data_4O86 # _model_server_result.job_id gXYIwrjYWEScf511oFd1Cg _model_server_result.datetime_utc '2025-01-02 20:10:45' _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":"H","auth_seq_id":507}' # _entry.id 4O86 # _exptl.entry_id 4O86 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "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 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 7 _struct_asym.id H _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 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "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 O1B ADP doub 7 n n PB O2B ADP sing 8 n n PB O3B ADP sing 9 n n PB O3A ADP sing 10 n n O2B HOB2 ADP sing 11 n n O3B HOB3 ADP sing 12 n n PA O1A ADP doub 13 n n PA O2A ADP sing 14 n n PA O3A ADP sing 15 n n PA O5' ADP sing 16 n n O2A HOA2 ADP sing 17 n n O5' C5' ADP sing 18 n n C5' C4' ADP sing 19 n n C5' "H5'1" ADP sing 20 n n C5' "H5'2" ADP sing 21 n n C4' O4' ADP sing 22 n n C4' C3' ADP sing 23 n n C4' H4' ADP sing 24 n n O4' C1' ADP sing 25 n n C3' O3' ADP sing 26 n n C3' C2' ADP sing 27 n n C3' H3' ADP sing 28 n n O3' HO3' ADP sing 29 n n C2' O2' ADP sing 30 n n C2' C1' ADP sing 31 n n C2' H2' ADP sing 32 n n O2' HO2' ADP sing 33 n n C1' N9 ADP sing 34 n n C1' H1' ADP sing 35 n n N9 C8 ADP sing 36 n y N9 C4 ADP sing 37 n y C8 N7 ADP doub 38 n y C8 H8 ADP sing 39 n n N7 C5 ADP sing 40 n y C5 C6 ADP sing 41 n y C5 C4 ADP doub 42 n y C6 N6 ADP sing 43 n n C6 N1 ADP doub 44 n y N6 HN61 ADP sing 45 n n N6 HN62 ADP sing 46 n n N1 C2 ADP sing 47 n y C2 N3 ADP doub 48 n y C2 H2 ADP sing 49 n n N3 C4 ADP sing 50 n y # _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 P PB ADP . . . H 7 24.886 -14.985 0.473 0.8 39.84 ? PB ADP 507 A 1 HETATM 2 O O1B ADP . . . H 7 24.555 -13.509 0.427 0.8 39.49 ? O1B ADP 507 A 1 HETATM 3 O O2B ADP . . . H 7 26.311 -15.331 0.096 0.8 37.74 ? O2B ADP 507 A 1 HETATM 4 O O3B ADP . . . H 7 23.845 -15.871 -0.189 0.8 36.36 ? O3B ADP 507 A 1 HETATM 5 P PA ADP . . . H 7 23.481 -15.711 2.846 0.8 38.08 ? PA ADP 507 A 1 HETATM 6 O O1A ADP . . . H 7 22.828 -14.473 3.412 0.8 38.75 ? O1A ADP 507 A 1 HETATM 7 O O2A ADP . . . H 7 22.649 -16.665 2.026 0.8 39.12 ? O2A ADP 507 A 1 HETATM 8 O O3A ADP . . . H 7 24.825 -15.307 2.05 0.8 38.18 ? O3A ADP 507 A 1 HETATM 9 O O5' ADP . . . H 7 24.132 -16.55 4.069 0.8 37.27 ? O5' ADP 507 A 1 HETATM 10 C C5' ADP . . . H 7 24.404 -17.955 3.964 0.8 32.62 ? C5' ADP 507 A 1 HETATM 11 C C4' ADP . . . H 7 25.759 -18.281 3.318 0.8 29.67 ? C4' ADP 507 A 1 HETATM 12 O O4' ADP . . . H 7 26.228 -19.537 3.827 0.8 28.09 ? O4' ADP 507 A 1 HETATM 13 C C3' ADP . . . H 7 25.658 -18.507 1.819 0.8 28.65 ? C3' ADP 507 A 1 HETATM 14 O O3' ADP . . . H 7 26.922 -18.193 1.226 0.8 28.16 ? O3' ADP 507 A 1 HETATM 15 C C2' ADP . . . H 7 25.387 -19.996 1.69 0.8 27.46 ? C2' ADP 507 A 1 HETATM 16 O O2' ADP . . . H 7 25.782 -20.532 0.428 0.8 26.96 ? O2' ADP 507 A 1 HETATM 17 C C1' ADP . . . H 7 26.228 -20.561 2.82 0.8 26.98 ? C1' ADP 507 A 1 HETATM 18 N N9 ADP . . . H 7 25.674 -21.803 3.42 0.8 25.88 ? N9 ADP 507 A 1 HETATM 19 C C8 ADP . . . H 7 24.373 -22.152 3.526 0.8 24.7 ? C8 ADP 507 A 1 HETATM 20 N N7 ADP . . . H 7 24.241 -23.344 4.153 0.8 24.23 ? N7 ADP 507 A 1 HETATM 21 C C5 ADP . . . H 7 25.486 -23.772 4.477 0.8 24.95 ? C5 ADP 507 A 1 HETATM 22 C C6 ADP . . . H 7 26.097 -24.954 5.147 0.8 24.37 ? C6 ADP 507 A 1 HETATM 23 N N6 ADP . . . H 7 25.34 -25.964 5.643 0.8 22.75 ? N6 ADP 507 A 1 HETATM 24 N N1 ADP . . . H 7 27.451 -24.998 5.25 0.8 25.29 ? N1 ADP 507 A 1 HETATM 25 C C2 ADP . . . H 7 28.251 -24.022 4.788 0.8 24.27 ? C2 ADP 507 A 1 HETATM 26 N N3 ADP . . . H 7 27.768 -22.929 4.179 0.8 24.75 ? N3 ADP 507 A 1 HETATM 27 C C4 ADP . . . H 7 26.427 -22.75 3.989 0.8 25.43 ? C4 ADP 507 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 328 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #