data_3LCB # _model_server_result.job_id F0AQGleDCb_mf1cDjHoJLw _model_server_result.datetime_utc '2024-11-09 02:44:04' _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 3lcb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":1760}' # _entry.id 3LCB # _exptl.entry_id 3LCB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 90 _cell.angle_gamma 120 _cell.entry_id 3LCB _cell.length_a 196.801 _cell.length_b 196.801 _cell.length_c 156.458 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3LCB _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dodecameric 12 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,E,F,G,K 1 1 D,N 1 2 B,C,H,I,J,L,M 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N 3 1,3,2 # 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' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 F N N ? 4 H 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 OD1 ASN 462 A ASN 462 1_555 G MG MG . A MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.289 ? metalc ? metalc2 A OD2 ASP 475 A ASP 475 1_555 G MG MG . A MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.729 ? metalc ? metalc3 A OD1 ASP 475 A ASP 475 1_555 G MG MG . A MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc4 G MG MG . A MG 579 1_555 F O1A ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc5 G MG MG . A MG 579 1_555 F O1G ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc6 G MG MG . A MG 579 1_555 F O1B ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? metalc ? metalc7 G MG MG . A MG 579 1_555 F O3B ATP . A ATP 1760 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.786 ? metalc ? metalc8 B OD1 ASN 462 B ASN 462 1_555 J MG MG . B MG 579 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc9 J MG MG . B MG 579 1_555 H O1B ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.88 ? metalc ? metalc10 J MG MG . B MG 579 1_555 H O3A ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc11 J MG MG . B MG 579 1_555 H O2B ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.866 ? metalc ? metalc12 J MG MG . B MG 579 1_555 H O5' ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc13 J MG MG . B MG 579 1_555 H O2A ATP . B ATP 1761 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.944 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 109 n n PG O2G ATP sing 110 n n PG O3G ATP sing 111 n n PG O3B ATP sing 112 n n O2G HOG2 ATP sing 113 n n O3G HOG3 ATP sing 114 n n PB O1B ATP doub 115 n n PB O2B ATP sing 116 n n PB O3B ATP sing 117 n n PB O3A ATP sing 118 n n O2B HOB2 ATP sing 119 n n PA O1A ATP doub 120 n n PA O2A ATP sing 121 n n PA O3A ATP sing 122 n n PA O5' ATP sing 123 n n O2A HOA2 ATP sing 124 n n O5' C5' ATP sing 125 n n C5' C4' ATP sing 126 n n C5' "H5'1" ATP sing 127 n n C5' "H5'2" ATP sing 128 n n C4' O4' ATP sing 129 n n C4' C3' ATP sing 130 n n C4' H4' ATP sing 131 n n O4' C1' ATP sing 132 n n C3' O3' ATP sing 133 n n C3' C2' ATP sing 134 n n C3' H3' ATP sing 135 n n O3' HO3' ATP sing 136 n n C2' O2' ATP sing 137 n n C2' C1' ATP sing 138 n n C2' H2' ATP sing 139 n n O2' HO2' ATP sing 140 n n C1' N9 ATP sing 141 n n C1' H1' ATP sing 142 n n N9 C8 ATP sing 143 n y N9 C4 ATP sing 144 n y C8 N7 ATP doub 145 n y C8 H8 ATP sing 146 n n N7 C5 ATP sing 147 n y C5 C6 ATP sing 148 n y C5 C4 ATP doub 149 n y C6 N6 ATP sing 150 n n C6 N1 ATP doub 151 n y N6 HN61 ATP sing 152 n n N6 HN62 ATP sing 153 n n N1 C2 ATP sing 154 n y C2 N3 ATP doub 155 n y C2 H2 ATP sing 156 n n N3 C4 ATP sing 157 n y # _atom_sites.entry_id 3LCB _atom_sites.fract_transf_matrix[1][1] 0.005081 _atom_sites.fract_transf_matrix[1][2] 0.002934 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005867 _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] 0.006391 _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 E 3 AMP A 1 1604 1604 AMP AMP . F 4 ATP A 1 1760 1760 ATP ATP . G 5 MG A 1 579 1 MG MG . H 4 ATP B 1 1761 1761 ATP ATP . I 3 AMP B 1 1604 1604 AMP AMP . J 5 MG B 1 579 1 MG MG . K 6 HOH A 1 580 8 HOH HOH . K 6 HOH A 2 581 15 HOH HOH . K 6 HOH A 3 582 20 HOH HOH . L 6 HOH B 1 580 7 HOH HOH . L 6 HOH B 2 581 9 HOH HOH . L 6 HOH B 3 582 13 HOH HOH . L 6 HOH B 4 583 19 HOH HOH . L 6 HOH B 5 584 21 HOH HOH . M 6 HOH C 1 417 1 HOH HOH . M 6 HOH C 2 418 3 HOH HOH . M 6 HOH C 3 419 6 HOH HOH . M 6 HOH C 4 420 12 HOH HOH . M 6 HOH C 5 421 14 HOH HOH . N 6 HOH D 1 417 2 HOH HOH . N 6 HOH D 2 418 4 HOH HOH . N 6 HOH D 3 419 5 HOH HOH . N 6 HOH D 4 420 10 HOH HOH . N 6 HOH D 5 421 11 HOH HOH . N 6 HOH D 6 422 16 HOH HOH . N 6 HOH D 7 423 17 HOH HOH . N 6 HOH D 8 424 18 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 PG ATP . . . F 4 -29.731 62.017 -53.451 1 70.41 ? PG ATP 1760 A 1 HETATM 2 O O1G ATP . . . F 4 -30.995 62.752 -53.844 1 69.44 ? O1G ATP 1760 A 1 HETATM 3 O O2G ATP . . . F 4 -29.202 62.476 -52.111 1 70.44 ? O2G ATP 1760 A 1 HETATM 4 O O3G ATP . . . F 4 -28.657 62.018 -54.52 1 70.15 ? O3G ATP 1760 A 1 HETATM 5 P PB ATP . . . F 4 -30.137 59.189 -54.255 1 67.4 ? PB ATP 1760 A 1 HETATM 6 O O1B ATP . . . F 4 -30.223 59.81 -55.629 1 67.37 ? O1B ATP 1760 A 1 HETATM 7 O O2B ATP . . . F 4 -28.959 58.325 -53.884 1 67.3 ? O2B ATP 1760 A 1 HETATM 8 O O3B ATP . . . F 4 -30.21 60.447 -53.203 1 69.39 ? O3B ATP 1760 A 1 HETATM 9 P PA ATP . . . F 4 -32.749 58.118 -54.895 1 64.51 ? PA ATP 1760 A 1 HETATM 10 O O1A ATP . . . F 4 -33.113 59.549 -55.194 1 63.97 ? O1A ATP 1760 A 1 HETATM 11 O O2A ATP . . . F 4 -33.692 57.242 -54.099 1 64.29 ? O2A ATP 1760 A 1 HETATM 12 O O3A ATP . . . F 4 -31.371 58.164 -54.045 1 65.27 ? O3A ATP 1760 A 1 HETATM 13 O O5' ATP . . . F 4 -32.547 57.406 -56.339 1 64.36 ? O5' ATP 1760 A 1 HETATM 14 C C5' ATP . . . F 4 -31.918 58.099 -57.419 1 64.36 ? C5' ATP 1760 A 1 HETATM 15 C C4' ATP . . . F 4 -32.838 58.413 -58.591 1 64.62 ? C4' ATP 1760 A 1 HETATM 16 O O4' ATP . . . F 4 -33.518 57.258 -59.079 1 64.9 ? O4' ATP 1760 A 1 HETATM 17 C C3' ATP . . . F 4 -33.93 59.427 -58.3 1 64.76 ? C3' ATP 1760 A 1 HETATM 18 O O3' ATP . . . F 4 -33.43 60.766 -58.358 1 65.3 ? O3' ATP 1760 A 1 HETATM 19 C C2' ATP . . . F 4 -34.928 59.122 -59.396 1 64.86 ? C2' ATP 1760 A 1 HETATM 20 O O2' ATP . . . F 4 -34.515 59.732 -60.627 1 64.5 ? O2' ATP 1760 A 1 HETATM 21 C C1' ATP . . . F 4 -34.825 57.615 -59.548 1 65.31 ? C1' ATP 1760 A 1 HETATM 22 N N9 ATP . . . F 4 -35.849 56.939 -58.705 1 65.64 ? N9 ATP 1760 A 1 HETATM 23 C C8 ATP . . . F 4 -35.62 56.408 -57.489 1 65.52 ? C8 ATP 1760 A 1 HETATM 24 N N7 ATP . . . F 4 -36.743 55.867 -56.968 1 65.91 ? N7 ATP 1760 A 1 HETATM 25 C C5 ATP . . . F 4 -37.729 56.042 -57.864 1 65.85 ? C5 ATP 1760 A 1 HETATM 26 C C6 ATP . . . F 4 -39.172 55.703 -57.939 1 65.77 ? C6 ATP 1760 A 1 HETATM 27 N N6 ATP . . . F 4 -39.777 55.049 -56.918 1 65.73 ? N6 ATP 1760 A 1 HETATM 28 N N1 ATP . . . F 4 -39.855 56.065 -59.051 1 65.36 ? N1 ATP 1760 A 1 HETATM 29 C C2 ATP . . . F 4 -39.249 56.712 -60.065 1 65.65 ? C2 ATP 1760 A 1 HETATM 30 N N3 ATP . . . F 4 -37.941 57.049 -60.064 1 66.03 ? N3 ATP 1760 A 1 HETATM 31 C C4 ATP . . . F 4 -37.138 56.749 -59.01 1 65.81 ? C4 ATP 1760 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #