data_1KSW # _model_server_result.job_id T2qqzWsrrvbJctLIWYhoew _model_server_result.datetime_utc '2025-04-21 06:22:34' _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 1ksw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":1}' # _entry.id 1KSW # _exptl.entry_id 1KSW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 517.324 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "N6-BENZYL ADENOSINE-5'-DIPHOSPHATE" _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 90 _cell.entry_id 1KSW _cell.length_a 50.81 _cell.length_b 87.68 _cell.length_c 106.28 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1KSW _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 A C GLN 445 A GLN 526 1_555 A N PTR 446 A PTR 527 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C PTR 446 A PTR 527 1_555 A N GLN 447 A GLN 528 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? # _chem_comp.formula 'C17 H21 N5 O10 P2' _chem_comp.formula_weight 517.324 _chem_comp.id NBS _chem_comp.mon_nstd_flag . _chem_comp.name "N6-BENZYL ADENOSINE-5'-DIPHOSPHATE" _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 PB O4P NBS sing 237 n n PB O5P NBS sing 238 n n PB O6P NBS doub 239 n n PB O3P NBS sing 240 n n O4P HOP4 NBS sing 241 n n O5P HOP5 NBS sing 242 n n PA O1P NBS sing 243 n n PA O2P NBS doub 244 n n PA O3P NBS sing 245 n n PA O5' NBS sing 246 n n O1P HOP1 NBS sing 247 n n O5' C5' NBS sing 248 n n C5' C4' NBS sing 249 n n C5' "H5'1" NBS sing 250 n n C5' "H5'2" NBS sing 251 n n C4' O4' NBS sing 252 n n C4' C3' NBS sing 253 n n C4' H4' NBS sing 254 n n O4' C1' NBS sing 255 n n C1' N9 NBS sing 256 n n C1' C2' NBS sing 257 n n C1' H1' NBS sing 258 n n N9 C4 NBS sing 259 n y N9 C8 NBS sing 260 n y C4 N3 NBS doub 261 n y C4 C5 NBS sing 262 n y N3 C2 NBS sing 263 n y C2 N1 NBS doub 264 n y C2 H2 NBS sing 265 n n N1 C6 NBS sing 266 n y C6 N6 NBS sing 267 n n C6 C5 NBS doub 268 n y N6 CB1 NBS sing 269 n n N6 H6 NBS sing 270 n n CB1 CB2 NBS sing 271 n n CB1 HB11 NBS sing 272 n n CB1 HB12 NBS sing 273 n n CB2 CB3 NBS doub 274 n y CB2 CB7 NBS sing 275 n y CB3 CB4 NBS sing 276 n y CB3 HB3 NBS sing 277 n n CB4 CB5 NBS doub 278 n y CB4 HB4 NBS sing 279 n n CB5 CB6 NBS sing 280 n y CB5 HB5 NBS sing 281 n n CB6 CB7 NBS doub 282 n y CB6 HB6 NBS sing 283 n n CB7 HB7 NBS sing 284 n n C5 N7 NBS sing 285 n y N7 C8 NBS doub 286 n y C8 H8 NBS sing 287 n n C2' O2' NBS sing 288 n n C2' C3' NBS sing 289 n n C2' H2' NBS sing 290 n n O2' "HO'2" NBS sing 291 n n C3' O3' NBS sing 292 n n C3' H3' NBS sing 293 n n O3' "HO'3" NBS sing 294 n n # _atom_sites.entry_id 1KSW _atom_sites.fract_transf_matrix[1][1] 0.019681 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011405 _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] 0.009409 _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 B 2 NBS A 1 1 1 NBS NBA . C 3 HOH A 1 534 3 HOH WAT . C 3 HOH A 2 535 4 HOH WAT . C 3 HOH A 3 536 5 HOH WAT . C 3 HOH A 4 537 6 HOH WAT . C 3 HOH A 5 538 8 HOH WAT . C 3 HOH A 6 539 9 HOH WAT . C 3 HOH A 7 540 10 HOH WAT . C 3 HOH A 8 541 11 HOH WAT . C 3 HOH A 9 542 12 HOH WAT . C 3 HOH A 10 543 14 HOH WAT . C 3 HOH A 11 544 15 HOH WAT . C 3 HOH A 12 545 18 HOH WAT . C 3 HOH A 13 546 22 HOH WAT . C 3 HOH A 14 547 25 HOH WAT . C 3 HOH A 15 548 26 HOH WAT . C 3 HOH A 16 549 27 HOH WAT . C 3 HOH A 17 550 28 HOH WAT . C 3 HOH A 18 551 29 HOH WAT . C 3 HOH A 19 552 30 HOH WAT . C 3 HOH A 20 553 33 HOH WAT . C 3 HOH A 21 554 34 HOH WAT . C 3 HOH A 22 555 36 HOH WAT . C 3 HOH A 23 556 37 HOH WAT . C 3 HOH A 24 557 38 HOH WAT . C 3 HOH A 25 558 41 HOH WAT . C 3 HOH A 26 559 44 HOH WAT . C 3 HOH A 27 560 48 HOH WAT . C 3 HOH A 28 561 49 HOH WAT . C 3 HOH A 29 562 50 HOH WAT . C 3 HOH A 30 563 51 HOH WAT . C 3 HOH A 31 564 52 HOH WAT . C 3 HOH A 32 565 53 HOH WAT . C 3 HOH A 33 566 55 HOH WAT . C 3 HOH A 34 567 58 HOH WAT . C 3 HOH A 35 568 62 HOH WAT . C 3 HOH A 36 569 66 HOH WAT . C 3 HOH A 37 570 72 HOH WAT . C 3 HOH A 38 571 73 HOH WAT . C 3 HOH A 39 572 74 HOH WAT . C 3 HOH A 40 573 76 HOH WAT . C 3 HOH A 41 574 79 HOH WAT . C 3 HOH A 42 575 81 HOH WAT . C 3 HOH A 43 576 82 HOH WAT . C 3 HOH A 44 577 87 HOH WAT . C 3 HOH A 45 578 88 HOH WAT . C 3 HOH A 46 579 93 HOH WAT . # 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 P PB NBS . . . B 2 -4.707 48.145 -1.934 1 96.51 ? PB NBS 1 A 1 HETATM 2 O O4P NBS . . . B 2 -5.024 48.685 -3.293 1 94.53 ? O4P NBS 1 A 1 HETATM 3 O O5P NBS . . . B 2 -5.808 48.284 -0.909 1 93.45 ? O5P NBS 1 A 1 HETATM 4 O O6P NBS . . . B 2 -3.972 46.826 -1.94 1 90.78 ? O6P NBS 1 A 1 HETATM 5 P PA NBS . . . B 2 -3.543 50.26 -0.276 1 84.39 ? PA NBS 1 A 1 HETATM 6 O O1P NBS . . . B 2 -2.687 51.406 -0.661 1 83.85 ? O1P NBS 1 A 1 HETATM 7 O O2P NBS . . . B 2 -4.848 50.534 0.382 1 84.83 ? O2P NBS 1 A 1 HETATM 8 O O3P NBS . . . B 2 -3.564 49.311 -1.621 1 90.86 ? O3P NBS 1 A 1 HETATM 9 O O5' NBS . . . B 2 -2.61 49.421 0.74 1 82.58 ? O5' NBS 1 A 1 HETATM 10 C C5' NBS . . . B 2 -1.573 48.533 0.307 1 76.59 ? C5' NBS 1 A 1 HETATM 11 C C4' NBS . . . B 2 -0.651 49.114 -0.784 1 68.86 ? C4' NBS 1 A 1 HETATM 12 O O4' NBS . . . B 2 -0.01 50.364 -0.381 1 64.41 ? O4' NBS 1 A 1 HETATM 13 C C1' NBS . . . B 2 1.284 50.048 0.196 1 61.19 ? C1' NBS 1 A 1 HETATM 14 N N9 NBS . . . B 2 1.216 50.221 1.663 1 58.72 ? N9 NBS 1 A 1 HETATM 15 C C4 NBS . . . B 2 2.281 50.338 2.523 1 55.58 ? C4 NBS 1 A 1 HETATM 16 N N3 NBS . . . B 2 3.589 50.268 2.2 1 58.59 ? N3 NBS 1 A 1 HETATM 17 C C2 NBS . . . B 2 4.356 50.437 3.278 1 54.22 ? C2 NBS 1 A 1 HETATM 18 N N1 NBS . . . B 2 3.983 50.648 4.538 1 49.25 ? N1 NBS 1 A 1 HETATM 19 C C6 NBS . . . B 2 2.667 50.715 4.839 1 48.66 ? C6 NBS 1 A 1 HETATM 20 N N6 NBS . . . B 2 2.3 50.986 6.161 1 43.46 ? N6 NBS 1 A 1 HETATM 21 C CB1 NBS . . . B 2 0.977 50.744 6.712 1 39.83 ? CB1 NBS 1 A 1 HETATM 22 C CB2 NBS . . . B 2 0.074 52.009 6.767 1 41.57 ? CB2 NBS 1 A 1 HETATM 23 C CB3 NBS . . . B 2 -0.834 52.16 7.806 1 39.05 ? CB3 NBS 1 A 1 HETATM 24 C CB4 NBS . . . B 2 -1.704 53.277 7.856 1 39.01 ? CB4 NBS 1 A 1 HETATM 25 C CB5 NBS . . . B 2 -1.641 54.242 6.839 1 41.94 ? CB5 NBS 1 A 1 HETATM 26 C CB6 NBS . . . B 2 -0.724 54.091 5.798 1 43.13 ? CB6 NBS 1 A 1 HETATM 27 C CB7 NBS . . . B 2 0.139 52.966 5.774 1 42.15 ? CB7 NBS 1 A 1 HETATM 28 C C5 NBS . . . B 2 1.754 50.56 3.772 1 52.01 ? C5 NBS 1 A 1 HETATM 29 N N7 NBS . . . B 2 0.37 50.566 3.712 1 54.36 ? N7 NBS 1 A 1 HETATM 30 C C8 NBS . . . B 2 0.107 50.359 2.457 1 55.34 ? C8 NBS 1 A 1 HETATM 31 C C2' NBS . . . B 2 1.602 48.606 -0.167 1 63.66 ? C2' NBS 1 A 1 HETATM 32 O O2' NBS . . . B 2 2.85 48.522 -0.85 1 63.13 ? O2' NBS 1 A 1 HETATM 33 C C3' NBS . . . B 2 0.47 48.143 -1.051 1 65.82 ? C3' NBS 1 A 1 HETATM 34 O O3' NBS . . . B 2 0.81 48.231 -2.417 1 66.91 ? O3' NBS 1 A 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 35 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 867 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 34 #