data_1MXB # _model_server_result.job_id Nm8x8Hze4UBtP63W7aUiHA _model_server_result.datetime_utc '2024-11-27 21:00:22' _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 1mxb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":385}' # _entry.id 1MXB # _exptl.entry_id 1MXB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 1MXB _cell.length_a 128.9 _cell.length_b 128.9 _cell.length_c 139.8 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1MXB _symmetry.cell_setting ? _symmetry.Int_Tables_number 180 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 62 2 2' # 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,PQS dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G 1 1,2 A,B,C,D,E,F,G 2 1,3,2,4 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 9_555 -x,-x+y,-z+1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 46.6 3 'crystal symmetry operation' 4_565 -x,-y+1,z -1 0 0 0 -1 0 0 0 1 -64.45 111.630675 0 4 'crystal symmetry operation' 12_565 x,x-y+1,-z+1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 -64.45 111.630675 46.6 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id G _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 16 A ASP 16 9_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.19 ? metalc ? metalc2 A OD1 ASP 16 A ASP 16 9_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc3 A OE1 GLU 42 A GLU 42 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc4 A OE2 GLU 42 A GLU 42 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.004 ? metalc ? metalc5 A O GLY 243 A GLY 243 1_555 F K K . A K 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc6 A O GLY 243 A GLY 243 9_555 F K K . A K 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.515 ? metalc ? metalc7 A O SER 263 A SER 263 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc8 A OD1 ASP 271 A ASP 271 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc9 A OD2 ASP 271 A ASP 271 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc10 B O4 PO4 . A PO4 384 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.247 ? metalc ? metalc11 B O2 PO4 . A PO4 384 1_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc12 G O2B ADP . A ADP 385 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc13 G O2A ADP . A ADP 385 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.994 ? metalc ? metalc14 G O1A ADP . A ADP 385 1_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.139 ? metalc ? metalc15 G O3B ADP . A ADP 385 1_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.897 ? # _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 1MXB _atom_sites.fract_transf_matrix[1][1] 0.007758 _atom_sites.fract_transf_matrix[1][2] 0.004479 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008958 _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] 0.007153 _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 PO4 A 1 384 384 PO4 PO4 . C 3 MG A 1 411 411 MG MG . D 3 MG A 1 412 412 MG MG . E 4 K A 1 413 413 K K . F 4 K A 1 414 414 K K . G 5 ADP A 1 385 385 ADP ADP . # 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 5 -13.661 42.709 18.1 1 41.17 ? PB ADP 385 A 1 HETATM 2 O O1B ADP . . . G 5 -12.332 43.319 18.343 1 38 ? O1B ADP 385 A 1 HETATM 3 O O2B ADP . . . G 5 -13.582 41.311 17.556 1 42.87 ? O2B ADP 385 A 1 HETATM 4 O O3B ADP . . . G 5 -14.553 42.862 19.275 1 43.01 ? O3B ADP 385 A 1 HETATM 5 P PA ADP . . . G 5 -15.911 43.082 16.651 1 55.64 ? PA ADP 385 A 1 HETATM 6 O O1A ADP . . . G 5 -16.687 43.243 17.931 1 66.29 ? O1A ADP 385 A 1 HETATM 7 O O2A ADP . . . G 5 -15.809 41.743 16.001 1 53.48 ? O2A ADP 385 A 1 HETATM 8 O O3A ADP . . . G 5 -14.379 43.59 16.913 1 54.2 ? O3A ADP 385 A 1 HETATM 9 O O5' ADP . . . G 5 -16.707 44.059 15.684 1 73.96 ? O5' ADP 385 A 1 HETATM 10 C C5' ADP . . . G 5 -17.281 43.657 14.442 1 97.8 ? C5' ADP 385 A 1 HETATM 11 C C4' ADP . . . G 5 -16.333 43.953 13.283 1 115.51 ? C4' ADP 385 A 1 HETATM 12 O O4' ADP . . . G 5 -16.938 44.837 12.323 1 122.13 ? O4' ADP 385 A 1 HETATM 13 C C3' ADP . . . G 5 -15.02 44.594 13.759 1 122.4 ? C3' ADP 385 A 1 HETATM 14 O O3' ADP . . . G 5 -13.967 43.613 13.843 1 123.18 ? O3' ADP 385 A 1 HETATM 15 C C2' ADP . . . G 5 -14.725 45.733 12.806 1 126.48 ? C2' ADP 385 A 1 HETATM 16 O O2' ADP . . . G 5 -13.547 45.455 12.033 1 130.18 ? O2' ADP 385 A 1 HETATM 17 C C1' ADP . . . G 5 -15.961 45.814 11.892 1 126.49 ? C1' ADP 385 A 1 HETATM 18 N N9 ADP . . . G 5 -16.551 47.176 11.782 1 118.13 ? N9 ADP 385 A 1 HETATM 19 C C8 ADP . . . G 5 -16.293 48.297 12.554 1 98.11 ? C8 ADP 385 A 1 HETATM 20 N N7 ADP . . . G 5 -16.407 49.418 11.888 1 95.84 ? N7 ADP 385 A 1 HETATM 21 C C5 ADP . . . G 5 -16.917 49.037 10.645 1 98.5 ? C5 ADP 385 A 1 HETATM 22 C C6 ADP . . . G 5 -17.498 49.777 9.586 1 97.01 ? C6 ADP 385 A 1 HETATM 23 N N6 ADP . . . G 5 -17.471 51.114 9.554 1 99.07 ? N6 ADP 385 A 1 HETATM 24 N N1 ADP . . . G 5 -18.187 49.104 8.643 1 100.16 ? N1 ADP 385 A 1 HETATM 25 C C2 ADP . . . G 5 -18.324 47.793 8.771 1 97.67 ? C2 ADP 385 A 1 HETATM 26 N N3 ADP . . . G 5 -17.779 46.964 9.66 1 99.87 ? N3 ADP 385 A 1 HETATM 27 C C4 ADP . . . G 5 -17.087 47.668 10.601 1 98.73 ? C4 ADP 385 A 1 HETATM 28 H HO3' ADP . . . G 5 -13.635 43.476 12.946 0 0 ? HO3' ADP 385 A 1 HETATM 29 H HO2' ADP . . . G 5 -12.911 45.047 12.631 0 0 ? HO2' ADP 385 A 1 HETATM 30 H HN61 ADP . . . G 5 -17.704 51.619 8.709 0 0 ? HN61 ADP 385 A 1 HETATM 31 H HN62 ADP . . . G 5 -17.289 51.625 10.409 0 0 ? HN62 ADP 385 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #