data_6IXW # _model_server_result.job_id p30f_S6QZXF8v4b-AVQfHg _model_server_result.datetime_utc '2024-10-19 12:22:41' _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 6ixw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 6IXW # _exptl.entry_id 6IXW _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 131.55 _cell.angle_gamma 90 _cell.entry_id 6IXW _cell.length_a 164.153 _cell.length_b 93.922 _cell.length_c 114.699 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6IXW _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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F 1 1 B,G,H 2 1 C,I,J,K 3 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 D N N ? 2 G N N ? 2 I 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 A OE1 GLU 127 C GLU 125 1_555 F MG MG . C MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc2 D O1B ADP . C ADP 401 1_555 E MG MG . C MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc3 G O1B ADP . B ADP 401 1_555 H MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.91 ? metalc ? metalc4 C OD1 ASP 227 A ASP 225 1_555 K MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.616 ? metalc ? metalc5 C OD2 ASP 227 A ASP 225 1_555 K MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc6 I O1B ADP . A ADP 401 1_555 J MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? # _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 6IXW _atom_sites.fract_transf_matrix[1][1] 0.006092 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005399 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010647 _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] 0.011649 _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 2 ADP C 1 401 380 ADP ADP . E 3 MG C 1 402 401 MG MG . F 3 MG C 1 403 1 MG MG . G 2 ADP B 1 401 380 ADP ADP . H 3 MG B 1 402 401 MG MG . I 2 ADP A 1 401 380 ADP ADP . J 3 MG A 1 402 401 MG MG . K 3 MG A 1 403 2 MG MG . # 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 . . . G 2 15.361 -4.928 23.035 1 67.09 ? PB ADP 401 B 1 HETATM 2 O O1B ADP . . . G 2 16.617 -4.822 22.177 1 69.96 ? O1B ADP 401 B 1 HETATM 3 O O2B ADP . . . G 2 14.215 -5.697 22.41 1 33.57 ? O2B ADP 401 B 1 HETATM 4 O O3B ADP . . . G 2 15.556 -5.268 24.497 1 41.58 ? O3B ADP 401 B 1 HETATM 5 P PA ADP . . . G 2 13.866 -2.601 22.283 1 62.68 ? PA ADP 401 B 1 HETATM 6 O O1A ADP . . . G 2 14.635 -1.837 21.227 1 67.65 ? O1A ADP 401 B 1 HETATM 7 O O2A ADP . . . G 2 12.788 -3.57 21.875 1 56.09 ? O2A ADP 401 B 1 HETATM 8 O O3A ADP . . . G 2 14.954 -3.376 23.172 1 76.27 ? O3A ADP 401 B 1 HETATM 9 O O5' ADP . . . G 2 13.232 -1.653 23.425 1 24.33 ? O5' ADP 401 B 1 HETATM 10 C C5' ADP . . . G 2 11.805 -1.644 23.513 1 73.23 ? C5' ADP 401 B 1 HETATM 11 C C4' ADP . . . G 2 11.259 -1.328 24.901 1 45.97 ? C4' ADP 401 B 1 HETATM 12 O O4' ADP . . . G 2 11.089 0.08 25 1 37.39 ? O4' ADP 401 B 1 HETATM 13 C C3' ADP . . . G 2 9.878 -1.951 25.104 1 63.26 ? C3' ADP 401 B 1 HETATM 14 O O3' ADP . . . G 2 9.915 -3.077 25.996 1 68.93 ? O3' ADP 401 B 1 HETATM 15 C C2' ADP . . . G 2 8.998 -0.869 25.682 1 61.13 ? C2' ADP 401 B 1 HETATM 16 O O2' ADP . . . G 2 8.866 -1.02 27.1 1 88.51 ? O2' ADP 401 B 1 HETATM 17 C C1' ADP . . . G 2 9.771 0.408 25.467 1 99.09 ? C1' ADP 401 B 1 HETATM 18 N N9 ADP . . . G 2 9.005 1.228 24.493 1 86.47 ? N9 ADP 401 B 1 HETATM 19 C C8 ADP . . . G 2 9.134 1.196 23.157 1 44.28 ? C8 ADP 401 B 1 HETATM 20 N N7 ADP . . . G 2 8.287 2.087 22.582 1 81.14 ? N7 ADP 401 B 1 HETATM 21 C C5 ADP . . . G 2 7.596 2.7 23.558 1 64.29 ? C5 ADP 401 B 1 HETATM 22 C C6 ADP . . . G 2 6.539 3.735 23.63 1 66.38 ? C6 ADP 401 B 1 HETATM 23 N N6 ADP . . . G 2 6.058 4.297 22.483 1 61.5 ? N6 ADP 401 B 1 HETATM 24 N N1 ADP . . . G 2 6.089 4.089 24.869 1 43.79 ? N1 ADP 401 B 1 HETATM 25 C C2 ADP . . . G 2 6.584 3.531 25.993 1 46.65 ? C2 ADP 401 B 1 HETATM 26 N N3 ADP . . . G 2 7.542 2.587 25.987 1 30.13 ? N3 ADP 401 B 1 HETATM 27 C C4 ADP . . . G 2 8.072 2.131 24.822 1 65.59 ? C4 ADP 401 B 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #