data_6NHK # _model_server_result.job_id maI-kum1xwnOWihtaL8sjw _model_server_result.datetime_utc '2024-11-21 23:27:07' _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 6nhk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":501}' # _entry.id 6NHK # _exptl.entry_id 6NHK _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 97.56 _cell.angle_gamma 90 _cell.entry_id 6NHK _cell.length_a 177.263 _cell.length_b 60.102 _cell.length_c 91.699 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NHK _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,J 1 1 B,G,H,I,K 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 G N 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 C O1B ADP . A ADP 501 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc2 D O1 PO4 . A PO4 502 1_555 E MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.796 ? metalc ? metalc3 B OD2 ASP 198 B ASP 244 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.92 ? metalc ? metalc4 G O1B ADP . B ADP 600 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc5 H O1 PO4 . B PO4 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? # _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 6NHK _atom_sites.fract_transf_matrix[1][1] 0.005641 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000749 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016638 _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] 0.011001 _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 C 2 ADP A 1 501 501 ADP ADP . D 3 PO4 A 1 502 502 PO4 PO4 . E 4 MG A 1 503 503 MG MG . F 5 GOL A 1 504 504 GOL GOL . G 2 ADP B 1 600 600 ADP ADP . H 3 PO4 B 1 601 601 PO4 PO4 . I 4 MG B 1 602 602 MG MG . J 6 HOH A 1 601 601 HOH HOH . J 6 HOH A 2 602 602 HOH HOH . J 6 HOH A 3 603 603 HOH HOH . J 6 HOH A 4 604 604 HOH HOH . J 6 HOH A 5 605 605 HOH HOH . J 6 HOH A 6 606 606 HOH HOH . K 6 HOH B 1 701 701 HOH HOH . K 6 HOH B 2 702 702 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 2 15.754 34.308 117.944 1 65.1 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . C 2 17.025 34.052 117.179 1 72.68 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . C 2 14.808 35.258 117.271 1 47.81 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . C 2 15.952 34.566 119.411 1 60.26 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . C 2 14.627 31.997 119.123 1 49.57 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . C 2 14.676 30.556 118.706 1 55.6 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . C 2 15.394 32.443 120.334 1 57.51 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . C 2 15.029 32.882 117.85 1 67.34 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . C 2 13.094 32.41 119.319 1 67.21 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . C 2 12.264 31.65 120.186 1 63 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . C 2 10.873 32.258 120.231 1 55.93 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . C 2 9.933 31.237 119.918 1 63.5 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . C 2 10.547 32.746 121.626 1 67.05 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . C 2 9.794 33.954 121.551 1 73.03 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . C 2 9.669 31.683 122.233 1 57.35 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . C 2 8.588 32.311 122.924 1 62.12 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . C 2 9.152 30.882 121.056 1 52.81 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . C 2 9.29 29.435 121.328 1 48.07 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . C 2 10.384 28.813 121.791 1 54.13 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . C 2 10.165 27.483 121.929 1 54.1 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . C 2 8.902 27.242 121.548 1 57.28 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . C 2 8.024 26.058 121.444 1 60.71 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . C 2 8.464 24.829 121.786 1 66.63 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . C 2 6.768 26.245 120.995 1 58.55 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . C 2 6.313 27.46 120.652 1 56.23 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . C 2 7.054 28.575 120.722 1 58.22 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . C 2 8.332 28.532 121.153 1 55.31 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #