data_8C1I # _model_server_result.job_id b33g0AHRExyubnfKzTeo2Q _model_server_result.datetime_utc '2024-10-10 01:24:01' _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 8c1i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8C1I # _exptl.entry_id 8C1I _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 8C1I _cell.length_a 81.429 _cell.length_b 81.429 _cell.length_c 167.262 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8C1I _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 _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 metalc ? metalc1 A OD2 ASP 151 A ASP 274 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.192 ? metalc ? metalc2 A OD1 ASP 151 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc3 A OD2 ASP 151 A ASP 274 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 B O1B ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc5 B O1A ADP . A ADP 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc6 B O3B ADP . A ADP 401 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? metalc ? metalc7 C MG MG . A MG 402 1_555 O O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc8 C MG MG . A MG 402 1_555 O O HOH . A HOH 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc9 D MG MG . A MG 403 1_555 F O2 T5L . A T5L 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.919 ? metalc ? metalc10 D MG MG . A MG 403 1_555 O O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? # _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 8C1I _atom_sites.fract_transf_matrix[1][1] 0.012281 _atom_sites.fract_transf_matrix[1][2] 0.00709 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01418 _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] 0.005979 _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 ADP A 1 401 1 ADP ADP . C 3 MG A 1 402 1 MG MG . D 3 MG A 1 403 2 MG MG . E 4 T1L A 1 404 4000 T1L 601 . 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 8 ACT A 1 413 1 ACT ACT . O 9 HOH A 1 501 25 HOH HOH . O 9 HOH A 2 502 2 HOH HOH . O 9 HOH A 3 503 24 HOH HOH . O 9 HOH A 4 504 5 HOH HOH . O 9 HOH A 5 505 36 HOH HOH . O 9 HOH A 6 506 23 HOH HOH . O 9 HOH A 7 507 16 HOH HOH . O 9 HOH A 8 508 12 HOH HOH . O 9 HOH A 9 509 44 HOH HOH . O 9 HOH A 10 510 15 HOH HOH . O 9 HOH A 11 511 41 HOH HOH . O 9 HOH A 12 512 9 HOH HOH . O 9 HOH A 13 513 27 HOH HOH . O 9 HOH A 14 514 45 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 . . . B 2 -10.105 -23.854 4.807 1 68.97 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . B 2 -10.817 -24.885 3.913 1 68.28 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . B 2 -9.543 -22.709 3.997 1 70.88 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . B 2 -10.974 -23.393 5.887 1 69.16 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . B 2 -8.538 -25.995 6.065 1 66.81 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . B 2 -9.634 -26.966 5.643 1 63.95 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . B 2 -8.431 -25.932 7.541 1 67.3 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . B 2 -8.819 -24.559 5.43 1 67.62 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . B 2 -7.172 -26.434 5.345 1 65.23 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . B 2 -6.969 -26.402 3.917 1 62.18 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . B 2 -6.269 -27.665 3.487 1 61.1 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . B 2 -4.947 -27.727 4.073 1 60.16 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . B 2 -6.932 -28.971 3.904 1 60.75 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . B 2 -8.032 -29.32 3.075 1 62.94 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . B 2 -5.756 -29.94 3.857 1 59.67 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . B 2 -5.439 -30.296 2.515 1 60.38 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . B 2 -4.644 -29.065 4.446 1 59.44 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . B 2 -4.551 -29.142 5.904 1 59.46 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . B 2 -5.223 -28.345 6.796 1 60.27 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . B 2 -4.969 -28.614 8.051 1 60.82 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . B 2 -4.054 -29.658 7.989 1 60.94 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . B 2 -3.353 -30.36 8.985 1 61.57 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . B 2 -3.485 -30.114 10.291 1 61.23 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . B 2 -2.492 -31.328 8.586 1 60.93 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . B 2 -2.359 -31.569 7.276 1 60.36 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . B 2 -2.959 -30.962 6.246 1 60.2 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . B 2 -3.801 -29.998 6.669 1 60.34 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #