data_4O86 # _model_server_result.job_id wPmtT3frNNafDER9VqKQ-Q _model_server_result.datetime_utc '2025-01-02 20:46:04' _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 4o86 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":502}' # _entry.id 4O86 # _exptl.entry_id 4O86 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 403.176 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "CYTIDINE-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 4O86 _cell.length_a 44.25 _cell.length_b 155.54 _cell.length_c 78.35 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O86 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,H,I _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_654 -x+1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 44.25 0 -39.175 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 metalc ? metalc1 F MG MG . A MG 505 1_555 G O3 PO4 . A PO4 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc2 F MG MG . A MG 505 1_555 G O4 PO4 . A PO4 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc3 F MG MG . A MG 505 1_555 H O3B ADP . A ADP 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? metalc ? metalc4 F MG MG . A MG 505 1_555 H O2A ADP . A ADP 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc5 F MG MG . A MG 505 1_555 I O HOH . A HOH 681 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.749 ? metalc ? metalc6 F MG MG . A MG 505 1_555 I O HOH . A HOH 687 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? # _chem_comp.formula 'C9 H15 N3 O11 P2' _chem_comp.formula_weight 403.176 _chem_comp.id CDP _chem_comp.mon_nstd_flag . _chem_comp.name "CYTIDINE-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 O3B PB CDP sing 156 n n PB O1B CDP doub 157 n n PB O2B CDP sing 158 n n PB O3A CDP sing 159 n n O3A PA CDP sing 160 n n PA O1A CDP doub 161 n n PA O2A CDP sing 162 n n PA O5' CDP sing 163 n n O5' C5' CDP sing 164 n n C5' C4' CDP sing 165 n n C5' "H5'1" CDP sing 166 n n C5' "H5'2" CDP sing 167 n n C4' O4' CDP sing 168 n n C4' C3' CDP sing 169 n n C4' H4' CDP sing 170 n n O4' C1' CDP sing 171 n n C3' O3' CDP sing 172 n n C3' C2' CDP sing 173 n n C3' H3' CDP sing 174 n n O3' HA CDP sing 175 n n C2' O2' CDP sing 176 n n C2' C1' CDP sing 177 n n C2' H2' CDP sing 178 n n O2' HB CDP sing 179 n n C1' N1 CDP sing 180 n n C1' H1' CDP sing 181 n n N1 C2 CDP sing 182 n n N1 C6 CDP sing 183 n n C2 O2 CDP doub 184 n n C2 N3 CDP sing 185 n n N3 C4 CDP doub 186 n n C4 N4 CDP sing 187 n n C4 C5 CDP sing 188 n n N4 H4N1 CDP sing 189 n n N4 H4N2 CDP sing 190 n n C5 C6 CDP doub 191 n n C5 H5 CDP sing 192 n n C6 H6 CDP sing 193 n n HO1 O2A CDP sing 194 n n HO2 O2B CDP sing 195 n n HO3 O3B CDP sing 196 n n # _atom_sites.entry_id 4O86 _atom_sites.fract_transf_matrix[1][1] 0.022599 _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] 0.006429 _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] 0.012763 _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 PO4 A 1 501 501 PO4 PO4 . C 3 CDP A 1 502 420 CDP CDP . D 4 C5P A 1 503 430 C5P C5P . E 5 ACT A 1 504 502 ACT ACT . F 6 MG A 1 505 505 MG MG . G 2 PO4 A 1 506 442 PO4 PO4 . H 7 ADP A 1 507 422 ADP ADP . I 8 HOH A 1 601 301 HOH HOH . I 8 HOH A 2 602 302 HOH HOH . I 8 HOH A 3 603 303 HOH HOH . I 8 HOH A 4 604 304 HOH HOH . I 8 HOH A 5 605 305 HOH HOH . I 8 HOH A 6 606 306 HOH HOH . I 8 HOH A 7 607 307 HOH HOH . I 8 HOH A 8 608 308 HOH HOH . I 8 HOH A 9 609 309 HOH HOH . I 8 HOH A 10 610 310 HOH HOH . I 8 HOH A 11 611 311 HOH HOH . I 8 HOH A 12 612 312 HOH HOH . I 8 HOH A 13 613 313 HOH HOH . I 8 HOH A 14 614 314 HOH HOH . I 8 HOH A 15 615 315 HOH HOH . I 8 HOH A 16 616 316 HOH HOH . I 8 HOH A 17 617 317 HOH HOH . I 8 HOH A 18 618 318 HOH HOH . I 8 HOH A 19 619 319 HOH HOH . I 8 HOH A 20 620 320 HOH HOH . I 8 HOH A 21 621 321 HOH HOH . I 8 HOH A 22 622 322 HOH HOH . I 8 HOH A 23 623 323 HOH HOH . I 8 HOH A 24 624 324 HOH HOH . I 8 HOH A 25 625 325 HOH HOH . I 8 HOH A 26 626 326 HOH HOH . I 8 HOH A 27 627 327 HOH HOH . I 8 HOH A 28 628 328 HOH HOH . I 8 HOH A 29 629 329 HOH HOH . I 8 HOH A 30 630 330 HOH HOH . I 8 HOH A 31 631 331 HOH HOH . I 8 HOH A 32 632 332 HOH HOH . I 8 HOH A 33 633 333 HOH HOH . I 8 HOH A 34 634 334 HOH HOH . I 8 HOH A 35 635 335 HOH HOH . I 8 HOH A 36 636 336 HOH HOH . I 8 HOH A 37 637 337 HOH HOH . I 8 HOH A 38 638 338 HOH HOH . I 8 HOH A 39 639 339 HOH HOH . I 8 HOH A 40 640 340 HOH HOH . I 8 HOH A 41 641 341 HOH HOH . I 8 HOH A 42 642 342 HOH HOH . I 8 HOH A 43 643 343 HOH HOH . I 8 HOH A 44 644 344 HOH HOH . I 8 HOH A 45 645 345 HOH HOH . I 8 HOH A 46 646 346 HOH HOH . I 8 HOH A 47 647 347 HOH HOH . I 8 HOH A 48 648 348 HOH HOH . I 8 HOH A 49 649 349 HOH HOH . I 8 HOH A 50 650 350 HOH HOH . I 8 HOH A 51 651 351 HOH HOH . I 8 HOH A 52 652 352 HOH HOH . I 8 HOH A 53 653 353 HOH HOH . I 8 HOH A 54 654 354 HOH HOH . I 8 HOH A 55 655 355 HOH HOH . I 8 HOH A 56 656 356 HOH HOH . I 8 HOH A 57 657 357 HOH HOH . I 8 HOH A 58 658 358 HOH HOH . I 8 HOH A 59 659 359 HOH HOH . I 8 HOH A 60 660 360 HOH HOH . I 8 HOH A 61 661 361 HOH HOH . I 8 HOH A 62 662 362 HOH HOH . I 8 HOH A 63 663 363 HOH HOH . I 8 HOH A 64 664 364 HOH HOH . I 8 HOH A 65 665 365 HOH HOH . I 8 HOH A 66 666 366 HOH HOH . I 8 HOH A 67 667 367 HOH HOH . I 8 HOH A 68 668 368 HOH HOH . I 8 HOH A 69 669 369 HOH HOH . I 8 HOH A 70 670 370 HOH HOH . I 8 HOH A 71 671 371 HOH HOH . I 8 HOH A 72 672 372 HOH HOH . I 8 HOH A 73 673 373 HOH HOH . I 8 HOH A 74 674 374 HOH HOH . I 8 HOH A 75 675 375 HOH HOH . I 8 HOH A 76 676 376 HOH HOH . I 8 HOH A 77 677 377 HOH HOH . I 8 HOH A 78 678 378 HOH HOH . I 8 HOH A 79 679 379 HOH HOH . I 8 HOH A 80 680 380 HOH HOH . I 8 HOH A 81 681 381 HOH HOH . I 8 HOH A 82 682 382 HOH HOH . I 8 HOH A 83 683 383 HOH HOH . I 8 HOH A 84 684 384 HOH HOH . I 8 HOH A 85 685 385 HOH HOH . I 8 HOH A 86 686 386 HOH HOH . I 8 HOH A 87 687 387 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 O O3B CDP . A . C 3 15.393 -11.866 -10.258 0.5 15.93 ? O3B CDP 502 A 1 HETATM 2 P PB CDP . A . C 3 14.43 -12.943 -9.837 0.5 16.39 ? PB CDP 502 A 1 HETATM 3 O O1B CDP . A . C 3 14.437 -13.175 -8.336 0.5 15.98 ? O1B CDP 502 A 1 HETATM 4 O O2B CDP . A . C 3 13.066 -12.855 -10.467 0.5 15.41 ? O2B CDP 502 A 1 HETATM 5 O O3A CDP . A . C 3 15.091 -14.286 -10.452 0.5 16.19 ? O3A CDP 502 A 1 HETATM 6 P PA CDP . A . C 3 14.27 -15.594 -10.92 0.5 16.32 ? PA CDP 502 A 1 HETATM 7 O O1A CDP . A . C 3 15.207 -16.479 -11.707 0.5 16.7 ? O1A CDP 502 A 1 HETATM 8 O O2A CDP . A . C 3 12.969 -15.196 -11.585 0.5 16.4 ? O2A CDP 502 A 1 HETATM 9 O O5' CDP . A . C 3 13.936 -16.302 -9.516 0.5 16.38 ? O5' CDP 502 A 1 HETATM 10 C C5' CDP . A . C 3 13.716 -17.708 -9.434 0.5 16.84 ? C5' CDP 502 A 1 HETATM 11 C C4' CDP . A . C 3 13.453 -18.091 -7.984 0.5 17.53 ? C4' CDP 502 A 1 HETATM 12 O O4' CDP . A . C 3 14.687 -18.19 -7.274 0.5 17.87 ? O4' CDP 502 A 1 HETATM 13 C C3' CDP . A . C 3 12.642 -17.019 -7.276 0.5 17.96 ? C3' CDP 502 A 1 HETATM 14 O O3' CDP . A . C 3 11.722 -17.648 -6.377 0.5 17.74 ? O3' CDP 502 A 1 HETATM 15 C C2' CDP . A . C 3 13.637 -16.222 -6.474 0.5 18.19 ? C2' CDP 502 A 1 HETATM 16 O O2' CDP . A . C 3 13.001 -15.796 -5.264 0.5 18.72 ? O2' CDP 502 A 1 HETATM 17 C C1' CDP . A . C 3 14.751 -17.225 -6.216 0.5 18.49 ? C1' CDP 502 A 1 HETATM 18 N N1 CDP . A . C 3 16.095 -16.626 -6.221 0.5 18.99 ? N1 CDP 502 A 1 HETATM 19 C C2 CDP . A . C 3 16.837 -16.547 -5.022 0.5 18.88 ? C2 CDP 502 A 1 HETATM 20 O O2 CDP . A . C 3 16.339 -16.965 -3.956 0.5 18.46 ? O2 CDP 502 A 1 HETATM 21 N N3 CDP . A . C 3 18.083 -16.014 -5.029 0.5 19.21 ? N3 CDP 502 A 1 HETATM 22 C C4 CDP . A . C 3 18.63 -15.563 -6.178 0.5 19.57 ? C4 CDP 502 A 1 HETATM 23 N N4 CDP . A . C 3 19.873 -15.03 -6.17 0.5 20.38 ? N4 CDP 502 A 1 HETATM 24 C C5 CDP . A . C 3 17.919 -15.635 -7.373 0.5 19.54 ? C5 CDP 502 A 1 HETATM 25 C C6 CDP . A . C 3 16.636 -16.185 -7.368 0.5 19.45 ? C6 CDP 502 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #