data_6YCZ # _model_server_result.job_id U5vKWReJLz1k_ZuGSvUHZQ _model_server_result.datetime_utc '2024-10-19 11:43:11' _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 6ycz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":905}' # _entry.id 6YCZ # _exptl.entry_id 6YCZ _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 6YCZ _cell.length_a 90.08 _cell.length_b 114.43 _cell.length_c 170.71 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6YCZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 _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 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 A OG1 THR 198 A THR 198 1_555 G MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.699 ? metalc ? metalc2 A OG SER 246 A SER 246 1_555 G MG MG . A MG 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc3 G MG MG . A MG 904 1_555 H O3B ADP . A ADP 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.492 ? metalc ? metalc4 G MG MG . A MG 904 1_555 K O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc5 G MG MG . A MG 904 1_555 K O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? # _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 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6YCZ _atom_sites.fract_transf_matrix[1][1] 0.011101 _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] 0.008739 _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] 0.005858 _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 D 4 SO4 A 1 901 901 SO4 SO4 . E 4 SO4 A 1 902 1001 SO4 SO4 . F 5 EDO A 1 903 1101 EDO EDO . G 6 MG A 1 904 1 MG MG . H 7 ADP A 1 905 1 ADP ADP . I 4 SO4 B 1 301 301 SO4 SO4 . J 5 EDO C 1 201 201 EDO EDO . K 8 HOH A 1 1001 411 HOH HOH . K 8 HOH A 2 1002 408 HOH HOH . K 8 HOH A 3 1003 412 HOH HOH . K 8 HOH A 4 1004 413 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 2.215 0.297 25.672 1 61.84 ? PB ADP 905 A 1 HETATM 2 O O1B ADP . . . H 7 1.523 1.309 24.737 1 64.29 ? O1B ADP 905 A 1 HETATM 3 O O2B ADP . . . H 7 1.555 0.252 27.054 1 58.11 -1 O2B ADP 905 A 1 HETATM 4 O O3B ADP . . . H 7 2.269 -1.008 25.052 1 65.54 ? O3B ADP 905 A 1 HETATM 5 P PA ADP . . . H 7 5.075 0.241 26.301 1 60.79 ? PA ADP 905 A 1 HETATM 6 O O1A ADP . . . H 7 5.857 -0.008 25.058 1 64.86 -1 O1A ADP 905 A 1 HETATM 7 O O2A ADP . . . H 7 4.895 -1.028 27.125 1 58.9 ? O2A ADP 905 A 1 HETATM 8 O O3A ADP . . . H 7 3.675 0.883 25.903 1 60.27 ? O3A ADP 905 A 1 HETATM 9 O O5' ADP . . . H 7 5.747 1.278 27.243 1 60.66 ? O5' ADP 905 A 1 HETATM 10 C C5' ADP . . . H 7 6.267 2.508 26.71 1 64.57 ? C5' ADP 905 A 1 HETATM 11 C C4' ADP . . . H 7 7.689 2.628 27.178 1 66.27 ? C4' ADP 905 A 1 HETATM 12 O O4' ADP . . . H 7 7.71 2.657 28.619 1 62.88 ? O4' ADP 905 A 1 HETATM 13 C C3' ADP . . . H 7 8.605 1.472 26.8 1 69.44 ? C3' ADP 905 A 1 HETATM 14 O O3' ADP . . . H 7 9.097 1.569 25.461 1 71.18 ? O3' ADP 905 A 1 HETATM 15 C C2' ADP . . . H 7 9.696 1.597 27.86 1 69.29 ? C2' ADP 905 A 1 HETATM 16 O O2' ADP . . . H 7 10.664 2.579 27.507 1 71.51 ? O2' ADP 905 A 1 HETATM 17 C C1' ADP . . . H 7 8.88 2.022 29.09 1 64.62 ? C1' ADP 905 A 1 HETATM 18 N N9 ADP . . . H 7 8.484 0.911 29.944 1 65.09 ? N9 ADP 905 A 1 HETATM 19 C C8 ADP . . . H 7 7.277 0.262 29.995 1 65.59 ? C8 ADP 905 A 1 HETATM 20 N N7 ADP . . . H 7 7.23 -0.712 30.872 1 64.23 ? N7 ADP 905 A 1 HETATM 21 C C5 ADP . . . H 7 8.492 -0.697 31.446 1 63.9 ? C5 ADP 905 A 1 HETATM 22 C C6 ADP . . . H 7 9.076 -1.47 32.466 1 66.37 ? C6 ADP 905 A 1 HETATM 23 N N6 ADP . . . H 7 8.463 -2.5 33.053 1 69.66 ? N6 ADP 905 A 1 HETATM 24 N N1 ADP . . . H 7 10.35 -1.178 32.824 1 66.91 ? N1 ADP 905 A 1 HETATM 25 C C2 ADP . . . H 7 10.995 -0.202 32.171 1 67.79 ? C2 ADP 905 A 1 HETATM 26 N N3 ADP . . . H 7 10.549 0.586 31.187 1 65.78 ? N3 ADP 905 A 1 HETATM 27 C C4 ADP . . . H 7 9.277 0.293 30.879 1 64.59 ? C4 ADP 905 A 1 # _model_server_stats.io_time_ms 22 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #