data_9D2P # _model_server_result.job_id acjun00VsdmjxHxWUgGzFg _model_server_result.datetime_utc '2025-08-23 22:57:50' _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 9d2p # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 9D2P # _exptl.entry_id 9D2P _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _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 120 _cell.entry_id 9D2P _cell.length_a 97.927 _cell.length_b 97.927 _cell.length_c 69.061 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9D2P _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall 'P 31 2"' _symmetry.space_group_name_H-M 'P 31 2 1' # _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 _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' 5_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -23.020333 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 D MG MG . A MG 403 1_555 F O1B ADP . A ADP 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc2 D MG MG . A MG 403 1_555 G O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc3 D MG MG . A MG 403 1_555 G O HOH . A HOH 535 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc4 D MG MG . A MG 403 1_555 G O HOH . A HOH 553 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc5 D MG MG . A MG 403 1_555 G O HOH . A HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc6 D MG MG . A MG 403 1_555 G O HOH . A HOH 558 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? # _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 8 n n PB O2B ADP sing 9 n n PB O3B ADP sing 10 n n PB O3A ADP sing 11 n n O2B HOB2 ADP sing 12 n n O3B HOB3 ADP sing 13 n n PA O1A ADP doub 14 n n PA O2A ADP sing 15 n n PA O3A ADP sing 16 n n PA O5' ADP sing 17 n n O2A HOA2 ADP sing 18 n n O5' C5' ADP sing 19 n n C5' C4' ADP sing 20 n n C5' "H5'1" ADP sing 21 n n C5' "H5'2" ADP sing 22 n n C4' O4' ADP sing 23 n n C4' C3' ADP sing 24 n n C4' H4' ADP sing 25 n n O4' C1' ADP sing 26 n n C3' O3' ADP sing 27 n n C3' C2' ADP sing 28 n n C3' H3' ADP sing 29 n n O3' HO3' ADP sing 30 n n C2' O2' ADP sing 31 n n C2' C1' ADP sing 32 n n C2' H2' ADP sing 33 n n O2' HO2' ADP sing 34 n n C1' N9 ADP sing 35 n n C1' H1' ADP sing 36 n n N9 C8 ADP sing 37 n y N9 C4 ADP sing 38 n y C8 N7 ADP doub 39 n y C8 H8 ADP sing 40 n n N7 C5 ADP sing 41 n y C5 C6 ADP sing 42 n y C5 C4 ADP doub 43 n y C6 N6 ADP sing 44 n n C6 N1 ADP doub 45 n y N6 HN61 ADP sing 46 n n N6 HN62 ADP sing 47 n n N1 C2 ADP sing 48 n y C2 N3 ADP doub 49 n y C2 H2 ADP sing 50 n n N3 C4 ADP sing 51 n y # _atom_sites.entry_id 9D2P _atom_sites.fract_transf_matrix[1][1] 0.010212 _atom_sites.fract_transf_matrix[1][2] 0.005896 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011791 _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] 0.01448 _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 MZI A 1 401 401 MZI LIG . C 3 ACY A 1 402 501 ACY ACT . D 4 MG A 1 403 1 MG MG . E 5 EDO A 1 404 1 EDO EDO . F 6 ADP A 1 405 1 ADP ADP . G 7 HOH A 1 501 204 HOH HOH . G 7 HOH A 2 502 4 HOH HOH . G 7 HOH A 3 503 98 HOH HOH . G 7 HOH A 4 504 228 HOH HOH . G 7 HOH A 5 505 54 HOH HOH . G 7 HOH A 6 506 227 HOH HOH . G 7 HOH A 7 507 221 HOH HOH . G 7 HOH A 8 508 195 HOH HOH . G 7 HOH A 9 509 230 HOH HOH . G 7 HOH A 10 510 210 HOH HOH . G 7 HOH A 11 511 55 HOH HOH . G 7 HOH A 12 512 57 HOH HOH . G 7 HOH A 13 513 72 HOH HOH . G 7 HOH A 14 514 20 HOH HOH . G 7 HOH A 15 515 84 HOH HOH . G 7 HOH A 16 516 198 HOH HOH . G 7 HOH A 17 517 237 HOH HOH . G 7 HOH A 18 518 63 HOH HOH . G 7 HOH A 19 519 62 HOH HOH . G 7 HOH A 20 520 15 HOH HOH . G 7 HOH A 21 521 220 HOH HOH . G 7 HOH A 22 522 59 HOH HOH . G 7 HOH A 23 523 26 HOH HOH . G 7 HOH A 24 524 50 HOH HOH . G 7 HOH A 25 525 34 HOH HOH . G 7 HOH A 26 526 203 HOH HOH . G 7 HOH A 27 527 190 HOH HOH . G 7 HOH A 28 528 162 HOH HOH . G 7 HOH A 29 529 196 HOH HOH . G 7 HOH A 30 530 214 HOH HOH . G 7 HOH A 31 531 232 HOH HOH . G 7 HOH A 32 532 212 HOH HOH . G 7 HOH A 33 533 209 HOH HOH . G 7 HOH A 34 534 11 HOH HOH . G 7 HOH A 35 535 5 HOH HOH . G 7 HOH A 36 536 216 HOH HOH . G 7 HOH A 37 537 22 HOH HOH . G 7 HOH A 38 538 218 HOH HOH . G 7 HOH A 39 539 200 HOH HOH . G 7 HOH A 40 540 78 HOH HOH . G 7 HOH A 41 541 74 HOH HOH . G 7 HOH A 42 542 179 HOH HOH . G 7 HOH A 43 543 236 HOH HOH . G 7 HOH A 44 544 242 HOH HOH . G 7 HOH A 45 545 10 HOH HOH . G 7 HOH A 46 546 36 HOH HOH . G 7 HOH A 47 547 240 HOH HOH . G 7 HOH A 48 548 205 HOH HOH . G 7 HOH A 49 549 226 HOH HOH . G 7 HOH A 50 550 48 HOH HOH . G 7 HOH A 51 551 56 HOH HOH . G 7 HOH A 52 552 241 HOH HOH . G 7 HOH A 53 553 6 HOH HOH . G 7 HOH A 54 554 207 HOH HOH . G 7 HOH A 55 555 161 HOH HOH . G 7 HOH A 56 556 177 HOH HOH . G 7 HOH A 57 557 222 HOH HOH . G 7 HOH A 58 558 7 HOH HOH . G 7 HOH A 59 559 186 HOH HOH . G 7 HOH A 60 560 118 HOH HOH . G 7 HOH A 61 561 18 HOH HOH . G 7 HOH A 62 562 66 HOH HOH . G 7 HOH A 63 563 206 HOH HOH . G 7 HOH A 64 564 27 HOH HOH . G 7 HOH A 65 565 97 HOH HOH . G 7 HOH A 66 566 192 HOH HOH . G 7 HOH A 67 567 40 HOH HOH . G 7 HOH A 68 568 2 HOH HOH . G 7 HOH A 69 569 88 HOH HOH . G 7 HOH A 70 570 183 HOH HOH . G 7 HOH A 71 571 238 HOH HOH . G 7 HOH A 72 572 51 HOH HOH . G 7 HOH A 73 573 193 HOH HOH . G 7 HOH A 74 574 23 HOH HOH . G 7 HOH A 75 575 33 HOH HOH . G 7 HOH A 76 576 32 HOH HOH . G 7 HOH A 77 577 149 HOH HOH . G 7 HOH A 78 578 82 HOH HOH . G 7 HOH A 79 579 119 HOH HOH . G 7 HOH A 80 580 92 HOH HOH . G 7 HOH A 81 581 194 HOH HOH . G 7 HOH A 82 582 47 HOH HOH . G 7 HOH A 83 583 17 HOH HOH . G 7 HOH A 84 584 37 HOH HOH . G 7 HOH A 85 585 185 HOH HOH . G 7 HOH A 86 586 135 HOH HOH . G 7 HOH A 87 587 60 HOH HOH . G 7 HOH A 88 588 29 HOH HOH . G 7 HOH A 89 589 201 HOH HOH . G 7 HOH A 90 590 71 HOH HOH . G 7 HOH A 91 591 213 HOH HOH . G 7 HOH A 92 592 35 HOH HOH . G 7 HOH A 93 593 219 HOH HOH . G 7 HOH A 94 594 223 HOH HOH . G 7 HOH A 95 595 38 HOH HOH . G 7 HOH A 96 596 211 HOH HOH . G 7 HOH A 97 597 189 HOH HOH . G 7 HOH A 98 598 124 HOH HOH . G 7 HOH A 99 599 8 HOH HOH . G 7 HOH A 100 600 235 HOH HOH . G 7 HOH A 101 601 197 HOH HOH . G 7 HOH A 102 602 79 HOH HOH . G 7 HOH A 103 603 202 HOH HOH . G 7 HOH A 104 604 231 HOH HOH . G 7 HOH A 105 605 229 HOH HOH . G 7 HOH A 106 606 208 HOH HOH . G 7 HOH A 107 607 16 HOH HOH . G 7 HOH A 108 608 170 HOH HOH . G 7 HOH A 109 609 215 HOH HOH . G 7 HOH A 110 610 182 HOH HOH . G 7 HOH A 111 611 61 HOH HOH . G 7 HOH A 112 612 122 HOH HOH . G 7 HOH A 113 613 234 HOH HOH . G 7 HOH A 114 614 53 HOH HOH . G 7 HOH A 115 615 19 HOH HOH . G 7 HOH A 116 616 239 HOH HOH . G 7 HOH A 117 617 21 HOH HOH . G 7 HOH A 118 618 58 HOH HOH . G 7 HOH A 119 619 178 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 . . . F 6 -26.891 -13.53 0.602 1 27.77 ? PB ADP 405 A 1 HETATM 2 O O1B ADP . . . F 6 -28.109 -14.149 1.232 1 26.32 ? O1B ADP 405 A 1 HETATM 3 O O2B ADP . . . F 6 -26.973 -13.572 -0.879 1 22.97 ? O2B ADP 405 A 1 HETATM 4 O O3B ADP . . . F 6 -25.665 -14.194 1.064 1 27.02 ? O3B ADP 405 A 1 HETATM 5 P PA ADP . . . F 6 -26.921 -11.382 2.456 1 28.19 ? PA ADP 405 A 1 HETATM 6 O O1A ADP . . . F 6 -28.344 -10.983 2.808 1 21.95 ? O1A ADP 405 A 1 HETATM 7 O O2A ADP . . . F 6 -26.407 -12.305 3.501 1 28.1 ? O2A ADP 405 A 1 HETATM 8 O O3A ADP . . . F 6 -26.824 -12.008 1.02 1 24.93 ? O3A ADP 405 A 1 HETATM 9 O O5' ADP . . . F 6 -26.038 -10.096 2.373 1 28.6 ? O5' ADP 405 A 1 HETATM 10 C C5' ADP . . . F 6 -24.848 -10.134 1.574 1 26.39 ? C5' ADP 405 A 1 HETATM 11 C C4' ADP . . . F 6 -24.365 -8.716 1.421 1 28.49 ? C4' ADP 405 A 1 HETATM 12 O O4' ADP . . . F 6 -24.162 -8.15 2.729 1 26.63 ? O4' ADP 405 A 1 HETATM 13 C C3' ADP . . . F 6 -23.006 -8.669 0.735 1 23.94 ? C3' ADP 405 A 1 HETATM 14 O O3' ADP . . . F 6 -23.17 -8.534 -0.678 1 25.3 ? O3' ADP 405 A 1 HETATM 15 C C2' ADP . . . F 6 -22.411 -7.383 1.338 1 26.08 ? C2' ADP 405 A 1 HETATM 16 O O2' ADP . . . F 6 -22.826 -6.251 0.57 1 24.06 ? O2' ADP 405 A 1 HETATM 17 C C1' ADP . . . F 6 -23.043 -7.304 2.743 1 23.13 ? C1' ADP 405 A 1 HETATM 18 N N9 ADP . . . F 6 -22.216 -7.766 3.829 1 23.52 ? N9 ADP 405 A 1 HETATM 19 C C8 ADP . . . F 6 -22.389 -7.405 5.104 1 26.07 ? C8 ADP 405 A 1 HETATM 20 N N7 ADP . . . F 6 -21.49 -8.013 5.863 1 26.26 ? N7 ADP 405 A 1 HETATM 21 C C5 ADP . . . F 6 -20.756 -8.768 5.06 1 29.11 ? C5 ADP 405 A 1 HETATM 22 C C6 ADP . . . F 6 -19.699 -9.591 5.368 1 32.76 ? C6 ADP 405 A 1 HETATM 23 N N6 ADP . . . F 6 -19.283 -9.707 6.629 1 37.8 ? N6 ADP 405 A 1 HETATM 24 N N1 ADP . . . F 6 -19.128 -10.245 4.347 1 29.66 ? N1 ADP 405 A 1 HETATM 25 C C2 ADP . . . F 6 -19.599 -10.079 3.123 1 27.99 ? C2 ADP 405 A 1 HETATM 26 N N3 ADP . . . F 6 -20.597 -9.31 2.81 1 26.97 ? N3 ADP 405 A 1 HETATM 27 C C4 ADP . . . F 6 -21.2 -8.628 3.795 1 25.45 ? C4 ADP 405 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 312 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #