data_5YH3 # _model_server_result.job_id dt6WI8Li0exaZ4_wgrSU0g _model_server_result.datetime_utc '2024-12-03 18:50:53' _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 5yh3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":701}' # _entry.id 5YH3 # _exptl.entry_id 5YH3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _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 90 _cell.entry_id 5YH3 _cell.length_a 78.469 _cell.length_b 192.747 _cell.length_c 226.669 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5YH3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F 1 1 C,D,G,H 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 ? 3 E N N ? 3 F N N ? 3 G N N ? 3 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 disulf ? disulf1 A SG CYS 147 A CYS 209 1_555 A SG CYS 257 A CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 A SG CYS 149 A CYS 211 1_555 A SG CYS 261 A CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 A SG CYS 252 A CYS 314 1_555 A SG CYS 268 A CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf4 A SG CYS 316 A CYS 378 1_555 A SG CYS 390 A CYS 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf5 A SG CYS 391 A CYS 453 1_555 A SG CYS 450 A CYS 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf6 B SG CYS 222 C CYS 362 1_555 B SG CYS 238 C CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf7 B SG CYS 227 C CYS 367 1_555 B SG CYS 231 C CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf8 B SG CYS 286 C CYS 426 1_555 B SG CYS 360 C CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf9 B SG CYS 361 C CYS 501 1_555 B SG CYS 420 C CYS 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 C SG CYS 147 B CYS 209 1_555 C SG CYS 257 B CYS 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf11 C SG CYS 149 B CYS 211 1_555 C SG CYS 261 B CYS 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf12 C SG CYS 252 B CYS 314 1_555 C SG CYS 268 B CYS 330 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf13 C SG CYS 316 B CYS 378 1_555 C SG CYS 390 B CYS 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf14 C SG CYS 391 B CYS 453 1_555 C SG CYS 450 B CYS 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf15 D SG CYS 222 D CYS 362 1_555 D SG CYS 238 D CYS 378 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf16 D SG CYS 227 D CYS 367 1_555 D SG CYS 231 D CYS 371 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf17 D SG CYS 286 D CYS 426 1_555 D SG CYS 360 D CYS 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf18 D SG CYS 361 D CYS 501 1_555 D SG CYS 420 D CYS 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _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 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 5YH3 _atom_sites.fract_transf_matrix[1][1] 0.012744 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005188 _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] 0.004412 _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 ATP A 1 701 701 ATP ATP . F 3 ATP A 1 702 702 ATP ATP . G 3 ATP B 1 701 701 ATP ATP . H 3 ATP B 1 702 702 ATP ATP . # 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 . . . G 3 -12.439 -0.644 -56.408 1 163.39 ? PG ATP 701 B 1 HETATM 2 O O1G ATP . . . G 3 -12.996 -1.759 -57.263 1 138.53 ? O1G ATP 701 B 1 HETATM 3 O O2G ATP . . . G 3 -11.765 -1.074 -55.132 1 109.96 ? O2G ATP 701 B 1 HETATM 4 O O3G ATP . . . G 3 -11.678 0.415 -57.172 1 137.59 ? O3G ATP 701 B 1 HETATM 5 P PB ATP . . . G 3 -14.087 1.595 -56.369 1 174.45 ? PB ATP 701 B 1 HETATM 6 O O1B ATP . . . G 3 -13.999 1.615 -57.878 1 141.99 ? O1B ATP 701 B 1 HETATM 7 O O2B ATP . . . G 3 -13.267 2.566 -55.552 1 127.12 ? O2B ATP 701 B 1 HETATM 8 O O3B ATP . . . G 3 -13.752 0.107 -55.872 1 139.79 ? O3B ATP 701 B 1 HETATM 9 P PA ATP . . . G 3 -16.804 1.297 -56.943 1 144.62 ? PA ATP 701 B 1 HETATM 10 O O1A ATP . . . G 3 -16.604 2.083 -58.217 1 130.83 ? O1A ATP 701 B 1 HETATM 11 O O2A ATP . . . G 3 -16.911 -0.208 -56.971 1 122.74 ? O2A ATP 701 B 1 HETATM 12 O O3A ATP . . . G 3 -15.63 1.701 -55.918 1 147.13 ? O3A ATP 701 B 1 HETATM 13 O O5' ATP . . . G 3 -18.115 1.887 -56.229 1 94.5 ? O5' ATP 701 B 1 HETATM 14 C C5' ATP . . . G 3 -18.632 3.133 -56.678 1 100.55 ? C5' ATP 701 B 1 HETATM 15 C C4' ATP . . . G 3 -19.802 2.943 -57.635 1 95.31 ? C4' ATP 701 B 1 HETATM 16 O O4' ATP . . . G 3 -20.931 3.642 -57.111 1 88.15 ? O4' ATP 701 B 1 HETATM 17 C C3' ATP . . . G 3 -19.481 3.565 -58.982 1 90.8 ? C3' ATP 701 B 1 HETATM 18 O O3' ATP . . . G 3 -20.089 2.81 -60.033 1 87.66 ? O3' ATP 701 B 1 HETATM 19 C C2' ATP . . . G 3 -20.113 4.938 -58.932 1 78.97 ? C2' ATP 701 B 1 HETATM 20 O O2' ATP . . . G 3 -20.701 5.233 -60.201 1 74.76 ? O2' ATP 701 B 1 HETATM 21 C C1' ATP . . . G 3 -21.169 4.851 -57.837 1 82.2 ? C1' ATP 701 B 1 HETATM 22 N N9 ATP . . . G 3 -21.035 5.983 -56.883 1 82.23 ? N9 ATP 701 B 1 HETATM 23 C C8 ATP . . . G 3 -20.373 5.932 -55.709 1 74.23 ? C8 ATP 701 B 1 HETATM 24 N N7 ATP . . . G 3 -20.432 7.119 -55.053 1 66.73 ? N7 ATP 701 B 1 HETATM 25 C C5 ATP . . . G 3 -21.151 7.963 -55.817 1 66.95 ? C5 ATP 701 B 1 HETATM 26 C C6 ATP . . . G 3 -21.595 9.375 -55.718 1 63.96 ? C6 ATP 701 B 1 HETATM 27 N N6 ATP . . . G 3 -21.274 10.139 -54.643 1 57.94 ? N6 ATP 701 B 1 HETATM 28 N N1 ATP . . . G 3 -22.334 9.876 -56.735 1 71.49 ? N1 ATP 701 B 1 HETATM 29 C C2 ATP . . . G 3 -22.661 9.128 -57.807 1 74.26 ? C2 ATP 701 B 1 HETATM 30 N N3 ATP . . . G 3 -22.293 7.841 -57.962 1 76.44 ? N3 ATP 701 B 1 HETATM 31 C C4 ATP . . . G 3 -21.549 7.21 -57.02 1 77.49 ? C4 ATP 701 B 1 # _model_server_stats.io_time_ms 78 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #