data_8C1K # _model_server_result.job_id JMWz_v7vZZ5UZ1lJlGr3kQ _model_server_result.datetime_utc '2024-11-22 22:36:45' _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 8c1k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 8C1K # _exptl.entry_id 8C1K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 8C1K _cell.length_a 82.142 _cell.length_b 82.142 _cell.length_c 169.177 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C1K _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,J,K,L,M,N,O,P _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 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 A OD2 ASP 151 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.104 ? metalc ? metalc2 A OD1 ASP 151 A ASP 274 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc3 A OD2 ASP 151 A ASP 274 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc4 C O1B ADP . A ADP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc5 C O1A ADP . A ADP 402 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc6 C O3B ADP . A ADP 402 1_555 E MG MG . A MG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.142 ? metalc ? metalc7 D MG MG . A MG 403 1_555 P O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc8 D MG MG . A MG 403 1_555 P O HOH . A HOH 519 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc9 E MG MG . A MG 404 1_555 F O2 T5L . A T5L 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc10 E MG MG . A MG 404 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? # _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 8C1K _atom_sites.fract_transf_matrix[1][1] 0.012174 _atom_sites.fract_transf_matrix[1][2] 0.007029 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014057 _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] 0.005911 _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 T4O A 1 401 4000 T4O 602 . C 3 ADP A 1 402 1 ADP ADP . D 4 MG A 1 403 1 MG MG . E 4 MG A 1 404 2 MG MG . F 5 T5L A 1 405 1 T5L CHA . G 6 SO4 A 1 406 1 SO4 SO4 . H 6 SO4 A 1 407 2 SO4 SO4 . I 6 SO4 A 1 408 3 SO4 SO4 . J 6 SO4 A 1 409 5 SO4 SO4 . K 6 SO4 A 1 410 6 SO4 SO4 . L 7 DMS A 1 411 1 DMS DMS . M 7 DMS A 1 412 2 DMS DMS . N 7 DMS A 1 413 3 DMS DMS . O 8 ACT A 1 414 1 ACT ACT . P 9 HOH A 1 501 56 HOH HOH . P 9 HOH A 2 502 4 HOH HOH . P 9 HOH A 3 503 81 HOH HOH . P 9 HOH A 4 504 33 HOH HOH . P 9 HOH A 5 505 35 HOH HOH . P 9 HOH A 6 506 75 HOH HOH . P 9 HOH A 7 507 78 HOH HOH . P 9 HOH A 8 508 2 HOH HOH . P 9 HOH A 9 509 77 HOH HOH . P 9 HOH A 10 510 79 HOH HOH . P 9 HOH A 11 511 8 HOH HOH . P 9 HOH A 12 512 7 HOH HOH . P 9 HOH A 13 513 76 HOH HOH . P 9 HOH A 14 514 11 HOH HOH . P 9 HOH A 15 515 36 HOH HOH . P 9 HOH A 16 516 28 HOH HOH . P 9 HOH A 17 517 25 HOH HOH . P 9 HOH A 18 518 64 HOH HOH . P 9 HOH A 19 519 34 HOH HOH . P 9 HOH A 20 520 68 HOH HOH . P 9 HOH A 21 521 74 HOH HOH . P 9 HOH A 22 522 1 HOH HOH . P 9 HOH A 23 523 10 HOH HOH . P 9 HOH A 24 524 52 HOH HOH . P 9 HOH A 25 525 24 HOH HOH . P 9 HOH A 26 526 80 HOH HOH . P 9 HOH A 27 527 70 HOH HOH . P 9 HOH A 28 528 38 HOH HOH . P 9 HOH A 29 529 23 HOH HOH . P 9 HOH A 30 530 65 HOH HOH . P 9 HOH A 31 531 49 HOH HOH . P 9 HOH A 32 532 13 HOH HOH . P 9 HOH A 33 533 82 HOH HOH . P 9 HOH A 34 534 17 HOH HOH . P 9 HOH A 35 535 14 HOH HOH . P 9 HOH A 36 536 55 HOH HOH . P 9 HOH A 37 537 58 HOH HOH . P 9 HOH A 38 538 27 HOH HOH . P 9 HOH A 39 539 12 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 . . . C 3 -10.014 -23.942 4.811 1 69.97 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . . . C 3 -10.78 -24.78 3.765 1 67.99 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . . . C 3 -9.276 -22.806 4.091 1 70.3 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . . . C 3 -10.94 -23.477 5.922 1 63.99 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . . . C 3 -8.487 -26.22 5.963 1 64.22 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . . . C 3 -9.526 -27.239 5.505 1 60.37 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . . . C 3 -8.466 -26.092 7.445 1 62.88 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . . . C 3 -8.757 -24.787 5.315 1 67.03 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . . . C 3 -7.079 -26.644 5.304 1 62.12 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . . . C 3 -6.899 -26.667 3.877 1 60.3 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . . . C 3 -6.258 -27.961 3.455 1 60.11 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . . . C 3 -4.92 -28.045 3.999 1 60.12 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . . . C 3 -6.935 -29.234 3.944 1 60.61 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . . . C 3 -8.084 -29.618 3.211 1 62.08 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . . . C 3 -5.798 -30.23 3.831 1 61.42 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . . . C 3 -5.573 -30.549 2.459 1 63.86 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . . . C 3 -4.652 -29.386 4.392 1 62.73 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . . . C 3 -4.558 -29.435 5.852 1 67.07 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . . . C 3 -5.214 -28.632 6.741 1 67.67 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . . . C 3 -4.99 -28.887 7.995 1 67.06 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . . . C 3 -4.089 -29.964 7.943 1 68.71 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . . . C 3 -3.473 -30.717 8.952 1 70.55 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . . . C 3 -3.663 -30.504 10.254 1 68.04 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . . . C 3 -2.655 -31.731 8.567 1 69.84 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . . . C 3 -2.497 -31.962 7.259 1 67.84 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . . . C 3 -3.035 -31.308 6.222 1 66.32 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . . . C 3 -3.824 -30.306 6.633 1 66.51 ? C4 ADP 402 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 68 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #