data_3GJL
# 
_entry.id   3GJL 
# 
_audit_conform.dict_name       mmcif_pdbx.dic 
_audit_conform.dict_version    5.380 
_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   3GJL         pdb_00003gjl 10.2210/pdb3gjl/pdb 
NDB   BD0112       ?            ?                   
RCSB  RCSB051941   ?            ?                   
WWPDB D_1000051941 ?            ?                   
# 
loop_
_pdbx_database_related.db_name 
_pdbx_database_related.db_id 
_pdbx_database_related.details 
_pdbx_database_related.content_type 
PDB 3GJH . unspecified 
PDB 3GJJ . unspecified 
PDB 3GJK . unspecified 
# 
_pdbx_database_status.status_code                     REL 
_pdbx_database_status.entry_id                        3GJL 
_pdbx_database_status.recvd_initial_deposition_date   2009-03-09 
_pdbx_database_status.deposit_site                    RCSB 
_pdbx_database_status.process_site                    PDBJ 
_pdbx_database_status.status_code_sf                  REL 
_pdbx_database_status.status_code_mr                  ? 
_pdbx_database_status.SG_entry                        ? 
_pdbx_database_status.pdb_format_compatible           Y 
_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 
'Takenaka, A.'     1  
'Juan, E.C.M.'     2  
'Shimizu, S.'      3  
'Haraguchi, T.'    4  
'Xiao, M.'         5  
'Kurose, T.'       6  
'Ohkubo, A.'       7  
'Sekine, M.'       8  
'Shibata, T.'      9  
'Millington, C.L.' 10 
'Williams, D.M.'   11 
# 
_citation.id                        primary 
_citation.title                     
;Insights into the stabilizing contributions of bicyclic cytosine analogues: crystal structures of DNA duplexes containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one
;
_citation.journal_abbrev            'To be Published' 
_citation.journal_volume            ? 
_citation.page_first                ? 
_citation.page_last                 ? 
_citation.year                      ? 
_citation.journal_id_ASTM           ? 
_citation.country                   ? 
_citation.journal_id_ISSN           ? 
_citation.journal_id_CSD            0353 
_citation.book_publisher            ? 
_citation.pdbx_database_id_PubMed   ? 
_citation.pdbx_database_id_DOI      ? 
# 
loop_
_citation_author.citation_id 
_citation_author.name 
_citation_author.ordinal 
_citation_author.identifier_ORCID 
primary 'Takenaka, A.'     1  ? 
primary 'Juan, E.C.M.'     2  ? 
primary 'Shimizu, S.'      3  ? 
primary 'Haraguchi, T.'    4  ? 
primary 'Xiao, M.'         5  ? 
primary 'Kurose, T.'       6  ? 
primary 'Ohkubo, A.'       7  ? 
primary 'Sekine, M.'       8  ? 
primary 'Shibata, T.'      9  ? 
primary 'Millington, C.M.' 10 ? 
primary 'William, D.M.'    11 ? 
# 
_cell.entry_id           3GJL 
_cell.length_a           26.477 
_cell.length_b           26.477 
_cell.length_c           98.958 
_cell.angle_alpha        90.00 
_cell.angle_beta         90.00 
_cell.angle_gamma        120.00 
_cell.Z_PDB              6 
_cell.pdbx_unique_axis   ? 
_cell.length_a_esd       ? 
_cell.length_b_esd       ? 
_cell.length_c_esd       ? 
_cell.angle_alpha_esd    ? 
_cell.angle_beta_esd     ? 
_cell.angle_gamma_esd    ? 
# 
_symmetry.entry_id                         3GJL 
_symmetry.space_group_name_H-M             'P 32 1 2' 
_symmetry.pdbx_full_space_group_name_H-M   ? 
_symmetry.cell_setting                     ? 
_symmetry.Int_Tables_number                153 
_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(*CP*GP*CP*GP*AP*A)-3'"      1818.231 1  ? ? ? ? 
2 polymer     syn "5'-D(P*TP*TP*(B7C)P*GP*CP*G)-3'" 1838.251 1  ? ? ? ? 
3 non-polymer syn 'SODIUM ION'                      22.990   1  ? ? ? ? 
4 water       nat water                             18.015   42 ? ? ? ? 
# 
loop_
_entity_poly.entity_id 
_entity_poly.type 
_entity_poly.nstd_linkage 
_entity_poly.nstd_monomer 
_entity_poly.pdbx_seq_one_letter_code 
_entity_poly.pdbx_seq_one_letter_code_can 
_entity_poly.pdbx_strand_id 
_entity_poly.pdbx_target_identifier 
1 polydeoxyribonucleotide no no  '(DC)(DG)(DC)(DG)(DA)(DA)'  CGCGAA A ? 
2 polydeoxyribonucleotide no yes '(DT)(DT)(B7C)(DG)(DC)(DG)' TTXGCG B ? 
# 
loop_
_entity_poly_seq.entity_id 
_entity_poly_seq.num 
_entity_poly_seq.mon_id 
_entity_poly_seq.hetero 
1 1 DC  n 
1 2 DG  n 
1 3 DC  n 
1 4 DG  n 
1 5 DA  n 
1 6 DA  n 
2 1 DT  n 
2 2 DT  n 
2 3 B7C n 
2 4 DG  n 
2 5 DC  n 
2 6 DG  n 
# 
loop_
_struct_ref.id 
_struct_ref.db_name 
_struct_ref.db_code 
_struct_ref.pdbx_db_accession 
_struct_ref.entity_id 
_struct_ref.pdbx_db_isoform 
_struct_ref.pdbx_seq_one_letter_code 
_struct_ref.pdbx_align_begin 
1 PDB 3GJL 3GJL 1 ? ? ? 
2 PDB 3GJL 3GJL 2 ? ? ? 
# 
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 3GJL A 1 ? 6 ? 3GJL 1 ? 6  ? 1 6  
2 2 3GJL B 1 ? 6 ? 3GJL 7 ? 12 ? 7 12 
# 
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 
B7C 'DNA linking' n '3-(2-deoxy-5-O-phosphono-beta-D-erythro-pentofuranosyl)-7,8-dihydropyrido[2,3-d]pyrimidin-2(3H)-one' ? 
'C12 H16 N3 O7 P' 345.245 
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  
NA  non-polymer   . 'SODIUM ION'                                                                                          ? 'Na 1' 
22.990  
# 
_exptl.entry_id          3GJL 
_exptl.method            'X-RAY DIFFRACTION' 
_exptl.crystals_number   1 
# 
_exptl_crystal.id                    1 
_exptl_crystal.density_meas          ? 
_exptl_crystal.density_Matthews      2.74 
_exptl_crystal.density_percent_sol   55.08 
_exptl_crystal.description           ? 
# 
_exptl_crystal_grow.crystal_id      1 
_exptl_crystal_grow.method          'VAPOR DIFFUSION, HANGING DROP' 
_exptl_crystal_grow.temp            293 
_exptl_crystal_grow.temp_details    ? 
_exptl_crystal_grow.pH              7.0 
_exptl_crystal_grow.pdbx_details    
;25mM Sodium cacodylate (pH7.0), 6mM Spermine, tetrahydrochloride, 50mM NaCl, 5% MPD , VAPOR DIFFUSION, HANGING DROP, temperature 293K
;
_exptl_crystal_grow.pdbx_pH_range   . 
# 
_diffrn.id                     1 
_diffrn.ambient_temp           100 
_diffrn.ambient_temp_details   ? 
_diffrn.crystal_id             1 
# 
_diffrn_detector.diffrn_id              1 
_diffrn_detector.detector               CCD 
_diffrn_detector.type                   'ADSC QUANTUM 270' 
_diffrn_detector.pdbx_collection_date   2006-12-17 
_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                    ? 
_diffrn_radiation.pdbx_diffrn_protocol             'SINGLE WAVELENGTH' 
_diffrn_radiation.pdbx_scattering_type             x-ray 
# 
_diffrn_radiation_wavelength.id           1 
_diffrn_radiation_wavelength.wavelength   1.00 
_diffrn_radiation_wavelength.wt           1.0 
# 
_diffrn_source.diffrn_id                   1 
_diffrn_source.source                      SYNCHROTRON 
_diffrn_source.type                        'PHOTON FACTORY BEAMLINE AR-NW12A' 
_diffrn_source.pdbx_synchrotron_site       'Photon Factory' 
_diffrn_source.pdbx_synchrotron_beamline   AR-NW12A 
_diffrn_source.pdbx_wavelength             ? 
_diffrn_source.pdbx_wavelength_list        1.00 
# 
_reflns.entry_id                     3GJL 
_reflns.observed_criterion_sigma_I   0 
_reflns.observed_criterion_sigma_F   0 
_reflns.d_resolution_low             50 
_reflns.d_resolution_high            1.92 
_reflns.number_obs                   3233 
_reflns.number_all                   3233 
_reflns.percent_possible_obs         99.4 
_reflns.pdbx_Rmerge_I_obs            0.064 
_reflns.pdbx_Rsym_value              ? 
_reflns.pdbx_netI_over_sigmaI        91.6 
_reflns.B_iso_Wilson_estimate        ? 
_reflns.pdbx_redundancy              20.7 
_reflns.R_free_details               ? 
_reflns.limit_h_max                  ? 
_reflns.limit_h_min                  ? 
_reflns.limit_k_max                  ? 
_reflns.limit_k_min                  ? 
_reflns.limit_l_max                  ? 
_reflns.limit_l_min                  ? 
_reflns.observed_criterion_F_max     ? 
_reflns.observed_criterion_F_min     ? 
_reflns.pdbx_chi_squared             ? 
_reflns.pdbx_scaling_rejects         ? 
_reflns.pdbx_diffrn_id               1 
_reflns.pdbx_ordinal                 1 
# 
_reflns_shell.d_res_high             1.92 
_reflns_shell.d_res_low              1.99 
_reflns_shell.percent_possible_all   100 
_reflns_shell.Rmerge_I_obs           0.291 
_reflns_shell.pdbx_Rsym_value        ? 
_reflns_shell.meanI_over_sigI_obs    15.9 
_reflns_shell.pdbx_redundancy        21.4 
_reflns_shell.percent_possible_obs   ? 
_reflns_shell.number_unique_all      ? 
_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                                 3GJL 
_refine.ls_number_reflns_obs                     3165 
_refine.ls_number_reflns_all                     3205 
_refine.pdbx_ls_sigma_I                          0 
_refine.pdbx_ls_sigma_F                          2 
_refine.pdbx_data_cutoff_high_absF               ? 
_refine.pdbx_data_cutoff_low_absF                ? 
_refine.pdbx_data_cutoff_high_rms_absF           ? 
_refine.ls_d_res_low                             22.34 
_refine.ls_d_res_high                            1.92 
_refine.ls_percent_reflns_obs                    99.3 
_refine.ls_R_factor_obs                          0.227 
_refine.ls_R_factor_all                          0.227 
_refine.ls_R_factor_R_work                       0.225 
_refine.ls_R_factor_R_free                       0.264 
_refine.ls_R_factor_R_free_error                 ? 
_refine.ls_R_factor_R_free_error_details         ? 
_refine.ls_percent_reflns_R_free                 4.4 
_refine.ls_number_reflns_R_free                  139 
_refine.ls_number_parameters                     ? 
_refine.ls_number_restraints                     ? 
_refine.occupancy_min                            ? 
_refine.occupancy_max                            ? 
_refine.correlation_coeff_Fo_to_Fc               0.952 
_refine.correlation_coeff_Fo_to_Fc_free          0.937 
_refine.B_iso_mean                               25.343 
_refine.aniso_B[1][1]                            -0.06 
_refine.aniso_B[2][2]                            -0.06 
_refine.aniso_B[3][3]                            0.09 
_refine.aniso_B[1][2]                            -0.03 
_refine.aniso_B[1][3]                            0.00 
_refine.aniso_B[2][3]                            0.00 
_refine.solvent_model_details                    MASK 
_refine.solvent_model_param_ksol                 ? 
_refine.solvent_model_param_bsol                 ? 
_refine.pdbx_solvent_vdw_probe_radii             1.40 
_refine.pdbx_solvent_ion_probe_radii             0.80 
_refine.pdbx_solvent_shrinkage_radii             0.80 
_refine.pdbx_ls_cross_valid_method               THROUGHOUT 
_refine.details                                  'HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS' 
_refine.pdbx_starting_model                      1ehv 
_refine.pdbx_method_to_determine_struct          'MOLECULAR REPLACEMENT' 
_refine.pdbx_isotropic_thermal_model             isotropic 
_refine.pdbx_stereochemistry_target_values       'Engh & Huber' 
_refine.pdbx_stereochem_target_val_spec_case     ? 
_refine.pdbx_R_Free_selection_details            RANDOM 
_refine.pdbx_overall_ESU_R                       0.162 
_refine.pdbx_overall_ESU_R_Free                  0.151 
_refine.overall_SU_ML                            0.094 
_refine.overall_SU_B                             3.325 
_refine.ls_redundancy_reflns_obs                 ? 
_refine.B_iso_min                                ? 
_refine.B_iso_max                                ? 
_refine.overall_SU_R_Cruickshank_DPI             ? 
_refine.overall_SU_R_free                        ? 
_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   246 
_refine_hist.pdbx_number_atoms_ligand         1 
_refine_hist.number_atoms_solvent             42 
_refine_hist.number_atoms_total               289 
_refine_hist.d_res_high                       1.92 
_refine_hist.d_res_low                        22.34 
# 
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 
r_bond_refined_d             0.013 0.021 ? 276 'X-RAY DIFFRACTION' ? 
r_bond_other_d               ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_angle_refined_deg          2.209 3.000 ? 423 'X-RAY DIFFRACTION' ? 
r_angle_other_deg            ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_dihedral_angle_1_deg       ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_dihedral_angle_2_deg       ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_dihedral_angle_3_deg       ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_dihedral_angle_4_deg       ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_chiral_restr               0.086 0.200 ? 46  'X-RAY DIFFRACTION' ? 
r_gen_planes_refined         0.011 0.020 ? 127 'X-RAY DIFFRACTION' ? 
r_gen_planes_other           ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_nbd_refined                0.154 0.200 ? 71  'X-RAY DIFFRACTION' ? 
r_nbd_other                  ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_nbtor_refined              0.312 0.200 ? 163 'X-RAY DIFFRACTION' ? 
r_nbtor_other                ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_xyhbond_nbd_refined        0.186 0.200 ? 12  'X-RAY DIFFRACTION' ? 
r_xyhbond_nbd_other          ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_metal_ion_refined          0.443 0.200 ? 1   'X-RAY DIFFRACTION' ? 
r_metal_ion_other            ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_symmetry_vdw_refined       0.447 0.200 ? 27  'X-RAY DIFFRACTION' ? 
r_symmetry_vdw_other         ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_symmetry_hbond_refined     0.062 0.200 ? 10  'X-RAY DIFFRACTION' ? 
r_symmetry_hbond_other       ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_symmetry_metal_ion_refined 0.457 0.200 ? 3   'X-RAY DIFFRACTION' ? 
r_symmetry_metal_ion_other   ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_mcbond_it                  ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_mcbond_other               ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_mcangle_it                 ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_scbond_it                  1.798 3.000 ? 333 'X-RAY DIFFRACTION' ? 
r_scangle_it                 2.407 4.500 ? 423 'X-RAY DIFFRACTION' ? 
r_rigid_bond_restr           ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_sphericity_free            ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
r_sphericity_bonded          ?     ?     ? ?   'X-RAY DIFFRACTION' ? 
# 
_refine_ls_shell.pdbx_total_number_of_bins_used   20 
_refine_ls_shell.d_res_high                       1.921 
_refine_ls_shell.d_res_low                        1.971 
_refine_ls_shell.number_reflns_R_work             206 
_refine_ls_shell.R_factor_R_work                  0.255 
_refine_ls_shell.percent_reflns_obs               100.00 
_refine_ls_shell.R_factor_R_free                  0.413 
_refine_ls_shell.R_factor_R_free_error            ? 
_refine_ls_shell.percent_reflns_R_free            ? 
_refine_ls_shell.number_reflns_R_free             11 
_refine_ls_shell.number_reflns_all                ? 
_refine_ls_shell.R_factor_all                     ? 
_refine_ls_shell.number_reflns_obs                ? 
_refine_ls_shell.redundancy_reflns_obs            ? 
_refine_ls_shell.pdbx_refine_id                   'X-RAY DIFFRACTION' 
# 
_struct.entry_id                  3GJL 
_struct.title                     'crystal structure of a DNA duplex containing 7,8-dihydropyridol[2,3-d]pyrimidin-2-one' 
_struct.pdbx_model_details        ? 
_struct.pdbx_CASP_flag            ? 
_struct.pdbx_model_type_details   ? 
# 
_struct_keywords.entry_id        3GJL 
_struct_keywords.pdbx_keywords   DNA 
_struct_keywords.text            'DNA, duplex, bicyclic cytosine, 7, 8-dihydropyridol[2, 3-d]pyrimidin-2-one' 
# 
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 2 ? 
C N N 3 ? 
D N N 4 ? 
E N N 4 ? 
# 
_struct_biol.id        1 
_struct_biol.details   ? 
# 
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 ? B DT  2 "O3'" ? ? ? 1_555 B B7C 3 P   ? ? B DT  8 B B7C 9  1_555 ? ? ? ? ? ? ?            1.588 ? ? 
covale2  covale both ? B B7C 3 "O3'" ? ? ? 1_555 B DG  4 P   ? ? B B7C 9 B DG  10 1_555 ? ? ? ? ? ? ?            1.606 ? ? 
metalc1  metalc ?    ? C NA  . NA    ? ? ? 1_555 B DG  6 OP1 ? ? B NA  1 B DG  12 1_555 ? ? ? ? ? ? ?            1.906 ? ? 
hydrog1  hydrog ?    ? A DG  2 N1    ? ? ? 1_555 B DC  5 N3  ? ? A DG  2 B DC  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog2  hydrog ?    ? A DG  2 N2    ? ? ? 1_555 B DC  5 O2  ? ? A DG  2 B DC  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog3  hydrog ?    ? A DG  2 O6    ? ? ? 1_555 B DC  5 N4  ? ? A DG  2 B DC  11 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog4  hydrog ?    ? A DC  3 N3    ? ? ? 1_555 B DG  4 N1  ? ? A DC  3 B DG  10 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog5  hydrog ?    ? A DC  3 N4    ? ? ? 1_555 B DG  4 O6  ? ? A DC  3 B DG  10 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog6  hydrog ?    ? A DC  3 O2    ? ? ? 1_555 B DG  4 N2  ? ? A DC  3 B DG  10 1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog7  hydrog ?    ? A DA  5 N1    ? ? ? 1_555 B DT  2 N3  ? ? A DA  5 B DT  8  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog8  hydrog ?    ? A DA  5 N6    ? ? ? 1_555 B DT  2 O4  ? ? A DA  5 B DT  8  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog9  hydrog ?    ? A DA  6 N1    ? ? ? 1_555 B DT  1 N3  ? ? A DA  6 B DT  7  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
hydrog10 hydrog ?    ? A DA  6 N6    ? ? ? 1_555 B DT  1 O4  ? ? A DA  6 B DT  7  1_555 ? ? ? ? ? ? WATSON-CRICK ?     ? ? 
# 
loop_
_struct_conn_type.id 
_struct_conn_type.criteria 
_struct_conn_type.reference 
covale ? ? 
metalc ? ? 
hydrog ? ? 
# 
_struct_site.id                   AC1 
_struct_site.pdbx_evidence_code   Software 
_struct_site.pdbx_auth_asym_id    B 
_struct_site.pdbx_auth_comp_id    NA 
_struct_site.pdbx_auth_seq_id     1 
_struct_site.pdbx_auth_ins_code   ? 
_struct_site.pdbx_num_residues    6 
_struct_site.details              'BINDING SITE FOR RESIDUE NA B 1' 
# 
loop_
_struct_site_gen.id 
_struct_site_gen.site_id 
_struct_site_gen.pdbx_num_res 
_struct_site_gen.label_comp_id 
_struct_site_gen.label_asym_id 
_struct_site_gen.label_seq_id 
_struct_site_gen.pdbx_auth_ins_code 
_struct_site_gen.auth_comp_id 
_struct_site_gen.auth_asym_id 
_struct_site_gen.auth_seq_id 
_struct_site_gen.label_atom_id 
_struct_site_gen.label_alt_id 
_struct_site_gen.symmetry 
_struct_site_gen.details 
1 AC1 6 DC A 1 ? DC A 1  . ? 6_456 ? 
2 AC1 6 DC A 1 ? DC A 1  . ? 1_455 ? 
3 AC1 6 DC B 5 ? DC B 11 . ? 1_555 ? 
4 AC1 6 DC B 5 ? DC B 11 . ? 6_566 ? 
5 AC1 6 DG B 6 ? DG B 12 . ? 1_555 ? 
6 AC1 6 DG B 6 ? DG B 12 . ? 6_566 ? 
# 
_database_PDB_matrix.entry_id          3GJL 
_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                    3GJL 
_atom_sites.fract_transf_matrix[1][1]   0.037769 
_atom_sites.fract_transf_matrix[1][2]   0.021806 
_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]   0.043611 
_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]   0.010105 
_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  
NA 
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 DC  1 1  1  DC  DC  A . n 
A 1 2 DG  2 2  2  DG  DG  A . n 
A 1 3 DC  3 3  3  DC  DC  A . n 
A 1 4 DG  4 4  4  DG  DG  A . n 
A 1 5 DA  5 5  5  DA  DA  A . n 
A 1 6 DA  6 6  6  DA  DA  A . n 
B 2 1 DT  1 7  7  DT  DT  B . n 
B 2 2 DT  2 8  8  DT  DT  B . n 
B 2 3 B7C 3 9  9  B7C B7C B . n 
B 2 4 DG  4 10 10 DG  DG  B . n 
B 2 5 DC  5 11 11 DC  DC  B . n 
B 2 6 DG  6 12 12 DG  DG  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 3 NA  1  1  1  NA  NA  B . 
D 4 HOH 1  7  1  HOH HOH A . 
D 4 HOH 2  8  8  HOH HOH A . 
D 4 HOH 3  9  9  HOH HOH A . 
D 4 HOH 4  10 2  HOH HOH A . 
D 4 HOH 5  11 11 HOH HOH A . 
D 4 HOH 6  12 12 HOH HOH A . 
D 4 HOH 7  16 16 HOH HOH A . 
D 4 HOH 8  17 6  HOH HOH A . 
D 4 HOH 9  27 27 HOH HOH A . 
D 4 HOH 10 28 28 HOH HOH A . 
D 4 HOH 11 29 29 HOH HOH A . 
D 4 HOH 12 30 30 HOH HOH A . 
D 4 HOH 13 31 31 HOH HOH A . 
D 4 HOH 14 34 34 HOH HOH A . 
D 4 HOH 15 35 35 HOH HOH A . 
D 4 HOH 16 36 36 HOH HOH A . 
D 4 HOH 17 37 37 HOH HOH A . 
E 4 HOH 1  3  3  HOH HOH B . 
E 4 HOH 2  4  4  HOH HOH B . 
E 4 HOH 3  5  5  HOH HOH B . 
E 4 HOH 4  13 13 HOH HOH B . 
E 4 HOH 5  14 14 HOH HOH B . 
E 4 HOH 6  15 15 HOH HOH B . 
E 4 HOH 7  16 7  HOH HOH B . 
E 4 HOH 8  17 17 HOH HOH B . 
E 4 HOH 9  18 18 HOH HOH B . 
E 4 HOH 10 19 19 HOH HOH B . 
E 4 HOH 11 20 20 HOH HOH B . 
E 4 HOH 12 21 21 HOH HOH B . 
E 4 HOH 13 22 22 HOH HOH B . 
E 4 HOH 14 23 23 HOH HOH B . 
E 4 HOH 15 24 24 HOH HOH B . 
E 4 HOH 16 25 25 HOH HOH B . 
E 4 HOH 17 26 26 HOH HOH B . 
E 4 HOH 18 27 10 HOH HOH B . 
E 4 HOH 19 32 32 HOH HOH B . 
E 4 HOH 20 33 33 HOH HOH B . 
E 4 HOH 21 38 38 HOH HOH B . 
E 4 HOH 22 39 39 HOH HOH B . 
E 4 HOH 23 40 40 HOH HOH B . 
E 4 HOH 24 41 41 HOH HOH B . 
E 4 HOH 25 42 42 HOH HOH B . 
# 
_pdbx_struct_mod_residue.id               1 
_pdbx_struct_mod_residue.label_asym_id    B 
_pdbx_struct_mod_residue.label_comp_id    B7C 
_pdbx_struct_mod_residue.label_seq_id     3 
_pdbx_struct_mod_residue.auth_asym_id     B 
_pdbx_struct_mod_residue.auth_comp_id     B7C 
_pdbx_struct_mod_residue.auth_seq_id      9 
_pdbx_struct_mod_residue.PDB_ins_code     ? 
_pdbx_struct_mod_residue.parent_comp_id   DC 
_pdbx_struct_mod_residue.details          ? 
# 
_pdbx_struct_assembly.id                   1 
_pdbx_struct_assembly.details              author_and_software_defined_assembly 
_pdbx_struct_assembly.method_details       PISA 
_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,E 
# 
loop_
_pdbx_struct_assembly_prop.biol_id 
_pdbx_struct_assembly_prop.type 
_pdbx_struct_assembly_prop.value 
_pdbx_struct_assembly_prop.details 
1 'ABSA (A^2)' 460  ? 
1 MORE         -3   ? 
1 'SSA (A^2)'  2660 ? 
# 
_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 
# 
_pdbx_struct_special_symmetry.id              1 
_pdbx_struct_special_symmetry.PDB_model_num   1 
_pdbx_struct_special_symmetry.auth_asym_id    B 
_pdbx_struct_special_symmetry.auth_comp_id    NA 
_pdbx_struct_special_symmetry.auth_seq_id     1 
_pdbx_struct_special_symmetry.PDB_ins_code    ? 
_pdbx_struct_special_symmetry.label_asym_id   C 
_pdbx_struct_special_symmetry.label_comp_id   NA 
_pdbx_struct_special_symmetry.label_seq_id    . 
# 
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 2010-03-31 
2 'Structure model' 1 1 2011-07-13 
3 'Structure model' 1 2 2023-11-01 
# 
_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' 'Data collection'           
3 3 'Structure model' 'Database references'       
4 3 'Structure model' 'Derived calculations'      
5 3 '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 3 'Structure model' chem_comp_atom                
2 3 'Structure model' chem_comp_bond                
3 3 'Structure model' database_2                    
4 3 'Structure model' pdbx_initial_refinement_model 
5 3 'Structure model' struct_conn                   
6 3 'Structure model' struct_site                   
# 
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  3 'Structure model' '_database_2.pdbx_DOI'                
2  3 'Structure model' '_database_2.pdbx_database_accession' 
3  3 'Structure model' '_struct_conn.pdbx_leaving_atom_flag' 
4  3 'Structure model' '_struct_conn.ptnr1_auth_comp_id'     
5  3 'Structure model' '_struct_conn.ptnr1_auth_seq_id'      
6  3 'Structure model' '_struct_conn.ptnr1_label_asym_id'    
7  3 'Structure model' '_struct_conn.ptnr1_label_atom_id'    
8  3 'Structure model' '_struct_conn.ptnr1_label_comp_id'    
9  3 'Structure model' '_struct_conn.ptnr1_label_seq_id'     
10 3 'Structure model' '_struct_conn.ptnr2_auth_comp_id'     
11 3 'Structure model' '_struct_conn.ptnr2_auth_seq_id'      
12 3 'Structure model' '_struct_conn.ptnr2_label_asym_id'    
13 3 'Structure model' '_struct_conn.ptnr2_label_atom_id'    
14 3 'Structure model' '_struct_conn.ptnr2_label_comp_id'    
15 3 'Structure model' '_struct_conn.ptnr2_label_seq_id'     
16 3 'Structure model' '_struct_site.pdbx_auth_asym_id'      
17 3 'Structure model' '_struct_site.pdbx_auth_comp_id'      
18 3 'Structure model' '_struct_site.pdbx_auth_seq_id'       
# 
loop_
_software.name 
_software.classification 
_software.version 
_software.citation_id 
_software.pdbx_ordinal 
HKL-2000 'data collection' .        ? 1 
AMoRE    phasing           .        ? 2 
REFMAC   refinement        5.2.0019 ? 3 
HKL-2000 'data reduction'  .        ? 4 
HKL-2000 'data scaling'    .        ? 5 
# 
_pdbx_validate_symm_contact.id                1 
_pdbx_validate_symm_contact.PDB_model_num     1 
_pdbx_validate_symm_contact.auth_atom_id_1    "O3'" 
_pdbx_validate_symm_contact.auth_asym_id_1    A 
_pdbx_validate_symm_contact.auth_comp_id_1    DA 
_pdbx_validate_symm_contact.auth_seq_id_1     6 
_pdbx_validate_symm_contact.PDB_ins_code_1    ? 
_pdbx_validate_symm_contact.label_alt_id_1    ? 
_pdbx_validate_symm_contact.site_symmetry_1   1_555 
_pdbx_validate_symm_contact.auth_atom_id_2    P 
_pdbx_validate_symm_contact.auth_asym_id_2    B 
_pdbx_validate_symm_contact.auth_comp_id_2    DT 
_pdbx_validate_symm_contact.auth_seq_id_2     7 
_pdbx_validate_symm_contact.PDB_ins_code_2    ? 
_pdbx_validate_symm_contact.label_alt_id_2    ? 
_pdbx_validate_symm_contact.site_symmetry_2   5_555 
_pdbx_validate_symm_contact.dist              1.65 
# 
loop_
_pdbx_validate_rmsd_angle.id 
_pdbx_validate_rmsd_angle.PDB_model_num 
_pdbx_validate_rmsd_angle.auth_atom_id_1 
_pdbx_validate_rmsd_angle.auth_asym_id_1 
_pdbx_validate_rmsd_angle.auth_comp_id_1 
_pdbx_validate_rmsd_angle.auth_seq_id_1 
_pdbx_validate_rmsd_angle.PDB_ins_code_1 
_pdbx_validate_rmsd_angle.label_alt_id_1 
_pdbx_validate_rmsd_angle.auth_atom_id_2 
_pdbx_validate_rmsd_angle.auth_asym_id_2 
_pdbx_validate_rmsd_angle.auth_comp_id_2 
_pdbx_validate_rmsd_angle.auth_seq_id_2 
_pdbx_validate_rmsd_angle.PDB_ins_code_2 
_pdbx_validate_rmsd_angle.label_alt_id_2 
_pdbx_validate_rmsd_angle.auth_atom_id_3 
_pdbx_validate_rmsd_angle.auth_asym_id_3 
_pdbx_validate_rmsd_angle.auth_comp_id_3 
_pdbx_validate_rmsd_angle.auth_seq_id_3 
_pdbx_validate_rmsd_angle.PDB_ins_code_3 
_pdbx_validate_rmsd_angle.label_alt_id_3 
_pdbx_validate_rmsd_angle.angle_value 
_pdbx_validate_rmsd_angle.angle_target_value 
_pdbx_validate_rmsd_angle.angle_deviation 
_pdbx_validate_rmsd_angle.angle_standard_deviation 
_pdbx_validate_rmsd_angle.linker_flag 
1 1 "O4'" A DG 2  ? ? "C1'" A DG 2  ? ? N9 A DG 2  ? ? 101.49 108.00 -6.51 0.70 N 
2 1 "O4'" A DG 4  ? ? "C1'" A DG 4  ? ? N9 A DG 4  ? ? 110.31 108.30 2.01  0.30 N 
3 1 "O4'" B DC 11 ? ? "C1'" B DC 11 ? ? N1 B DC 11 ? ? 110.84 108.30 2.54  0.30 N 
# 
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 
B7C OP3    O  N N 1   
B7C P      P  N N 2   
B7C OP1    O  N N 3   
B7C OP2    O  N N 4   
B7C "O5'"  O  N N 5   
B7C N1     N  N N 6   
B7C C6     C  N N 7   
B7C C2     C  N N 8   
B7C O2     O  N N 9   
B7C N3     N  N N 10  
B7C C4     C  N N 11  
B7C N4     N  N N 12  
B7C C5     C  N N 13  
B7C C7     C  N N 14  
B7C C8     C  N N 15  
B7C C9     C  N N 16  
B7C "C2'"  C  N N 17  
B7C "C5'"  C  N N 18  
B7C "C4'"  C  N R 19  
B7C "O4'"  O  N N 20  
B7C "C1'"  C  N R 21  
B7C "C3'"  C  N S 22  
B7C "O3'"  O  N N 23  
B7C HOP3   H  N N 24  
B7C HOP1   H  N N 25  
B7C H6     H  N N 26  
B7C HN4    H  N N 27  
B7C H7     H  N N 28  
B7C H8     H  N N 29  
B7C H9     H  N N 30  
B7C H9A    H  N N 31  
B7C "H2'"  H  N N 32  
B7C "H2'A" H  N N 33  
B7C "H5'"  H  N N 34  
B7C "H5'A" H  N N 35  
B7C "H4'"  H  N N 36  
B7C "H1'"  H  N N 37  
B7C "H3'"  H  N N 38  
B7C "HO3'" H  N N 39  
DA  OP3    O  N N 40  
DA  P      P  N N 41  
DA  OP1    O  N N 42  
DA  OP2    O  N N 43  
DA  "O5'"  O  N N 44  
DA  "C5'"  C  N N 45  
DA  "C4'"  C  N R 46  
DA  "O4'"  O  N N 47  
DA  "C3'"  C  N S 48  
DA  "O3'"  O  N N 49  
DA  "C2'"  C  N N 50  
DA  "C1'"  C  N R 51  
DA  N9     N  Y N 52  
DA  C8     C  Y N 53  
DA  N7     N  Y N 54  
DA  C5     C  Y N 55  
DA  C6     C  Y N 56  
DA  N6     N  N N 57  
DA  N1     N  Y N 58  
DA  C2     C  Y N 59  
DA  N3     N  Y N 60  
DA  C4     C  Y N 61  
DA  HOP3   H  N N 62  
DA  HOP2   H  N N 63  
DA  "H5'"  H  N N 64  
DA  "H5''" H  N N 65  
DA  "H4'"  H  N N 66  
DA  "H3'"  H  N N 67  
DA  "HO3'" H  N N 68  
DA  "H2'"  H  N N 69  
DA  "H2''" H  N N 70  
DA  "H1'"  H  N N 71  
DA  H8     H  N N 72  
DA  H61    H  N N 73  
DA  H62    H  N N 74  
DA  H2     H  N N 75  
DC  OP3    O  N N 76  
DC  P      P  N N 77  
DC  OP1    O  N N 78  
DC  OP2    O  N N 79  
DC  "O5'"  O  N N 80  
DC  "C5'"  C  N N 81  
DC  "C4'"  C  N R 82  
DC  "O4'"  O  N N 83  
DC  "C3'"  C  N S 84  
DC  "O3'"  O  N N 85  
DC  "C2'"  C  N N 86  
DC  "C1'"  C  N R 87  
DC  N1     N  N N 88  
DC  C2     C  N N 89  
DC  O2     O  N N 90  
DC  N3     N  N N 91  
DC  C4     C  N N 92  
DC  N4     N  N N 93  
DC  C5     C  N N 94  
DC  C6     C  N N 95  
DC  HOP3   H  N N 96  
DC  HOP2   H  N N 97  
DC  "H5'"  H  N N 98  
DC  "H5''" H  N N 99  
DC  "H4'"  H  N N 100 
DC  "H3'"  H  N N 101 
DC  "HO3'" H  N N 102 
DC  "H2'"  H  N N 103 
DC  "H2''" H  N N 104 
DC  "H1'"  H  N N 105 
DC  H41    H  N N 106 
DC  H42    H  N N 107 
DC  H5     H  N N 108 
DC  H6     H  N N 109 
DG  OP3    O  N N 110 
DG  P      P  N N 111 
DG  OP1    O  N N 112 
DG  OP2    O  N N 113 
DG  "O5'"  O  N N 114 
DG  "C5'"  C  N N 115 
DG  "C4'"  C  N R 116 
DG  "O4'"  O  N N 117 
DG  "C3'"  C  N S 118 
DG  "O3'"  O  N N 119 
DG  "C2'"  C  N N 120 
DG  "C1'"  C  N R 121 
DG  N9     N  Y N 122 
DG  C8     C  Y N 123 
DG  N7     N  Y N 124 
DG  C5     C  Y N 125 
DG  C6     C  N N 126 
DG  O6     O  N N 127 
DG  N1     N  N N 128 
DG  C2     C  N N 129 
DG  N2     N  N N 130 
DG  N3     N  N N 131 
DG  C4     C  Y N 132 
DG  HOP3   H  N N 133 
DG  HOP2   H  N N 134 
DG  "H5'"  H  N N 135 
DG  "H5''" H  N N 136 
DG  "H4'"  H  N N 137 
DG  "H3'"  H  N N 138 
DG  "HO3'" H  N N 139 
DG  "H2'"  H  N N 140 
DG  "H2''" H  N N 141 
DG  "H1'"  H  N N 142 
DG  H8     H  N N 143 
DG  H1     H  N N 144 
DG  H21    H  N N 145 
DG  H22    H  N N 146 
DT  OP3    O  N N 147 
DT  P      P  N N 148 
DT  OP1    O  N N 149 
DT  OP2    O  N N 150 
DT  "O5'"  O  N N 151 
DT  "C5'"  C  N N 152 
DT  "C4'"  C  N R 153 
DT  "O4'"  O  N N 154 
DT  "C3'"  C  N S 155 
DT  "O3'"  O  N N 156 
DT  "C2'"  C  N N 157 
DT  "C1'"  C  N R 158 
DT  N1     N  N N 159 
DT  C2     C  N N 160 
DT  O2     O  N N 161 
DT  N3     N  N N 162 
DT  C4     C  N N 163 
DT  O4     O  N N 164 
DT  C5     C  N N 165 
DT  C7     C  N N 166 
DT  C6     C  N N 167 
DT  HOP3   H  N N 168 
DT  HOP2   H  N N 169 
DT  "H5'"  H  N N 170 
DT  "H5''" H  N N 171 
DT  "H4'"  H  N N 172 
DT  "H3'"  H  N N 173 
DT  "HO3'" H  N N 174 
DT  "H2'"  H  N N 175 
DT  "H2''" H  N N 176 
DT  "H1'"  H  N N 177 
DT  H3     H  N N 178 
DT  H71    H  N N 179 
DT  H72    H  N N 180 
DT  H73    H  N N 181 
DT  H6     H  N N 182 
HOH O      O  N N 183 
HOH H1     H  N N 184 
HOH H2     H  N N 185 
NA  NA     NA N N 186 
# 
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 
B7C OP3   P      sing N N 1   
B7C P     OP1    sing N N 2   
B7C P     OP2    doub N N 3   
B7C P     "O5'"  sing N N 4   
B7C "O5'" "C5'"  sing N N 5   
B7C N1    C6     sing N N 6   
B7C N1    C2     sing N N 7   
B7C N1    "C1'"  sing N N 8   
B7C C6    C5     doub N N 9   
B7C C2    O2     doub N N 10  
B7C C2    N3     sing N N 11  
B7C N3    C4     doub N N 12  
B7C C4    N4     sing N N 13  
B7C C4    C5     sing N N 14  
B7C N4    C9     sing N N 15  
B7C C5    C7     sing N N 16  
B7C C7    C8     doub N N 17  
B7C C8    C9     sing N N 18  
B7C "C2'" "C1'"  sing N N 19  
B7C "C2'" "C3'"  sing N N 20  
B7C "C5'" "C4'"  sing N N 21  
B7C "C4'" "O4'"  sing N N 22  
B7C "C4'" "C3'"  sing N N 23  
B7C "O4'" "C1'"  sing N N 24  
B7C "C3'" "O3'"  sing N N 25  
B7C OP3   HOP3   sing N N 26  
B7C OP1   HOP1   sing N N 27  
B7C C6    H6     sing N N 28  
B7C N4    HN4    sing N N 29  
B7C C7    H7     sing N N 30  
B7C C8    H8     sing N N 31  
B7C C9    H9     sing N N 32  
B7C C9    H9A    sing N N 33  
B7C "C2'" "H2'"  sing N N 34  
B7C "C2'" "H2'A" sing N N 35  
B7C "C5'" "H5'"  sing N N 36  
B7C "C5'" "H5'A" sing N N 37  
B7C "C4'" "H4'"  sing N N 38  
B7C "C1'" "H1'"  sing N N 39  
B7C "C3'" "H3'"  sing N N 40  
B7C "O3'" "HO3'" sing N N 41  
DA  OP3   P      sing N N 42  
DA  OP3   HOP3   sing N N 43  
DA  P     OP1    doub N N 44  
DA  P     OP2    sing N N 45  
DA  P     "O5'"  sing N N 46  
DA  OP2   HOP2   sing N N 47  
DA  "O5'" "C5'"  sing N N 48  
DA  "C5'" "C4'"  sing N N 49  
DA  "C5'" "H5'"  sing N N 50  
DA  "C5'" "H5''" sing N N 51  
DA  "C4'" "O4'"  sing N N 52  
DA  "C4'" "C3'"  sing N N 53  
DA  "C4'" "H4'"  sing N N 54  
DA  "O4'" "C1'"  sing N N 55  
DA  "C3'" "O3'"  sing N N 56  
DA  "C3'" "C2'"  sing N N 57  
DA  "C3'" "H3'"  sing N N 58  
DA  "O3'" "HO3'" sing N N 59  
DA  "C2'" "C1'"  sing N N 60  
DA  "C2'" "H2'"  sing N N 61  
DA  "C2'" "H2''" sing N N 62  
DA  "C1'" N9     sing N N 63  
DA  "C1'" "H1'"  sing N N 64  
DA  N9    C8     sing Y N 65  
DA  N9    C4     sing Y N 66  
DA  C8    N7     doub Y N 67  
DA  C8    H8     sing N N 68  
DA  N7    C5     sing Y N 69  
DA  C5    C6     sing Y N 70  
DA  C5    C4     doub Y N 71  
DA  C6    N6     sing N N 72  
DA  C6    N1     doub Y N 73  
DA  N6    H61    sing N N 74  
DA  N6    H62    sing N N 75  
DA  N1    C2     sing Y N 76  
DA  C2    N3     doub Y N 77  
DA  C2    H2     sing N N 78  
DA  N3    C4     sing Y N 79  
DC  OP3   P      sing N N 80  
DC  OP3   HOP3   sing N N 81  
DC  P     OP1    doub N N 82  
DC  P     OP2    sing N N 83  
DC  P     "O5'"  sing N N 84  
DC  OP2   HOP2   sing N N 85  
DC  "O5'" "C5'"  sing N N 86  
DC  "C5'" "C4'"  sing N N 87  
DC  "C5'" "H5'"  sing N N 88  
DC  "C5'" "H5''" sing N N 89  
DC  "C4'" "O4'"  sing N N 90  
DC  "C4'" "C3'"  sing N N 91  
DC  "C4'" "H4'"  sing N N 92  
DC  "O4'" "C1'"  sing N N 93  
DC  "C3'" "O3'"  sing N N 94  
DC  "C3'" "C2'"  sing N N 95  
DC  "C3'" "H3'"  sing N N 96  
DC  "O3'" "HO3'" sing N N 97  
DC  "C2'" "C1'"  sing N N 98  
DC  "C2'" "H2'"  sing N N 99  
DC  "C2'" "H2''" sing N N 100 
DC  "C1'" N1     sing N N 101 
DC  "C1'" "H1'"  sing N N 102 
DC  N1    C2     sing N N 103 
DC  N1    C6     sing N N 104 
DC  C2    O2     doub N N 105 
DC  C2    N3     sing N N 106 
DC  N3    C4     doub N N 107 
DC  C4    N4     sing N N 108 
DC  C4    C5     sing N N 109 
DC  N4    H41    sing N N 110 
DC  N4    H42    sing N N 111 
DC  C5    C6     doub N N 112 
DC  C5    H5     sing N N 113 
DC  C6    H6     sing N N 114 
DG  OP3   P      sing N N 115 
DG  OP3   HOP3   sing N N 116 
DG  P     OP1    doub N N 117 
DG  P     OP2    sing N N 118 
DG  P     "O5'"  sing N N 119 
DG  OP2   HOP2   sing N N 120 
DG  "O5'" "C5'"  sing N N 121 
DG  "C5'" "C4'"  sing N N 122 
DG  "C5'" "H5'"  sing N N 123 
DG  "C5'" "H5''" sing N N 124 
DG  "C4'" "O4'"  sing N N 125 
DG  "C4'" "C3'"  sing N N 126 
DG  "C4'" "H4'"  sing N N 127 
DG  "O4'" "C1'"  sing N N 128 
DG  "C3'" "O3'"  sing N N 129 
DG  "C3'" "C2'"  sing N N 130 
DG  "C3'" "H3'"  sing N N 131 
DG  "O3'" "HO3'" sing N N 132 
DG  "C2'" "C1'"  sing N N 133 
DG  "C2'" "H2'"  sing N N 134 
DG  "C2'" "H2''" sing N N 135 
DG  "C1'" N9     sing N N 136 
DG  "C1'" "H1'"  sing N N 137 
DG  N9    C8     sing Y N 138 
DG  N9    C4     sing Y N 139 
DG  C8    N7     doub Y N 140 
DG  C8    H8     sing N N 141 
DG  N7    C5     sing Y N 142 
DG  C5    C6     sing N N 143 
DG  C5    C4     doub Y N 144 
DG  C6    O6     doub N N 145 
DG  C6    N1     sing N N 146 
DG  N1    C2     sing N N 147 
DG  N1    H1     sing N N 148 
DG  C2    N2     sing N N 149 
DG  C2    N3     doub N N 150 
DG  N2    H21    sing N N 151 
DG  N2    H22    sing N N 152 
DG  N3    C4     sing N N 153 
DT  OP3   P      sing N N 154 
DT  OP3   HOP3   sing N N 155 
DT  P     OP1    doub N N 156 
DT  P     OP2    sing N N 157 
DT  P     "O5'"  sing N N 158 
DT  OP2   HOP2   sing N N 159 
DT  "O5'" "C5'"  sing N N 160 
DT  "C5'" "C4'"  sing N N 161 
DT  "C5'" "H5'"  sing N N 162 
DT  "C5'" "H5''" sing N N 163 
DT  "C4'" "O4'"  sing N N 164 
DT  "C4'" "C3'"  sing N N 165 
DT  "C4'" "H4'"  sing N N 166 
DT  "O4'" "C1'"  sing N N 167 
DT  "C3'" "O3'"  sing N N 168 
DT  "C3'" "C2'"  sing N N 169 
DT  "C3'" "H3'"  sing N N 170 
DT  "O3'" "HO3'" sing N N 171 
DT  "C2'" "C1'"  sing N N 172 
DT  "C2'" "H2'"  sing N N 173 
DT  "C2'" "H2''" sing N N 174 
DT  "C1'" N1     sing N N 175 
DT  "C1'" "H1'"  sing N N 176 
DT  N1    C2     sing N N 177 
DT  N1    C6     sing N N 178 
DT  C2    O2     doub N N 179 
DT  C2    N3     sing N N 180 
DT  N3    C4     sing N N 181 
DT  N3    H3     sing N N 182 
DT  C4    O4     doub N N 183 
DT  C4    C5     sing N N 184 
DT  C5    C7     sing N N 185 
DT  C5    C6     doub N N 186 
DT  C7    H71    sing N N 187 
DT  C7    H72    sing N N 188 
DT  C7    H73    sing N N 189 
DT  C6    H6     sing N N 190 
HOH O     H1     sing N N 191 
HOH O     H2     sing N N 192 
# 
loop_
_ndb_struct_conf_na.entry_id 
_ndb_struct_conf_na.feature 
3GJL 'double helix'         
3GJL 'mismatched base pair' 
# 
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 2 1_555 B DC 5 1_555 -0.226 -0.180 0.269  -7.982 -0.800  -1.478 1 A_DG2:DC11_B A 2 ? B 11 ? 19 1 
1 A DC 3 1_555 B DG 4 1_555 0.257  -0.113 0.148  -2.087 2.293   0.953  2 A_DC3:DG10_B A 3 ? B 10 ? 19 1 
1 A DA 5 1_555 B DT 2 1_555 -0.009 -0.089 -0.017 1.800  -18.773 4.442  3 A_DA5:DT8_B  A 5 ? B 8  ? 20 1 
1 A DA 6 1_555 B DT 1 1_555 -0.002 -0.085 0.038  -0.067 -18.820 5.475  4 A_DA6:DT7_B  A 6 ? B 7  ? 20 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 2 1_555 B DC 5 1_555 A DC 3 1_555 B DG 4 1_555 0.873 0.334  3.360 1.419  -6.238 36.851 1.362  -1.170 3.292 -9.778 -2.224 
37.383 1 AA_DG2DC3:DG10DC11_BB A 2 ? B 11 ? A 3 ? B 10 ? 
1 A DC 3 1_555 B DG 4 1_555 A DA 5 1_555 B DT 2 1_555 0.004 0.099  6.374 3.719  4.817  67.276 -0.272 0.275  6.360 4.339  -3.350 
67.518 2 AA_DC3DA5:DT8DG10_BB  A 3 ? B 10 ? A 5 ? B 8  ? 
1 A DA 5 1_555 B DT 2 1_555 A DA 6 1_555 B DT 1 1_555 0.090 -0.285 3.269 -0.408 -2.459 35.567 -0.108 -0.207 3.279 -4.019 0.666  
35.652 3 AA_DA5DA6:DT7DT8_BB   A 5 ? B 8  ? A 6 ? B 7  ? 
# 
loop_
_pdbx_entity_nonpoly.entity_id 
_pdbx_entity_nonpoly.name 
_pdbx_entity_nonpoly.comp_id 
3 'SODIUM ION' NA  
4 water        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   1EHV 
_pdbx_initial_refinement_model.details          ? 
#