data_1MXC # _model_server_result.job_id f6Ha65ZDe8FRFFWfwmd-lA _model_server_result.datetime_utc '2024-11-24 04:02:36' _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 1mxc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":385}' # _entry.id 1MXC # _exptl.entry_id 1MXC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 506.097 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "8-BROMOADENOSINE-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 1MXC _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 1MXC _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 OD1 ASP 16 A ASP 16 9_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc2 A OD2 ASP 16 A ASP 16 9_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc3 A OE1 GLU 42 A GLU 42 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.676 ? metalc ? metalc4 A OE2 GLU 42 A GLU 42 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.112 ? metalc ? metalc5 A OG1 THR 242 A THR 242 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.698 ? metalc ? metalc6 A O GLY 243 A GLY 243 1_555 F K K . A K 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc7 A O GLY 243 A GLY 243 9_555 F K K . A K 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.534 ? metalc ? metalc8 A O SER 263 A SER 263 1_555 E K K . A K 413 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc9 A OD1 ASP 271 A ASP 271 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc10 A OD2 ASP 271 A ASP 271 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.147 ? metalc ? metalc11 B O4 PO4 . A PO4 384 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc12 B O2 PO4 . A PO4 384 1_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc13 G O2B ABP . A ABP 385 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc14 G O2A ABP . A ABP 385 1_555 C MG MG . A MG 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.867 ? metalc ? metalc15 G O1A ABP . A ABP 385 1_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.135 ? metalc ? metalc16 G O3B ABP . A ABP 385 1_555 D MG MG . A MG 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.82 ? # _chem_comp.formula 'C10 H14 Br N5 O10 P2' _chem_comp.formula_weight 506.097 _chem_comp.id ABP _chem_comp.mon_nstd_flag . _chem_comp.name "8-BROMOADENOSINE-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 ABP doub 1 n n PB O2B ABP sing 2 n n PB O3B ABP sing 3 n n PB O3A ABP sing 4 n n O2B HOB2 ABP sing 5 n n O3B HOB3 ABP sing 6 n n PA O1A ABP doub 7 n n PA O2A ABP sing 8 n n PA O3A ABP sing 9 n n PA O5' ABP sing 10 n n O2A HOA2 ABP sing 11 n n O5' C5' ABP sing 12 n n C5' C4' ABP sing 13 n n C5' "H5'1" ABP sing 14 n n C5' "H5'2" ABP sing 15 n n C4' O4' ABP sing 16 n n C4' C3' ABP sing 17 n n C4' H4' ABP sing 18 n n O4' C1' ABP sing 19 n n C3' O3' ABP sing 20 n n C3' C2' ABP sing 21 n n C3' H3' ABP sing 22 n n O3' HO3' ABP sing 23 n n C2' O2' ABP sing 24 n n C2' C1' ABP sing 25 n n C2' H2' ABP sing 26 n n O2' HO2' ABP sing 27 n n C1' N9 ABP sing 28 n n C1' H1' ABP sing 29 n n N9 C8 ABP sing 30 n y N9 C4 ABP sing 31 n y C8 BR8 ABP sing 32 n n C8 N7 ABP doub 33 n y N7 C5 ABP sing 34 n y C5 C6 ABP sing 35 n y C5 C4 ABP doub 36 n y C6 N6 ABP sing 37 n n C6 N1 ABP doub 38 n y N6 HN61 ABP sing 39 n n N6 HN62 ABP sing 40 n n N1 C2 ABP sing 41 n y C2 N3 ABP doub 42 n y C2 H2 ABP sing 43 n n N3 C4 ABP sing 44 n y # _atom_sites.entry_id 1MXC _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 ABP A 1 385 385 ABP ABP . # 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 ABP . . . G 5 -13.607 42.755 18.052 1 40.42 ? PB ABP 385 A 1 HETATM 2 O O1B ABP . . . G 5 -12.278 43.339 18.372 1 34.5 ? O1B ABP 385 A 1 HETATM 3 O O2B ABP . . . G 5 -13.526 41.358 17.491 1 37.88 ? O2B ABP 385 A 1 HETATM 4 O O3B ABP . . . G 5 -14.549 42.887 19.184 1 41.48 ? O3B ABP 385 A 1 HETATM 5 P PA ABP . . . G 5 -15.783 43.109 16.516 1 46.64 ? PA ABP 385 A 1 HETATM 6 O O1A ABP . . . G 5 -16.637 43.251 17.749 1 49.81 ? O1A ABP 385 A 1 HETATM 7 O O2A ABP . . . G 5 -15.624 41.761 15.875 1 34.34 ? O2A ABP 385 A 1 HETATM 8 O O3A ABP . . . G 5 -14.289 43.663 16.881 1 46.36 ? O3A ABP 385 A 1 HETATM 9 O O5' ABP . . . G 5 -16.527 44.1 15.505 1 62.56 ? O5' ABP 385 A 1 HETATM 10 C C5' ABP . . . G 5 -17.024 43.772 14.206 1 86.35 ? C5' ABP 385 A 1 HETATM 11 C C4' ABP . . . G 5 -16.06 44.213 13.091 1 102.22 ? C4' ABP 385 A 1 HETATM 12 O O4' ABP . . . G 5 -16.604 45.262 12.255 1 106.41 ? O4' ABP 385 A 1 HETATM 13 C C3' ABP . . . G 5 -14.723 44.722 13.626 1 106.62 ? C3' ABP 385 A 1 HETATM 14 O O3' ABP . . . G 5 -13.812 43.63 13.874 1 111.27 ? O3' ABP 385 A 1 HETATM 15 C C2' ABP . . . G 5 -14.234 45.719 12.581 1 109.87 ? C2' ABP 385 A 1 HETATM 16 O O2' ABP . . . G 5 -13.281 45.096 11.696 1 112.83 ? O2' ABP 385 A 1 HETATM 17 C C1' ABP . . . G 5 -15.505 46.101 11.792 1 107.56 ? C1' ABP 385 A 1 HETATM 18 N N9 ABP . . . G 5 -15.872 47.571 11.769 1 99.9 ? N9 ABP 385 A 1 HETATM 19 C C8 ABP . . . G 5 -15.279 48.756 12.287 1 93.43 ? C8 ABP 385 A 1 HETATM 20 BR BR8 ABP . . . G 5 -14.059 48.963 13.747 1 94.89 ? BR8 ABP 385 A 1 HETATM 21 N N7 ABP . . . G 5 -15.685 49.831 11.662 1 90.97 ? N7 ABP 385 A 1 HETATM 22 C C5 ABP . . . G 5 -16.627 49.389 10.739 1 92.94 ? C5 ABP 385 A 1 HETATM 23 C C6 ABP . . . G 5 -17.287 50.05 9.679 1 92.56 ? C6 ABP 385 A 1 HETATM 24 N N6 ABP . . . G 5 -17.399 51.376 9.622 1 92.55 ? N6 ABP 385 A 1 HETATM 25 N N1 ABP . . . G 5 -17.922 49.296 8.76 1 90.14 ? N1 ABP 385 A 1 HETATM 26 C C2 ABP . . . G 5 -17.983 47.986 8.944 1 89.58 ? C2 ABP 385 A 1 HETATM 27 N N3 ABP . . . G 5 -17.418 47.241 9.889 1 91.28 ? N3 ABP 385 A 1 HETATM 28 C C4 ABP . . . G 5 -16.755 48.026 10.796 1 93.18 ? C4 ABP 385 A 1 HETATM 29 H HO2' ABP . . . G 5 -12.991 44.28 12.128 0 0 ? HO2' ABP 385 A 1 HETATM 30 H HN61 ABP . . . G 5 -17.343 51.917 10.477 0 0 ? HN61 ABP 385 A 1 HETATM 31 H HN62 ABP . . . G 5 -17.618 51.832 8.747 0 0 ? HN62 ABP 385 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 338 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #