origx_vector[2]   0.00000 
_database_PDB_matrix.origx_vector[3]   0.00000 
# 
_atom_sites.entry_id                    1Y8V 
_atom_sites.fract_transf_matrix[1][1]   0.040272 
_atom_sites.fract_transf_matrix[1][2]   0.000000 
_atom_sites.fract_transf_matrix[1][3]   0.000000 
_atom_sites.fract_transf_matrix[2][1]   0.000000 
_atom_sites.fract_transf_matrix[2][2]   0.022068 
_atom_sites.fract_transf_matrix[2][3]   0.000000 
_atom_sites.fract_transf_matrix[3][1]   0.000000 
_atom_sites.fract_transf_matrix[3][2]   0.000000 
_atom_sites.fract_transf_matrix[3][3]   0.021890 
_atom_sites.fract_transf_vector[1]      0.00000 
_atom_sites.fract_transf_vector[2]      0.00000 
_atom_sites.fract_transf_vector[3]      0.00000 
# 
loop_
_atom_type.symbol 
C 
N 
O 
P 
# 
loop_
_pdbx_poly_seq_scheme.asym_id 
_pdbx_poly_seq_scheme.entity_id 
_pdbx_poly_seq_scheme.seq_id 
_pdbx_poly_seq_scheme.mon_id 
_pdbx_poly_seq_scheme.ndb_seq_num 
_pdbx_poly_seq_scheme.pdb_seq_num 
_pdbx_poly_seq_scheme.auth_seq_num 
_pdbx_poly_seq_scheme.pdb_mon_id 
_pdbx_poly_seq_scheme.auth_mon_id 
_pdbx_poly_seq_scheme.pdb_strand_id 
_pdbx_poly_seq_scheme.pdb_ins_code 
_pdbx_poly_seq_scheme.hetero 
A 1 1  DG  1  1  1  DG  G   A . n 
A 1 2  DC  2  2  2  DC  C   A . n 
A 1 3  DG  3  3  3  DG  G   A . n 
A 1 4  DT  4  4  4  DT  T   A . n 
A 1 5  DA  5  5  5  DA  A   A . n 
A 1 6  P2T 6  6  6  P2T PRL A . n 
A 1 7  DA  7  7  7  DA  A   A . n 
A 1 8  DC  8  8  8  DC  C   A . n 
A 1 9  DG  9  9  9  DG  G   A . n 
A 1 10 DC  10 10 10 DC  C   A . n 
B 1 1  DG  1  11 11 DG  G   B . n 
B 1 2  DC  2  12 12 DC  C   B . n 
B 1 3  DG  3  13 13 DG  G   B . n 
B 1 4  DT  4  14 14 DT  T   B . n 
B 1 5  DA  5  15 15 DA  A   B . n 
B 1 6  P2T 6  16 16 P2T PRL B . n 
B 1 7  DA  7  17 17 DA  A   B . n 
B 1 8  DC  8  18 18 DC  C   B . n 
B 1 9  DG  9  19 19 DG  G   B . n 
B 1 10 DC  10 20 20 DC  C   B . n 
# 
loop_
_pdbx_nonpoly_scheme.asym_id 
_pdbx_nonpoly_scheme.entity_id 
_pdbx_nonpoly_scheme.mon_id 
_pdbx_nonpoly_scheme.ndb_seq_num 
_pdbx_nonpoly_scheme.pdb_seq_num 
_pdbx_nonpoly_scheme.auth_seq_num 
_pdbx_nonpoly_scheme.pdb_mon_id 
_pdbx_nonpoly_scheme.auth_mon_id 
_pdbx_nonpoly_scheme.pdb_strand_id 
_pdbx_nonpoly_scheme.pdb_ins_code 
C 2 HOH 1  101 101 HOH HOH A . 
C 2 HOH 2  102 102 HOH HOH A . 
C 2 HOH 3  103 103 HOH HOH A . 
C 2 HOH 4  106 106 HOH HOH A . 
C 2 HOH 5  107 107 HOH HOH A . 
C 2 HOH 6  108 108 HOH HOH A . 
C 2 HOH 7  109 109 HOH HOH A . 
C 2 HOH 8  110 110 HOH HOH A . 
C 2 HOH 9  111 111 HOH HOH A . 
C 2 HOH 10 112 112 HOH HOH A . 
C 2 HOH 11 113 113 HOH HOH A . 
C 2 HOH 12 114 114 HOH HOH A . 
C 2 HOH 13 115 115 HOH HOH A . 
C 2 HOH 14 119 119 HOH HOH A . 
C 2 HOH 15 120 120 HOH HOH A . 
C 2 HOH 16 121 121 HOH HOH A . 
C 2 HOH 17 122 122 HOH HOH A . 
C 2 HOH 18 123 123 HOH HOH A . 
C 2 HOH 19 124 124 HOH HOH A . 
C 2 HOH 20 125 125 HOH HOH A . 
C 2 HOH 21 127 127 HOH HOH A . 
C 2 HOH 22 128 128 HOH HOH A . 
C 2 HOH 23 129 129 HOH HOH A . 
C 2 HOH 24 130 130 HOH HOH A . 
C 2 HOH 25 131 131 HOH HOH A . 
C 2 HOH 26 135 135 HOH HOH A . 
C 2 HOH 27 142 142 HOH HOH A . 
C 2 HOH 28 143 143 HOH HOH A . 
C 2 HOH 29 146 146 HOH HOH A . 
C 2 HOH 30 147 147 HOH HOH A . 
C 2 HOH 31 148 148 HOH HOH A . 
C 2 HOH 32 150 150 HOH HOH A . 
C 2 HOH 33 156 156 HOH HOH A . 
C 2 HOH 34 158 158 HOH HOH A . 
C 2 HOH 35 159 159 HOH HOH A . 
C 2 HOH 36 160 160 HOH HOH A . 
C 2 HOH 37 161 161 HOH HOH A . 
C 2 HOH 38 163 163 HOH HOH A . 
C 2 HOH 39 164 164 HOH HOH A . 
C 2 HOH 40 165 165 HOH HOH A . 
C 2 HOH 41 166 166 HOH HOH A . 
C 2 HOH 42 168 168 HOH HOH A . 
C 2 HOH 43 170 170 HOH HOH A . 
C 2 HOH 44 173 173 HOH HOH A . 
C 2 HOH 45 174 174 HOH HOH A . 
C 2 HOH 46 175 175 HOH HOH A . 
C 2 HOH 47 176 176 HOH HOH A . 
C 2 HOH 48 177 177 HOH HOH A . 
C 2 HOH 49 179 179 HOH HOH A . 
C 2 HOH 50 182 182 HOH HOH A . 
C 2 HOH 51 185 185 HOH HOH A . 
C 2 HOH 52 187 187 HOH HOH A . 
C 2 HOH 53 188 188 HOH HOH A . 
C 2 HOH 54 194 194 HOH HOH A . 
C 2 HOH 55 195 195 HOH HOH A . 
C 2 HOH 56 197 197 HOH HOH A . 
C 2 HOH 57 200 200 HOH HOH A . 
C 2 HOH 58 201 201 HOH HOH A . 
C 2 HOH 59 203 203 HOH HOH A . 
C 2 HOH 60 204 204 HOH HOH A . 
C 2 HOH 61 205 205 HOH HOH A . 
C 2 HOH 62 211 211 HOH HOH A . 
D 2 HOH 1  104 104 HOH HOH B . 
D 2 HOH 2  105 105 HOH HOH B . 
D 2 HOH 3  116 116 HOH HOH B . 
D 2 HOH 4  117 117 HOH HOH B . 
D 2 HOH 5  118 118 HOH HOH B . 
D 2 HOH 6  126 126 HOH HOH B . 
D 2 HOH 7  132 132 HOH HOH B . 
D 2 HOH 8  133 133 HOH HOH B . 
D 2 HOH 9  134 134 HOH HOH B . 
D 2 HOH 10 136 136 HOH HOH B . 
D 2 HOH 11 137 137 HOH HOH B . 
D 2 HOH 12 138 138 HOH HOH B . 
D 2 HOH 13 139 139 HOH HOH B . 
D 2 HOH 14 140 140 HOH HOH B . 
D 2 HOH 15 141 141 HOH HOH B . 
D 2 HOH 16 144 144 HOH HOH B . 
D 2 HOH 17 145 145 HOH HOH B . 
D 2 HOH 18 149 149 HOH HOH B . 
D 2 HOH 19 151 151 HOH HOH B . 
D 2 HOH 20 152 152 HOH HOH B . 
D 2 HOH 21 153 153 HOH HOH B . 
D 2 HOH 22 154 154 HOH HOH B . 
D 2 HOH 23 155 155 HOH HOH B . 
D 2 HOH 24 157 157 HOH HOH B . 
D 2 HOH 25 162 162 HOH HOH B . 
D 2 HOH 26 167 167 HOH HOH B . 
D 2 HOH 27 169 169 HOH HOH B . 
D 2 HOH 28 171 171 HOH HOH B . 
D 2 HOH 29 172 172 HOH HOH B . 
D 2 HOH 30 178 178 HOH HOH B . 
D 2 HOH 31 180 180 HOH HOH B . 
D 2 HOH 32 181 181 HOH HOH B . 
D 2 HOH 33 183 183 HOH HOH B . 
D 2 HOH 34 184 184 HOH HOH B . 
D 2 HOH 35 186 186 HOH HOH B . 
D 2 HOH 36 189 189 HOH HOH B . 
D 2 HOH 37 190 190 HOH HOH B . 
D 2 HOH 38 191 191 HOH HOH B . 
D 2 HOH 39 192 192 HOH HOH B . 
D 2 HOH 40 193 193 HOH HOH B . 
D 2 HOH 41 196 196 HOH HOH B . 
D 2 HOH 42 198 198 HOH HOH B . 
D 2 HOH 43 199 199 HOH HOH B . 
D 2 HOH 44 202 202 HOH HOH B . 
D 2 HOH 45 206 206 HOH HOH B . 
D 2 HOH 46 207 207 HOH HOH B . 
D 2 HOH 47 208 208 HOH HOH B . 
D 2 HOH 48 209 209 HOH HOH B . 
D 2 HOH 49 210 210 HOH HOH B . 
D 2 HOH 50 212 212 HOH HOH B . 
D 2 HOH 51 213 213 HOH HOH B . 
D 2 HOH 52 214 214 HOH HOH B . 
D 2 HOH 53 215 215 HOH HOH B . 
D 2 HOH 54 216 216 HOH HOH B . 
D 2 HOH 55 217 217 HOH HOH B . 
D 2 HOH 56 218 218 HOH HOH B . 
D 2 HOH 57 219 219 HOH HOH B . 
# 
loop_
_pdbx_struct_mod_residue.id 
_pdbx_struct_mod_residue.label_asym_id 
_pdbx_struct_mod_residue.label_comp_id 
_pdbx_struct_mod_residue.label_seq_id 
_pdbx_struct_mod_residue.auth_asym_id 
_pdbx_struct_mod_residue.auth_comp_id 
_pdbx_struct_mod_residue.auth_seq_id 
_pdbx_struct_mod_residue.PDB_ins_code 
_pdbx_struct_mod_residue.parent_comp_id 
_pdbx_struct_mod_residue.details 
1 A P2T 6 A P2T 6  ? DT 
;2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE
;
2 B P2T 6 B P2T 16 ? DT 
;2'-O-PROPYL THYMIDINE-5-MONOPHOSPHATE
;
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_defined_assembly 
_pdbx_struct_assembly.method_details       ? 
_pdbx_struct_assembly.oligomeric_details   dimeric 
_pdbx_struct_assembly.oligomeric_count     2 
# 
_pdbx_struct_assembly_gen.assembly_id       1 
_pdbx_struct_assembly_gen.oper_expression   1 
_pdbx_struct_assembly_gen.asym_id_list      A,B,C,D 
# 
_pdbx_struct_oper_list.id                   1 
_pdbx_struct_oper_list.type                 'identity operation' 
_pdbx_struct_oper_list.name                 1_555 
_pdbx_struct_oper_list.symmetry_operation   x,y,z 
_pdbx_struct_oper_list.matrix[1][1]         1.0000000000 
_pdbx_struct_oper_list.matrix[1][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[1][3]         0.0000000000 
_pdbx_struct_oper_list.vector[1]            0.0000000000 
_pdbx_struct_oper_list.matrix[2][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[2][2]         1.0000000000 
_pdbx_struct_oper_list.matrix[2][3]         0.0000000000 
_pdbx_struct_oper_list.vector[2]            0.0000000000 
_pdbx_struct_oper_list.matrix[3][1]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][2]         0.0000000000 
_pdbx_struct_oper_list.matrix[3][3]         1.0000000000 
_pdbx_struct_oper_list.vector[3]            0.0000000000 
# 
loop_
_pdbx_audit_revision_history.ordinal 
_pdbx_audit_revision_history.data_content_type 
_pdbx_audit_revision_history.major_revision 
_pdbx_audit_revision_history.minor_revision 
_pdbx_audit_revision_history.revision_date 
1 'Structure model' 1 0 2005-06-28 
2 'Structure model' 1 1 2008-04-30 
3 'Structure model' 1 2 2011-07-13 
4 'Structure model' 1 3 2023-08-23 
# 
_pdbx_audit_revision_details.ordinal             1 
_pdbx_audit_revision_details.revision_ordinal    1 
_pdbx_audit_revision_details.data_content_type   'Structure model' 
_pdbx_audit_revision_details.provider            repository 
_pdbx_audit_revision_details.type                'Initial release' 
_pdbx_audit_revision_details.description         ? 
_pdbx_audit_revision_details.details             ? 
# 
loop_
_pdbx_audit_revision_group.ordinal 
_pdbx_audit_revision_group.revision_ordinal 
_pdbx_audit_revision_group.data_content_type 
_pdbx_audit_revision_group.group 
1 2 'Structure model' 'Version format compliance' 
2 3 'Structure model' 'Version format compliance' 
3 4 'Structure model' 'Data collection'           
4 4 'Structure model' 'Database references'       
5 4 'Structure model' 'Derived calculations'      
6 4 'Structure model' 'Refinement description'    
# 
loop_
_pdbx_audit_revision_category.ordinal 
_pdbx_audit_revision_category.revision_ordinal 
_pdbx_audit_revision_category.data_content_type 
_pdbx_audit_revision_category.category 
1 4 'Structure model' chem_comp_atom                
2 4 'Structure model' chem_comp_bond                
3 4 'Structure model' database_2                    
4 4 'Structure model' pdbx_initial_refinement_model 
5 4 'Structure model' struct_conn                   
# 
loop_
_pdbx_audit_revision_item.ordinal 
_pdbx_audit_revision_item.revision_ordinal 
_pdbx_audit_revision_item.data_content_type 
_pdbx_audit_revision_item.item 
1 4 'Structure model' '_database_2.pdbx_DOI'                
2 4 'Structure model' '_database_2.pdbx_database_accession' 
3 4 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
DENZO     'data reduction' . ? 1 
SCALEPACK 'data scaling'   . ? 2 
AMoRE     phasing          . ? 3 
CNS       refinement       . ? 4 
# 
loop_
_chem_comp_atom.comp_id 
_chem_comp_atom.atom_id 
_chem_comp_atom.type_symbol 
_chem_comp_atom.pdbx_aromatic_flag 
_chem_comp_atom.pdbx_stereo_config 
_chem_comp_atom.pdbx_ordinal 
DA  OP3    O N N 1   
DA  P      P N N 2   
DA  OP1    O N N 3   
DA  OP2    O N N 4   
DA  "O5'"  O N N 5   
DA  "C5'"  C N N 6   
DA  "C4'"  C N R 7   
DA  "O4'"  O N N 8   
DA  "C3'"  C N S 9   
DA  "O3'"  O N N 10  
DA  "C2'"  C N N 11  
DA  "C1'"  C N R 12  
DA  N9     N Y N 13  
DA  C8     C Y N 14  
DA  N7     N Y N 15  
DA  C5     C Y N 16  
DA  C6     C Y N 17  
DA  N6     N N N 18  
DA  N1     N Y N 19  
DA  C2     C Y N 20  
DA  N3     N Y N 21  
DA  C4     C Y N 22  
DA  HOP3   H N N 23  
DA  HOP2   H N N 24  
DA  "H5'"  H N N 25  
DA  "H5''" H N N 26  
DA  "H4'"  H N N 27  
DA  "H3'"  H N N 28  
DA  "HO3'" H N N 29  
DA  "H2'"  H N N 30  
DA  "H2''" H N N 31  
DA  "H1'"  H N N 32  
DA  H8     H N N 33  
DA  H61    H N N 34  
DA  H62    H N N 35  
DA  H2     H N N 36  
DC  OP3    O N N 37  
DC  P      P N N 38  
DC  OP1    O N N 39  
DC  OP2    O N N 40  
DC  "O5'"  O N N 41  
DC  "C5'"  C N N 42  
DC  "C4'"  C N R 43  
DC  "O4'"  O N N 44  
DC  "C3'"  C N S 45  
DC  "O3'"  O N N 46  
DC  "C2'"  C N N 47  
DC  "C1'"  C N R 48  
DC  N1     N N N 49  
DC  C2     C N N 50  
DC  O2     O N N 51  
DC  N3     N N N 52  
DC  C4     C N N 53  
DC  N4     N N N 54  
DC  C5     C N N 55  
DC  C6     C N N 56  
DC  HOP3   H N N 57  
DC  HOP2   H N N 58  
DC  "H5'"  H N N 59  
DC  "H5''" H N N 60  
DC  "H4'"  H N N 61  
DC  "H3'"  H N N 62  
DC  "HO3'" H N N 63  
DC  "H2'"  H N N 64  
DC  "H2''" H N N 65  
DC  "H1'"  H N N 66  
DC  H41    H N N 67  
DC  H42    H N N 68  
DC  H5     H N N 69  
DC  H6     H N N 70  
DG  OP3    O N N 71  
DG  P      P N N 72  
DG  OP1    O N N 73  
DG  OP2    O N N 74  
DG  "O5'"  O N N 75  
DG  "C5'"  C N N 76  
DG  "C4'"  C N R 77  
DG  "O4'"  O N N 78  
DG  "C3'"  C N S 79  
DG  "O3'"  O N N 80  
DG  "C2'"  C N N 81  
DG  "C1'"  C N R 82  
DG  N9     N Y N 83  
DG  C8     C Y N 84  
DG  N7     N Y N 85  
DG  C5     C Y N 86  
DG  C6     C N N 87  
DG  O6     O N N 88  
DG  N1     N N N 89  
DG  C2     C N N 90  
DG  N2     N N N 91  
DG  N3     N N N 92  
DG  C4     C Y N 93  
DG  HOP3   H N N 94  
DG  HOP2   H N N 95  
DG  "H5'"  H N N 96  
DG  "H5''" H N N 97  
DG  "H4'"  H N N 98  
DG  "H3'"  H N N 99  
DG  "HO3'" H N N 100 
DG  "H2'"  H N N 101 
DG  "H2''" H N N 102 
DG  "H1'"  H N N 103 
DG  H8     H N N 104 
DG  H1     H N N 105 
DG  H21    H N N 106 
DG  H22    H N N 107 
DT  OP3    O N N 108 
DT  P      P N N 109 
DT  OP1    O N N 110 
DT  OP2    O N N 111 
DT  "O5'"  O N N 112 
DT  "C5'"  C N N 113 
DT  "C4'"  C N R 114 
DT  "O4'"  O N N 115 
DT  "C3'"  C N S 116 
DT  "O3'"  O N N 117 
DT  "C2'"  C N N 118 
DT  "C1'"  C N R 119 
DT  N1     N N N 120 
DT  C2     C N N 121 
DT  O2     O N N 122 
DT  N3     N N N 123 
DT  C4     C N N 124 
DT  O4     O N N 125 
DT  C5     C N N 126 
DT  C7     C N N 127 
DT  C6     C N N 128 
DT  HOP3   H N N 129 
DT  HOP2   H N N 130 
DT  "H5'"  H N N 131 
DT  "H5''" H N N 132 
DT  "H4'"  H N N 133 
DT  "H3'"  H N N 134 
DT  "HO3'" H N N 135 
DT  "H2'"  H N N 136 
DT  "H2''" H N N 137 
DT  "H1'"  H N N 138 
DT  H3     H N N 139 
DT  H71    H N N 140 
DT  H72    H N N 141 
DT  H73    H N N 142 
DT  H6     H N N 143 
HOH O      O N N 144 
HOH H1     H N N 145 
HOH H2     H N N 146 
P2T P      P N N 147 
P2T OP1    O N N 148 
P2T OP2    O N N 149 
P2T "O5'"  O N N 150 
P2T "C5'"  C N N 151 
P2T "C4'"  C N R 152 
P2T "O4'"  O N N 153 
P2T "C1'"  C N R 154 
P2T N1     N N N 155 
P2T C6     C N N 156 
P2T C2     C N N 157 
P2T O2     O N N 158 
P2T N3     N N N 159 
P2T C4     C N N 160 
P2T O4     O N N 161 
P2T C5     C N N 162 
P2T C5M    C N N 163 
P2T "C2'"  C N R 164 
P2T "O2'"  O N N 165 
P2T "CB'"  C N N 166 
P2T "CC'"  C N N 167 
P2T "CD'"  C N N 168 
P2T "C3'"  C N R 169 
P2T "O3'"  O N N 170 
P2T OP3    O N N 171 
P2T HOP2   H N N 172 
P2T "H5'"  H N N 173 
P2T "H5''" H N N 174 
P2T "H4'"  H N N 175 
P2T "H1'"  H N N 176 
P2T H6     H N N 177 
P2T HN3    H N N 178 
P2T H71    H N N 179 
P2T H72    H N N 180 
P2T H73    H N N 181 
P2T "H2'"  H N N 182 
P2T "HB'1" H N N 183 
P2T "HB'2" H N N 184 
P2T "HC'1" H N N 185 
P2T "HC'2" H N N 186 
P2T "HD'1" H N N 187 
P2T "HD'2" H N N 188 
P2T "HD'3" H N N 189 
P2T "H3'"  H N N 190 
P2T "HO3'" H N N 191 
P2T HOP3   H N N 192 
# 
loop_
_chem_comp_bond.comp_id 
_chem_comp_bond.atom_id_1 
_chem_comp_bond.atom_id_2 
_chem_comp_bond.value_order 
_chem_comp_bond.pdbx_aromatic_flag 
_chem_comp_bond.pdbx_stereo_config 
_chem_comp_bond.pdbx_ordinal 
DA  OP3   P      sing N N 1   
DA  OP3   HOP3   sing N N 2   
DA  P     OP1    doub N N 3   
DA  P     OP2    sing N N 4   
DA  P     "O5'"  sing N N 5   
DA  OP2   HOP2   sing N N 6   
DA  "O5'" "C5'"  sing N N 7   
DA  "C5'" "C4'"  sing N N 8   
DA  "C5'" "H5'"  sing N N 9   
DA  "C5'" "H5''" sing N N 10  
DA  "C4'" "O4'"  sing N N 11  
DA  "C4'" "C3'"  sing N N 12  
DA  "C4'" "H4'"  sing N N 13  
DA  "O4'" "C1'"  sing N N 14  
DA  "C3'" "O3'"  sing N N 15  
DA  "C3'" "C2'"  sing N N 16  
DA  "C3'" "H3'"  sing N N 17  
DA  "O3'" "HO3'" sing N N 18  
DA  "C2'" "C1'"  sing N N 19  
DA  "C2'" "H2'"  sing N N 20  
DA  "C2'" "H2''" sing N N 21  
DA  "C1'" N9     sing N N 22  
DA  "C1'" "H1'"  sing N N 23  
DA  N9    C8     sing Y N 24  
DA  N9    C4     sing Y N 25  
DA  C8    N7     doub Y N 26  
DA  C8    H8     sing N N 27  
DA  N7    C5     sing Y N 28  
DA  C5    C6     sing Y N 29  
DA  C5    C4     doub Y N 30  
DA  C6    N6     sing N N 31  
DA  C6    N1     doub Y N 32  
DA  N6    H61    sing N N 33  
DA  N6    H62    sing N N 34  
DA  N1    C2     sing Y N 35  
DA  C2    N3     doub Y N 36  
DA  C2    H2     sing N N 37  
DA  N3    C4     sing Y N 38  
DC  OP3   P      sing N N 39  
DC  OP3   HOP3   sing N N 40  
DC  P     OP1    doub N N 41  
DC  P     OP2    sing N N 42  
DC  P     "O5'"  sing N N 43  
DC  OP2   HOP2   sing N N 44  
DC  "O5'" "C5'"  sing N N 45  
DC  "C5'" "C4'"  sing N N 46  
DC  "C5'" "H5'"  sing N N 47  
DC  "C5'" "H5''" sing N N 48  
DC  "C4'" "O4'"  sing N N 49  
DC  "C4'" "C3'"  sing N N 50  
DC  "C4'" "H4'"  sing N N 51  
DC  "O4'" "C1'"  sing N N 52  
DC  "C3'" "O3'"  sing N N 53  
DC  "C3'" "C2'"  sing N N 54  
DC  "C3'" "H3'"  sing N N 55  
DC  "O3'" "HO3'" sing N N 56  
DC  "C2'" "C1'"  sing N N 57  
DC  "C2'" "H2'"  sing N N 58  
DC  "C2'" "H2''" sing N N 59  
DC  "C1'" N1     sing N N 60  
DC  "C1'" "H1'"  sing N N 61  
DC  N1    C2     sing N N 62  
DC  N1    C6     sing N N 63  
DC  C2    O2     doub N N 64  
DC  C2    N3     sing N N 65  
DC  N3    C4     doub N N 66  
DC  C4    N4     sing N N 67  
DC  C4    C5     sing N N 68  
DC  N4    H41    sing N N 69  
DC  N4    H42    sing N N 70  
DC  C5    C6     doub N N 71  
DC  C5    H5     sing N N 72  
DC  C6    H6     sing N N 73  
DG  OP3   P      sing N N 74  
DG  OP3   HOP3   sing N N 75  
DG  P     OP1    doub N N 76  
DG  P     OP2    sing N N 77  
DG  P     "O5'"  sing N N 78  
DG  OP2   HOP2   sing N N 79  
DG  "O5'" "C5'"  sing N N 80  
DG  "C5'" "C4'"  sing N N 81  
DG  "C5'" "H5'"  sing N N 82  
DG  "C5'" "H5''" sing N N 83  
DG  "C4'" "O4'"  sing N N 84  
DG  "C4'" "C3'"  sing N N 85  
DG  "C4'" "H4'"  sing N N 86  
DG  "O4'" "C1'"  sing N N 87  
DG  "C3'" "O3'"  sing N N 88  
DG  "C3'" "C2'"  sing N N 89  
DG  "C3'" "H3'"  sing N N 90  
DG  "O3'" "HO3'" sing N N 91  
DG  "C2'" "C1'"  sing N N 92  
DG  "C2'" "H2'"  sing N N 93  
DG  "C2'" "H2''" sing N N 94  
DG  "C1'" N9     sing N N 95  
DG  "C1'" "H1'"  sing N N 96  
DG  N9    C8     sing Y N 97  
DG  N9    C4     sing Y N 98  
DG  C8    N7     doub Y N 99  
DG  C8    H8     sing N N 100 
DG  N7    C5     sing Y N 101 
DG  C5    C6     sing N N 102 
DG  C5    C4     doub Y N 103 
DG  C6    O6     doub N N 104 
DG  C6    N1     sing N N 105 
DG  N1    C2     sing N N 106 
DG  N1    H1     sing N N 107 
DG  C2    N2     sing N N 108 
DG  C2    N3     doub N N 109 
DG  N2    H21    sing N N 110 
DG  N2    H22    sing N N 111 
DG  N3    C4     sing N N 112 
DT  OP3   P      sing N N 113 
DT  OP3   HOP3   sing N N 114 
DT  P     OP1    doub N N 115 
DT  P     OP2    sing N N 116 
DT  P     "O5'"  sing N N 117 
DT  OP2   HOP2   sing N N 118 
DT  "O5'" "C5'"  sing N N 119 
DT  "C5'" "C4'"  sing N N 120 
DT  "C5'" "H5'"  sing N N 121 
DT  "C5'" "H5''" sing N N 122 
DT  "C4'" "O4'"  sing N N 123 
DT  "C4'" "C3'"  sing N N 124 
DT  "C4'" "H4'"  sing N N 125 
DT  "O4'" "C1'"  sing N N 126 
DT  "C3'" "O3'"  sing N N 127 
DT  "C3'" "C2'"  sing N N 128 
DT  "C3'" "H3'"  sing N N 129 
DT  "O3'" "HO3'" sing N N 130 
DT  "C2'" "C1'"  sing N N 131 
DT  "C2'" "H2'"  sing N N 132 
DT  "C2'" "H2''" sing N N 133 
DT  "C1'" N1     sing N N 134 
DT  "C1'" "H1'"  sing N N 135 
DT  N1    C2     sing N N 136 
DT  N1    C6     sing N N 137 
DT  C2    O2     doub N N 138 
DT  C2    N3     sing N N 139 
DT  N3    C4     sing N N 140 
DT  N3    H3     sing N N 141 
DT  C4    O4     doub N N 142 
DT  C4    C5     sing N N 143 
DT  C5    C7     sing N N 144 
DT  C5    C6     doub N N 145 
DT  C7    H71    sing N N 146 
DT  C7    H72    sing N N 147 
DT  C7    H73    sing N N 148 
DT  C6    H6     sing N N 149 
HOH O     H1     sing N N 150 
HOH O     H2     sing N N 151 
P2T P     OP1    doub N N 152 
P2T P     OP2    sing N N 153 
P2T P     "O5'"  sing N N 154 
P2T P     OP3    sing N N 155 
P2T OP2   HOP2   sing N N 156 
P2T "O5'" "C5'"  sing N N 157 
P2T "C5'" "C4'"  sing N N 158 
P2T "C5'" "H5'"  sing N N 159 
P2T "C5'" "H5''" sing N N 160 
P2T "C4'" "O4'"  sing N N 161 
P2T "C4'" "C3'"  sing N N 162 
P2T "C4'" "H4'"  sing N N 163 
P2T "O4'" "C1'"  sing N N 164 
P2T "C1'" N1     sing N N 165 
P2T "C1'" "C2'"  sing N N 166 
P2T "C1'" "H1'"  sing N N 167 
P2T N1    C6     sing N N 168 
P2T N1    C2     sing N N 169 
P2T C6    C5     doub N N 170 
P2T C6    H6     sing N N 171 
P2T C2    O2     doub N N 172 
P2T C2    N3     sing N N 173 
P2T N3    C4     sing N N 174 
P2T N3    HN3    sing N N 175 
P2T C4    O4     doub N N 176 
P2T C4    C5     sing N N 177 
P2T C5    C5M    sing N N 178 
P2T C5M   H71    sing N N 179 
P2T C5M   H72    sing N N 180 
P2T C5M   H73    sing N N 181 
P2T "C2'" "O2'"  sing N N 182 
P2T "C2'" "C3'"  sing N N 183 
P2T "C2'" "H2'"  sing N N 184 
P2T "O2'" "CB'"  sing N N 185 
P2T "CB'" "CC'"  sing N N 186 
P2T "CB'" "HB'1" sing N N 187 
P2T "CB'" "HB'2" sing N N 188 
P2T "CC'" "CD'"  sing N N 189 
P2T "CC'" "HC'1" sing N N 190 
P2T "CC'" "HC'2" sing N N 191 
P2T "CD'" "HD'1" sing N N 192 
P2T "CD'" "HD'2" sing N N 193 
P2T "CD'" "HD'3" sing N N 194 
P2T "C3'" "O3'"  sing N N 195 
P2T "C3'" "H3'"  sing N N 196 
P2T "O3'" "HO3'" sing N N 197 
P2T OP3   HOP3   sing N N 198 
# 
_ndb_struct_conf_na.entry_id   1Y8V 
_ndb_struct_conf_na.feature    'a-form double helix' 
# 
loop_
_ndb_struct_na_base_pair.model_number 
_ndb_struct_na_base_pair.i_label_asym_id 
_ndb_struct_na_base_pair.i_label_comp_id 
_ndb_struct_na_base_pair.i_label_seq_id 
_ndb_struct_na_base_pair.i_symmetry 
_ndb_struct_na_base_pair.j_label_asym_id 
_ndb_struct_na_base_pair.j_label_comp_id 
_ndb_struct_na_base_pair.j_label_seq_id 
_ndb_struct_na_base_pair.j_symmetry 
_ndb_struct_na_base_pair.shear 
_ndb_struct_na_base_pair.stretch 
_ndb_struct_na_base_pair.stagger 
_ndb_struct_na_base_pair.buckle 
_ndb_struct_na_base_pair.propeller 
_ndb_struct_na_base_pair.opening 
_ndb_struct_na_base_pair.pair_number 
_ndb_struct_na_base_pair.pair_name 
_ndb_struct_na_base_pair.i_auth_asym_id 
_ndb_struct_na_base_pair.i_auth_seq_id 
_ndb_struct_na_base_pair.i_PDB_ins_code 
_ndb_struct_na_base_pair.j_auth_asym_id 
_ndb_struct_na_base_pair.j_auth_seq_id 
_ndb_struct_na_base_pair.j_PDB_ins_code 
_ndb_struct_na_base_pair.hbond_type_28 
_ndb_struct_na_base_pair.hbond_type_12 
1 A DG  1  1_555 B DC  10 1_555 -0.315 -0.171 0.196  1.596  -5.119  -0.972 1  A_DG1:DC20_B  A 1  ? B 20 ? 19 1 
1 A DC  2  1_555 B DG  9  1_555 0.112  0.006  0.095  4.473  -13.329 1.535  2  A_DC2:DG19_B  A 2  ? B 19 ? 19 1 
1 A DG  3  1_555 B DC  8  1_555 -0.284 -0.208 0.073  -6.466 -15.469 0.315  3  A_DG3:DC18_B  A 3  ? B 18 ? 19 1 
1 A DT  4  1_555 B DA  7  1_555 -0.185 -0.110 -0.024 -6.080 -17.343 -0.350 4  A_DT4:DA17_B  A 4  ? B 17 ? 20 1 
1 A DA  5  1_555 B P2T 6  1_555 0.133  -0.078 0.199  -1.062 -11.155 -4.834 5  A_DA5:P2T16_B A 5  ? B 16 ? 20 1 
1 A P2T 6  1_555 B DA  5  1_555 -0.151 -0.139 0.221  6.405  -12.392 3.569  6  A_P2T6:DA15_B A 6  ? B 15 ? 20 1 
1 A DA  7  1_555 B DT  4  1_555 -0.015 -0.124 0.082  6.226  -12.313 2.744  7  A_DA7:DT14_B  A 7  ? B 14 ? 20 1 
1 A DC  8  1_555 B DG  3  1_555 0.129  -0.185 -0.162 10.289 -13.195 0.952  8  A_DC8:DG13_B  A 8  ? B 13 ? 19 1 
1 A DG  9  1_555 B DC  2  1_555 -0.201 -0.124 -0.087 -7.235 -10.383 1.312  9  A_DG9:DC12_B  A 9  ? B 12 ? 19 1 
1 A DC  10 1_555 B DG  1  1_555 0.195  -0.151 0.048  -2.615 2.067   0.230  10 A_DC10:DG11_B A 10 ? B 11 ? 19 1 
# 
loop_
_ndb_struct_na_base_pair_step.model_number 
_ndb_struct_na_base_pair_step.i_label_asym_id_1 
_ndb_struct_na_base_pair_step.i_label_comp_id_1 
_ndb_struct_na_base_pair_step.i_label_seq_id_1 
_ndb_struct_na_base_pair_step.i_symmetry_1 
_ndb_struct_na_base_pair_step.j_label_asym_id_1 
_ndb_struct_na_base_pair_step.j_label_comp_id_1 
_ndb_struct_na_base_pair_step.j_label_seq_id_1 
_ndb_struct_na_base_pair_step.j_symmetry_1 
_ndb_struct_na_base_pair_step.i_label_asym_id_2 
_ndb_struct_na_base_pair_step.i_label_comp_id_2 
_ndb_struct_na_base_pair_step.i_label_seq_id_2 
_ndb_struct_na_base_pair_step.i_symmetry_2 
_ndb_struct_na_base_pair_step.j_label_asym_id_2 
_ndb_struct_na_base_pair_step.j_label_comp_id_2 
_ndb_struct_na_base_pair_step.j_label_seq_id_2 
_ndb_struct_na_base_pair_step.j_symmetry_2 
_ndb_struct_na_base_pair_step.shift 
_ndb_struct_na_base_pair_step.slide 
_ndb_struct_na_base_pair_step.rise 
_ndb_struct_na_base_pair_step.tilt 
_ndb_struct_na_base_pair_step.roll 
_ndb_struct_na_base_pair_step.twist 
_ndb_struct_na_base_pair_step.x_displacement 
_ndb_struct_na_base_pair_step.y_displacement 
_ndb_struct_na_base_pair_step.helical_rise 
_ndb_struct_na_base_pair_step.inclination 
_ndb_struct_na_base_pair_step.tip 
_ndb_struct_na_base_pair_step.helical_twist 
_ndb_struct_na_base_pair_step.step_number 
_ndb_struct_na_base_pair_step.step_name 
_ndb_struct_na_base_pair_step.i_auth_asym_id_1 
_ndb_struct_na_base_pair_step.i_auth_seq_id_1 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.j_auth_asym_id_1 
_ndb_struct_na_base_pair_step.j_auth_seq_id_1 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_1 
_ndb_struct_na_base_pair_step.i_auth_asym_id_2 
_ndb_struct_na_base_pair_step.i_auth_seq_id_2 
_ndb_struct_na_base_pair_step.i_PDB_ins_code_2 
_ndb_struct_na_base_pair_step.j_auth_asym_id_2 
_ndb_struct_na_base_pair_step.j_auth_seq_id_2 
_ndb_struct_na_base_pair_step.j_PDB_ins_code_2 
1 A DG  1 1_555 B DC  10 1_555 A DC  2  1_555 B DG  9 1_555 0.313  -1.510 3.235 2.150  -0.290 38.677 -2.242 -0.210 3.258 -0.438 
-3.244 38.736 1 AA_DG1DC2:DG19DC20_BB   A 1 ? B 20 ? A 2  ? B 19 ? 
1 A DC  2 1_555 B DG  9  1_555 A DG  3  1_555 B DC  8 1_555 0.164  -2.264 3.429 1.567  10.660 25.420 -7.132 0.006  2.314 22.955 
-3.375 27.575 2 AA_DC2DG3:DC18DG19_BB   A 2 ? B 19 ? A 3  ? B 18 ? 
1 A DG  3 1_555 B DC  8  1_555 A DT  4  1_555 B DA  7 1_555 -1.086 -1.428 3.190 -1.842 5.145  36.448 -2.926 1.480  3.017 8.169  
2.925  36.841 3 AA_DG3DT4:DA17DC18_BB   A 3 ? B 18 ? A 4  ? B 17 ? 
1 A DT  4 1_555 B DA  7  1_555 A DA  5  1_555 B P2T 6 1_555 0.572  -1.550 3.141 0.484  18.501 24.588 -5.885 -1.004 1.617 37.409 
-0.979 30.689 4 AA_DT4DA5:P2T16DA17_BB  A 4 ? B 17 ? A 5  ? B 16 ? 
1 A DA  5 1_555 B P2T 6  1_555 A P2T 6  1_555 B DA  5 1_555 0.681  -1.356 3.125 0.829  4.889  31.728 -3.265 -1.094 2.906 8.874  
-1.505 32.103 5 AA_DA5P2T6:DA15P2T16_BB A 5 ? B 16 ? A 6  ? B 15 ? 
1 A P2T 6 1_555 B DA  5  1_555 A DA  7  1_555 B DT  4 1_555 -0.079 -1.412 3.091 0.991  13.561 30.884 -4.337 0.276  2.284 24.056 
-1.758 33.678 6 AA_P2T6DA7:DT14DA15_BB  A 6 ? B 15 ? A 7  ? B 14 ? 
1 A DA  7 1_555 B DT  4  1_555 A DC  8  1_555 B DG  3 1_555 0.148  -1.711 3.279 1.456  4.094  30.881 -3.940 -0.006 3.036 7.640  
-2.717 31.178 7 AA_DA7DC8:DG13DT14_BB   A 7 ? B 14 ? A 8  ? B 13 ? 
1 A DC  8 1_555 B DG  3  1_555 A DG  9  1_555 B DC  2 1_555 -0.345 -1.909 3.650 -0.241 13.057 29.250 -5.825 0.582  2.587 24.382 
0.451  31.975 8 AA_DC8DG9:DC12DG13_BB   A 8 ? B 13 ? A 9  ? B 12 ? 
1 A DG  9 1_555 B DC  2  1_555 A DC  10 1_555 B DG  1 1_555 0.228  -1.492 3.251 0.665  3.159  35.286 -2.904 -0.280 3.113 5.197  
-1.094 35.428 9 AA_DG9DC10:DG11DC12_BB  A 9 ? B 12 ? A 10 ? B 11 ? 
# 
_pdbx_entity_nonpoly.entity_id   2 
_pdbx_entity_nonpoly.name        water 
_pdbx_entity_nonpoly.comp_id     HOH 
# 
_pdbx_initial_refinement_model.id               1 
_pdbx_initial_refinement_model.entity_id_list   ? 
_pdbx_initial_refinement_model.type             'experimental model' 
_pdbx_initial_refinement_model.source_name      PDB 
_pdbx_initial_refinement_model.accession_code   410D 
_pdbx_initial_refinement_model.details          ? 
#