data_8EVF # _model_server_result.job_id EqKo2j9y4Yd_02wdbXuhAw _model_server_result.datetime_utc '2025-01-12 19:16:07' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 8evf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 8EVF # _exptl.entry_id 8EVF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 8EVF _cell.length_a 98.671 _cell.length_b 98.671 _cell.length_c 81.736 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EVF _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1 # _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 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.id _struct_conn.ptnr1_label_asym_id _struct_conn.ptnr1_label_atom_id _struct_conn.ptnr1_label_comp_id _struct_conn.ptnr1_label_seq_id _struct_conn.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _struct_conn.ptnr2_label_asym_id _struct_conn.ptnr2_label_atom_id _struct_conn.ptnr2_label_comp_id _struct_conn.ptnr2_label_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_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order covale ? covale1 B O3' DG 4 T DG 4 1_555 B P X6H 5 T X6H 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.604 ? covale ? covale2 B O3' X6H 5 T X6H 5 1_555 B P DT 6 T DT 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.605 ? metalc ? metalc1 A OD1 ASP 16 A ASP 13 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.085 ? metalc ? metalc2 A OD2 ASP 16 A ASP 13 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc3 A OD2 ASP 16 A ASP 13 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.249 ? metalc ? metalc4 A O MET 17 A MET 14 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc5 A OD2 ASP 118 A ASP 115 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.29 ? metalc ? metalc6 A OD1 ASP 118 A ASP 115 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.124 ? metalc ? metalc7 A OE1 GLU 119 A GLU 116 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.26 ? metalc ? metalc8 D O2A DCP . A DCP 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.694 ? metalc ? metalc9 D O3A DCP . A DCP 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.115 ? metalc ? metalc10 D O2B DCP . A DCP 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.458 ? metalc ? metalc11 D O3B DCP . A DCP 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.174 ? metalc ? metalc12 D O2G DCP . A DCP 501 1_555 E CA CA . A CA 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc13 D O2A DCP . A DCP 501 1_555 F CA CA . A CA 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.293 ? metalc ? metalc14 F CA CA . A CA 503 1_555 C O3' DG 8 P DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? hydrog WATSON-CRICK hydrog1 B N3 DT 6 T DT 6 1_555 C N1 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 B O4 DT 6 T DT 6 1_555 C N6 DA 7 P DA 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 B N1 DG 7 T DG 7 1_555 C N3 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 B N2 DG 7 T DG 7 1_555 C O2 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 B O6 DG 7 T DG 7 1_555 C N4 DC 6 P DC 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 B N1 DA 8 T DA 8 1_555 C N3 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 B N6 DA 8 T DA 8 1_555 C O4 DT 5 P DT 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 B N3 DC 9 T DC 9 1_555 C N1 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 B N4 DC 9 T DC 9 1_555 C O6 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 B O2 DC 9 T DC 9 1_555 C N2 DG 4 P DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 B N1 DG 10 T DG 10 1_555 C N3 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 B N2 DG 10 T DG 10 1_555 C O2 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 B O6 DG 10 T DG 10 1_555 C N4 DC 3 P DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 B N3 DC 11 T DC 11 1_555 C N1 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 B N4 DC 11 T DC 11 1_555 C O6 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 B O2 DC 11 T DC 11 1_555 C N2 DG 2 P DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 B N3 DT 12 T DT 12 1_555 C N1 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 B O4 DT 12 T DT 12 1_555 C N6 DA 1 P DA 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DCP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYCYTIDINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag N1 C2 DCP sing 156 n n N1 C6 DCP sing 157 n n N1 C1' DCP sing 158 n n C2 N3 DCP sing 159 n n C2 O2 DCP doub 160 n n N3 C4 DCP doub 161 n n C4 C5 DCP sing 162 n n C4 N4 DCP sing 163 n n C5 C6 DCP doub 164 n n C5 H5 DCP sing 165 n n C6 H6 DCP sing 166 n n N4 HN41 DCP sing 167 n n N4 HN42 DCP sing 168 n n C1' C2' DCP sing 169 n n C1' O4' DCP sing 170 n n C1' H1' DCP sing 171 n n C2' C3' DCP sing 172 n n C2' "H2'1" DCP sing 173 n n C2' "H2'2" DCP sing 174 n n C3' C4' DCP sing 175 n n C3' O3' DCP sing 176 n n C3' H3' DCP sing 177 n n C4' O4' DCP sing 178 n n C4' C5' DCP sing 179 n n C4' H4' DCP sing 180 n n O3' HO3' DCP sing 181 n n C5' O5' DCP sing 182 n n C5' "H5'1" DCP sing 183 n n C5' "H5'2" DCP sing 184 n n O5' PA DCP sing 185 n n PA O1A DCP doub 186 n n PA O2A DCP sing 187 n n PA O3A DCP sing 188 n n O2A HOA2 DCP sing 189 n n O3A PB DCP sing 190 n n PB O1B DCP doub 191 n n PB O2B DCP sing 192 n n PB O3B DCP sing 193 n n O2B HOB2 DCP sing 194 n n O3B PG DCP sing 195 n n PG O1G DCP doub 196 n n PG O2G DCP sing 197 n n PG O3G DCP sing 198 n n O2G HOG2 DCP sing 199 n n O3G HOG3 DCP sing 200 n n # _atom_sites.entry_id 8EVF _atom_sites.fract_transf_matrix[1][1] 0.010135 _atom_sites.fract_transf_matrix[1][2] 0.005851 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011703 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.012235 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_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_ins_code D 4 DCP A 1 501 501 DCP DCP . E 5 CA A 1 502 1 CA CA . F 5 CA A 1 503 2 CA CA . G 6 HOH A 1 601 7 HOH HOH . G 6 HOH A 2 602 5 HOH HOH . G 6 HOH A 3 603 13 HOH HOH . G 6 HOH A 4 604 18 HOH HOH . G 6 HOH A 5 605 23 HOH HOH . G 6 HOH A 6 606 24 HOH HOH . G 6 HOH A 7 607 12 HOH HOH . G 6 HOH A 8 608 4 HOH HOH . G 6 HOH A 9 609 9 HOH HOH . G 6 HOH A 10 610 21 HOH HOH . G 6 HOH A 11 611 11 HOH HOH . G 6 HOH A 12 612 20 HOH HOH . G 6 HOH A 13 613 22 HOH HOH . G 6 HOH A 14 614 10 HOH HOH . G 6 HOH A 15 615 3 HOH HOH . G 6 HOH A 16 616 17 HOH HOH . G 6 HOH A 17 617 14 HOH HOH . G 6 HOH A 18 618 6 HOH HOH . G 6 HOH A 19 619 25 HOH HOH . G 6 HOH A 20 620 19 HOH HOH . G 6 HOH A 21 621 8 HOH HOH . G 6 HOH A 22 622 15 HOH HOH . G 6 HOH A 23 623 16 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 N N1 DCP . . . D 4 51.585 4.498 -18.05 1 48.96 ? N1 DCP 501 A 1 HETATM 2 C C2 DCP . . . D 4 52.827 4.901 -18.552 1 52.56 ? C2 DCP 501 A 1 HETATM 3 N N3 DCP . . . D 4 53.552 4.017 -19.291 1 52.91 ? N3 DCP 501 A 1 HETATM 4 C C4 DCP . . . D 4 53.081 2.782 -19.532 1 50.19 ? C4 DCP 501 A 1 HETATM 5 C C5 DCP . . . D 4 51.819 2.354 -19.027 1 51.91 ? C5 DCP 501 A 1 HETATM 6 C C6 DCP . . . D 4 51.114 3.232 -18.299 1 47.11 ? C6 DCP 501 A 1 HETATM 7 O O2 DCP . . . D 4 53.226 6.042 -18.312 1 51.62 ? O2 DCP 501 A 1 HETATM 8 N N4 DCP . . . D 4 53.835 1.954 -20.256 1 46.51 ? N4 DCP 501 A 1 HETATM 9 C C1' DCP . . . D 4 50.813 5.472 -17.249 1 45.43 ? C1' DCP 501 A 1 HETATM 10 C C2' DCP . . . D 4 49.982 6.441 -18.077 1 36.06 ? C2' DCP 501 A 1 HETATM 11 C C3' DCP . . . D 4 48.634 5.743 -18.167 1 34.52 ? C3' DCP 501 A 1 HETATM 12 C C4' DCP . . . D 4 48.543 5.019 -16.827 1 38.14 ? C4' DCP 501 A 1 HETATM 13 O O4' DCP . . . D 4 49.906 4.75 -16.43 1 47.22 ? O4' DCP 501 A 1 HETATM 14 O O3' DCP . . . D 4 47.581 6.699 -18.283 1 32.76 ? O3' DCP 501 A 1 HETATM 15 C C5' DCP . . . D 4 47.775 3.723 -16.876 1 42.45 ? C5' DCP 501 A 1 HETATM 16 O O5' DCP . . . D 4 48.051 3.088 -18.142 1 47.08 ? O5' DCP 501 A 1 HETATM 17 P PA DCP . . . D 4 47.134 1.931 -18.7 1 37.66 ? PA DCP 501 A 1 HETATM 18 O O1A DCP . . . D 4 47.926 0.93 -19.443 1 47.17 ? O1A DCP 501 A 1 HETATM 19 O O2A DCP . . . D 4 46.273 1.414 -17.55 1 40.41 ? O2A DCP 501 A 1 HETATM 20 O O3A DCP . . . D 4 46.171 2.672 -19.696 1 37.99 ? O3A DCP 501 A 1 HETATM 21 P PB DCP . . . D 4 45.493 4.104 -19.81 1 40.53 ? PB DCP 501 A 1 HETATM 22 O O1B DCP . . . D 4 46.337 5.045 -20.574 1 37.17 ? O1B DCP 501 A 1 HETATM 23 O O2B DCP . . . D 4 45.104 4.536 -18.396 1 42.91 ? O2B DCP 501 A 1 HETATM 24 O O3B DCP . . . D 4 44.154 3.734 -20.568 1 45.32 ? O3B DCP 501 A 1 HETATM 25 P PG DCP . . . D 4 43.339 2.442 -21.041 1 37.53 ? PG DCP 501 A 1 HETATM 26 O O1G DCP . . . D 4 44.016 1.794 -22.199 1 33.36 ? O1G DCP 501 A 1 HETATM 27 O O2G DCP . . . D 4 43.274 1.556 -19.795 1 45.78 ? O2G DCP 501 A 1 HETATM 28 O O3G DCP . . . D 4 41.935 2.966 -21.354 1 38.45 ? O3G DCP 501 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 582 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #