data_5SVM # _model_server_result.job_id JBvhjxpL1epoSZvLQ-irAA _model_server_result.datetime_utc '2024-11-05 21:00:58' _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 5svm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":401}' # _entry.id 5SVM # _exptl.entry_id 5SVM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 7 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 90 _cell.entry_id 5SVM _cell.length_a 172.64 _cell.length_b 172.64 _cell.length_c 172.64 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SVM _symmetry.cell_setting ? _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 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,C,D,E,F,G,H,I,P 1 1,2,4 B,J,K,L,M,N,O,Q 2 1,3,5 # 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' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 3 'crystal symmetry operation' 6_555 z+1/2,-x+1/2,-y 0 0 1 -1 0 0 0 -1 0 86.32 86.32 0 4 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 5 'crystal symmetry operation' 12_554 -y+1/2,-z,x-1/2 0 -1 0 0 0 -1 1 0 0 86.32 0 -86.32 # _struct_asym.details ? _struct_asym.entity_id 7 _struct_asym.id J _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 disulf ? disulf1 A SG CYS 106 A CYS 107 1_555 A SG CYS 152 A CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf2 A SG CYS 115 A CYS 116 1_555 A SG CYS 136 A CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf3 A SG CYS 121 A CYS 122 1_555 A SG CYS 146 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 202 A CYS 203 1_555 A SG CYS 212 A CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 246 A CYS 247 1_555 A SG CYS 255 A CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 B SG CYS 106 B CYS 107 1_555 B SG CYS 152 B CYS 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf7 B SG CYS 115 B CYS 116 1_555 B SG CYS 136 B CYS 137 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf8 B SG CYS 121 B CYS 122 1_555 B SG CYS 146 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 202 B CYS 203 1_555 B SG CYS 212 B CYS 213 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf10 B SG CYS 246 B CYS 247 1_555 B SG CYS 255 B CYS 256 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 A ND2 ASN 169 A ASN 170 1_555 C C1 NAG . A NAG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale2 A ND2 ASN 193 A ASN 194 1_555 D C1 NAG . A NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.436 ? covale ? covale3 A ND2 ASN 289 A ASN 290 1_555 E C1 NAG . A NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? covale ? covale4 B ND2 ASN 169 B ASN 170 1_555 K C1 NAG . B NAG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 B ND2 ASN 193 B ASN 194 1_555 L C1 NAG . B NAG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.449 ? covale ? covale6 B ND2 ASN 289 B ASN 290 1_555 M C1 NAG . B NAG 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? metalc ? metalc1 F OAI 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc2 F OAC 6AT . A 6AT 404 1_555 G NA NA . A NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.011 ? metalc ? metalc3 G NA NA . A NA 405 1_555 P O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.884 ? metalc ? metalc4 G NA NA . A NA 405 1_555 P O HOH . A HOH 511 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.65 ? metalc ? metalc5 G NA NA . A NA 405 1_555 P O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc6 G NA NA . A NA 405 1_555 P O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc7 B OD2 ASP 157 B ASP 158 1_555 N NA NA . B NA 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc8 N NA NA . B NA 405 1_555 Q O HOH . B HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.002 ? metalc ? metalc9 N NA NA . B NA 405 1_555 Q O HOH . B HOH 512 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.961 ? # _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 123 n n PG O2G ATP sing 124 n n PG O3G ATP sing 125 n n PG O3B ATP sing 126 n n O2G HOG2 ATP sing 127 n n O3G HOG3 ATP sing 128 n n PB O1B ATP doub 129 n n PB O2B ATP sing 130 n n PB O3B ATP sing 131 n n PB O3A ATP sing 132 n n O2B HOB2 ATP sing 133 n n PA O1A ATP doub 134 n n PA O2A ATP sing 135 n n PA O3A ATP sing 136 n n PA O5' ATP sing 137 n n O2A HOA2 ATP sing 138 n n O5' C5' ATP sing 139 n n C5' C4' ATP sing 140 n n C5' "H5'1" ATP sing 141 n n C5' "H5'2" ATP sing 142 n n C4' O4' ATP sing 143 n n C4' C3' ATP sing 144 n n C4' H4' ATP sing 145 n n O4' C1' ATP sing 146 n n C3' O3' ATP sing 147 n n C3' C2' ATP sing 148 n n C3' H3' ATP sing 149 n n O3' HO3' ATP sing 150 n n C2' O2' ATP sing 151 n n C2' C1' ATP sing 152 n n C2' H2' ATP sing 153 n n O2' HO2' ATP sing 154 n n C1' N9 ATP sing 155 n n C1' H1' ATP sing 156 n n N9 C8 ATP sing 157 n y N9 C4 ATP sing 158 n y C8 N7 ATP doub 159 n y C8 H8 ATP sing 160 n n N7 C5 ATP sing 161 n y C5 C6 ATP sing 162 n y C5 C4 ATP doub 163 n y C6 N6 ATP sing 164 n n C6 N1 ATP doub 165 n y N6 HN61 ATP sing 166 n n N6 HN62 ATP sing 167 n n N1 C2 ATP sing 168 n y C2 N3 ATP doub 169 n y C2 H2 ATP sing 170 n n N3 C4 ATP sing 171 n y # _atom_sites.entry_id 5SVM _atom_sites.fract_transf_matrix[1][1] 0.005792 _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] 0.005792 _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] 0.005792 _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 C 2 NAG A 1 401 500 NAG NAG . D 2 NAG A 1 402 501 NAG NAG . E 2 NAG A 1 403 502 NAG NAG . F 3 6AT A 1 404 1 6AT LIG . G 4 NA A 1 405 4 NA NA . H 5 TRS A 1 406 1 TRS TRS . I 6 EDO A 1 407 1 EDO EDO . J 7 ATP B 1 401 402 ATP ATP . K 2 NAG B 1 402 500 NAG NAG . L 2 NAG B 1 403 501 NAG NAG . M 2 NAG B 1 404 502 NAG NAG . N 4 NA B 1 405 3 NA NA . O 6 EDO B 1 406 2 EDO EDO . P 8 HOH A 1 501 20 HOH HOH . P 8 HOH A 2 502 40 HOH HOH . P 8 HOH A 3 503 52 HOH HOH . P 8 HOH A 4 504 3 HOH HOH . P 8 HOH A 5 505 44 HOH HOH . P 8 HOH A 6 506 6 HOH HOH . P 8 HOH A 7 507 1 HOH HOH . P 8 HOH A 8 508 5 HOH HOH . P 8 HOH A 9 509 4 HOH HOH . P 8 HOH A 10 510 11 HOH HOH . P 8 HOH A 11 511 43 HOH HOH . P 8 HOH A 12 512 14 HOH HOH . P 8 HOH A 13 513 26 HOH HOH . P 8 HOH A 14 514 49 HOH HOH . P 8 HOH A 15 515 54 HOH HOH . P 8 HOH A 16 516 15 HOH HOH . P 8 HOH A 17 517 45 HOH HOH . P 8 HOH A 18 518 42 HOH HOH . P 8 HOH A 19 519 2 HOH HOH . Q 8 HOH B 1 501 29 HOH HOH . Q 8 HOH B 2 502 22 HOH HOH . Q 8 HOH B 3 503 48 HOH HOH . Q 8 HOH B 4 504 37 HOH HOH . Q 8 HOH B 5 505 36 HOH HOH . Q 8 HOH B 6 506 23 HOH HOH . Q 8 HOH B 7 507 33 HOH HOH . Q 8 HOH B 8 508 51 HOH HOH . Q 8 HOH B 9 509 19 HOH HOH . Q 8 HOH B 10 510 50 HOH HOH . Q 8 HOH B 11 511 28 HOH HOH . Q 8 HOH B 12 512 32 HOH HOH . Q 8 HOH B 13 513 16 HOH HOH . Q 8 HOH B 14 514 35 HOH HOH . Q 8 HOH B 15 515 53 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 . . . J 7 37.666 35.167 -19.018 1 80.42 ? PG ATP 401 B 1 HETATM 2 O O1G ATP . . . J 7 36.642 34.615 -19.986 1 69.63 ? O1G ATP 401 B 1 HETATM 3 O O2G ATP . . . J 7 37.098 36.066 -17.945 1 90.62 ? O2G ATP 401 B 1 HETATM 4 O O3G ATP . . . J 7 38.923 35.692 -19.672 1 52.86 ? O3G ATP 401 B 1 HETATM 5 P PB ATP . . . J 7 37.579 32.42 -18.544 1 72.99 ? PB ATP 401 B 1 HETATM 6 O O1B ATP . . . J 7 38.005 32.012 -19.936 1 73.5 ? O1B ATP 401 B 1 HETATM 7 O O2B ATP . . . J 7 36.113 32.439 -18.183 1 66.17 ? O2B ATP 401 B 1 HETATM 8 O O3B ATP . . . J 7 38.168 33.879 -18.203 1 71.28 ? O3B ATP 401 B 1 HETATM 9 P PA ATP . . . J 7 39.902 31.106 -17.523 1 63.73 ? PA ATP 401 B 1 HETATM 10 O O1A ATP . . . J 7 40.552 31.789 -18.706 1 67.16 ? O1A ATP 401 B 1 HETATM 11 O O2A ATP . . . J 7 39.963 29.602 -17.37 1 66.91 ? O2A ATP 401 B 1 HETATM 12 O O3A ATP . . . J 7 38.346 31.531 -17.438 1 74.56 ? O3A ATP 401 B 1 HETATM 13 O O5' ATP . . . J 7 40.431 31.811 -16.179 1 59.47 ? O5' ATP 401 B 1 HETATM 14 C C5' ATP . . . J 7 39.933 31.369 -14.921 1 73.46 ? C5' ATP 401 B 1 HETATM 15 C C4' ATP . . . J 7 39.557 32.599 -14.112 1 72.64 ? C4' ATP 401 B 1 HETATM 16 O O4' ATP . . . J 7 40.71 33.425 -13.96 1 58.83 ? O4' ATP 401 B 1 HETATM 17 C C3' ATP . . . J 7 38.489 33.449 -14.793 1 80.38 ? C3' ATP 401 B 1 HETATM 18 O O3' ATP . . . J 7 37.402 33.679 -13.888 1 103.61 ? O3' ATP 401 B 1 HETATM 19 C C2' ATP . . . J 7 39.166 34.752 -15.161 1 65.91 ? C2' ATP 401 B 1 HETATM 20 O O2' ATP . . . J 7 38.316 35.883 -14.946 1 87.61 ? O2' ATP 401 B 1 HETATM 21 C C1' ATP . . . J 7 40.374 34.784 -14.244 1 78.45 ? C1' ATP 401 B 1 HETATM 22 N N9 ATP . . . J 7 41.547 35.449 -14.849 1 68.69 ? N9 ATP 401 B 1 HETATM 23 C C8 ATP . . . J 7 42.266 34.958 -15.872 1 71.05 ? C8 ATP 401 B 1 HETATM 24 N N7 ATP . . . J 7 43.285 35.8 -16.178 1 69.79 ? N7 ATP 401 B 1 HETATM 25 C C5 ATP . . . J 7 43.219 36.841 -15.333 1 62.11 ? C5 ATP 401 B 1 HETATM 26 C C6 ATP . . . J 7 43.994 38.078 -15.112 1 66.19 ? C6 ATP 401 B 1 HETATM 27 N N6 ATP . . . J 7 45.058 38.346 -15.894 1 61.23 ? N6 ATP 401 B 1 HETATM 28 N N1 ATP . . . J 7 43.6 38.914 -14.122 1 72.19 ? N1 ATP 401 B 1 HETATM 29 C C2 ATP . . . J 7 42.535 38.641 -13.344 1 64.2 ? C2 ATP 401 B 1 HETATM 30 N N3 ATP . . . J 7 41.79 37.528 -13.498 1 73.55 ? N3 ATP 401 B 1 HETATM 31 C C4 ATP . . . J 7 42.071 36.609 -14.456 1 64.26 ? C4 ATP 401 B 1 HETATM 32 H "H5'1" ATP . . . J 7 39.057 30.733 -15.067 1 88.16 ? "H5'1" ATP 401 B 1 HETATM 33 H "H5'2" ATP . . . J 7 40.697 30.793 -14.396 1 88.16 ? "H5'2" ATP 401 B 1 HETATM 34 H H4' ATP . . . J 7 39.187 32.281 -13.127 1 87.17 ? H4' ATP 401 B 1 HETATM 35 H H3' ATP . . . J 7 38.139 32.943 -15.704 1 96.46 ? H3' ATP 401 B 1 HETATM 36 H HO3' ATP . . . J 7 36.728 34.218 -14.324 1 124.33 ? HO3' ATP 401 B 1 HETATM 37 H H2' ATP . . . J 7 39.5 34.71 -16.207 1 79.09 ? H2' ATP 401 B 1 HETATM 38 H HO2' ATP . . . J 7 37.53 35.806 -15.504 1 105.13 ? HO2' ATP 401 B 1 HETATM 39 H H1' ATP . . . J 7 40.095 35.299 -13.314 1 94.14 ? H1' ATP 401 B 1 HETATM 40 H H8 ATP . . . J 7 42.059 34.026 -16.383 1 85.26 ? H8 ATP 401 B 1 HETATM 41 H HN61 ATP . . . J 7 45.591 39.192 -15.75 1 73.48 ? HN61 ATP 401 B 1 HETATM 42 H HN62 ATP . . . J 7 45.322 37.701 -16.625 1 73.48 ? HN62 ATP 401 B 1 HETATM 43 H H2 ATP . . . J 7 42.265 39.344 -12.566 1 77.04 ? H2 ATP 401 B 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 43 #