data_8RGJ # _model_server_result.job_id R6smsfa3zsJyBfxXHz9k8w _model_server_result.datetime_utc '2025-03-01 07:23:21' _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 8rgj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":401}' # _entry.id 8RGJ # _exptl.entry_id 8RGJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _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 90 _cell.entry_id 8RGJ _cell.length_a 135.85 _cell.length_b 135.85 _cell.length_c 78.634 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8RGJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 90 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 4 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 C N N ? 3 F 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 covale ? covale1 B C ILE 217 B ILE 199 1_555 B N CSO 218 B CSO 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.359 ? covale ? covale2 B C CSO 218 B CSO 200 1_555 B N GLU 219 B GLU 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 8RGJ _atom_sites.fract_transf_matrix[1][1] 0.007361 _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] 0.007361 _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] 0.012717 _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 3 ACP A 1 401 401 ACP ACP . D 4 ACT A 1 402 1 ACT ACT . E 5 GOL A 1 403 1 GOL GOL . F 3 ACP B 1 401 401 ACP ACP . G 6 HOH A 1 501 20 HOH HOH . G 6 HOH A 2 502 18 HOH HOH . G 6 HOH A 3 503 27 HOH HOH . G 6 HOH A 4 504 112 HOH HOH . G 6 HOH A 5 505 15 HOH HOH . G 6 HOH A 6 506 35 HOH HOH . G 6 HOH A 7 507 166 HOH HOH . G 6 HOH A 8 508 145 HOH HOH . G 6 HOH A 9 509 69 HOH HOH . G 6 HOH A 10 510 38 HOH HOH . G 6 HOH A 11 511 4 HOH HOH . G 6 HOH A 12 512 148 HOH HOH . G 6 HOH A 13 513 9 HOH HOH . G 6 HOH A 14 514 28 HOH HOH . G 6 HOH A 15 515 32 HOH HOH . G 6 HOH A 16 516 1 HOH HOH . G 6 HOH A 17 517 82 HOH HOH . G 6 HOH A 18 518 63 HOH HOH . G 6 HOH A 19 519 19 HOH HOH . G 6 HOH A 20 520 40 HOH HOH . G 6 HOH A 21 521 171 HOH HOH . G 6 HOH A 22 522 190 HOH HOH . G 6 HOH A 23 523 111 HOH HOH . G 6 HOH A 24 524 110 HOH HOH . G 6 HOH A 25 525 106 HOH HOH . G 6 HOH A 26 526 33 HOH HOH . G 6 HOH A 27 527 184 HOH HOH . G 6 HOH A 28 528 109 HOH HOH . G 6 HOH A 29 529 167 HOH HOH . G 6 HOH A 30 530 174 HOH HOH . G 6 HOH A 31 531 195 HOH HOH . G 6 HOH A 32 532 198 HOH HOH . G 6 HOH A 33 533 54 HOH HOH . G 6 HOH A 34 534 161 HOH HOH . G 6 HOH A 35 535 14 HOH HOH . G 6 HOH A 36 536 183 HOH HOH . G 6 HOH A 37 537 156 HOH HOH . G 6 HOH A 38 538 144 HOH HOH . G 6 HOH A 39 539 2 HOH HOH . G 6 HOH A 40 540 157 HOH HOH . G 6 HOH A 41 541 107 HOH HOH . G 6 HOH A 42 542 73 HOH HOH . G 6 HOH A 43 543 11 HOH HOH . G 6 HOH A 44 544 97 HOH HOH . G 6 HOH A 45 545 165 HOH HOH . G 6 HOH A 46 546 48 HOH HOH . G 6 HOH A 47 547 136 HOH HOH . G 6 HOH A 48 548 154 HOH HOH . G 6 HOH A 49 549 158 HOH HOH . G 6 HOH A 50 550 147 HOH HOH . G 6 HOH A 51 551 31 HOH HOH . G 6 HOH A 52 552 10 HOH HOH . G 6 HOH A 53 553 188 HOH HOH . G 6 HOH A 54 554 113 HOH HOH . G 6 HOH A 55 555 176 HOH HOH . G 6 HOH A 56 556 140 HOH HOH . G 6 HOH A 57 557 64 HOH HOH . G 6 HOH A 58 558 72 HOH HOH . G 6 HOH A 59 559 143 HOH HOH . G 6 HOH A 60 560 138 HOH HOH . G 6 HOH A 61 561 191 HOH HOH . G 6 HOH A 62 562 189 HOH HOH . G 6 HOH A 63 563 101 HOH HOH . G 6 HOH A 64 564 173 HOH HOH . G 6 HOH A 65 565 146 HOH HOH . G 6 HOH A 66 566 41 HOH HOH . G 6 HOH A 67 567 175 HOH HOH . G 6 HOH A 68 568 59 HOH HOH . G 6 HOH A 69 569 36 HOH HOH . G 6 HOH A 70 570 70 HOH HOH . G 6 HOH A 71 571 181 HOH HOH . H 6 HOH B 1 501 45 HOH HOH . H 6 HOH B 2 502 24 HOH HOH . H 6 HOH B 3 503 115 HOH HOH . H 6 HOH B 4 504 5 HOH HOH . H 6 HOH B 5 505 23 HOH HOH . H 6 HOH B 6 506 26 HOH HOH . H 6 HOH B 7 507 37 HOH HOH . H 6 HOH B 8 508 62 HOH HOH . H 6 HOH B 9 509 43 HOH HOH . H 6 HOH B 10 510 21 HOH HOH . H 6 HOH B 11 511 170 HOH HOH . H 6 HOH B 12 512 6 HOH HOH . H 6 HOH B 13 513 83 HOH HOH . H 6 HOH B 14 514 177 HOH HOH . H 6 HOH B 15 515 178 HOH HOH . H 6 HOH B 16 516 84 HOH HOH . H 6 HOH B 17 517 13 HOH HOH . H 6 HOH B 18 518 60 HOH HOH . H 6 HOH B 19 519 193 HOH HOH . H 6 HOH B 20 520 102 HOH HOH . H 6 HOH B 21 521 117 HOH HOH . H 6 HOH B 22 522 58 HOH HOH . H 6 HOH B 23 523 87 HOH HOH . H 6 HOH B 24 524 44 HOH HOH . H 6 HOH B 25 525 34 HOH HOH . H 6 HOH B 26 526 104 HOH HOH . H 6 HOH B 27 527 137 HOH HOH . H 6 HOH B 28 528 79 HOH HOH . H 6 HOH B 29 529 65 HOH HOH . H 6 HOH B 30 530 153 HOH HOH . H 6 HOH B 31 531 125 HOH HOH . H 6 HOH B 32 532 159 HOH HOH . H 6 HOH B 33 533 197 HOH HOH . H 6 HOH B 34 534 128 HOH HOH . H 6 HOH B 35 535 123 HOH HOH . H 6 HOH B 36 536 29 HOH HOH . H 6 HOH B 37 537 39 HOH HOH . H 6 HOH B 38 538 194 HOH HOH . H 6 HOH B 39 539 164 HOH HOH . H 6 HOH B 40 540 103 HOH HOH . H 6 HOH B 41 541 91 HOH HOH . H 6 HOH B 42 542 3 HOH HOH . H 6 HOH B 43 543 131 HOH HOH . H 6 HOH B 44 544 126 HOH HOH . H 6 HOH B 45 545 187 HOH HOH . H 6 HOH B 46 546 132 HOH HOH . H 6 HOH B 47 547 169 HOH HOH . H 6 HOH B 48 548 118 HOH HOH . H 6 HOH B 49 549 196 HOH HOH . H 6 HOH B 50 550 96 HOH HOH . H 6 HOH B 51 551 129 HOH HOH . H 6 HOH B 52 552 180 HOH HOH . H 6 HOH B 53 553 68 HOH HOH . H 6 HOH B 54 554 150 HOH HOH . H 6 HOH B 55 555 114 HOH HOH . H 6 HOH B 56 556 152 HOH HOH . H 6 HOH B 57 557 88 HOH HOH . H 6 HOH B 58 558 55 HOH HOH . H 6 HOH B 59 559 119 HOH HOH . H 6 HOH B 60 560 163 HOH HOH . H 6 HOH B 61 561 8 HOH HOH . H 6 HOH B 62 562 149 HOH HOH . H 6 HOH B 63 563 185 HOH HOH . H 6 HOH B 64 564 77 HOH HOH . H 6 HOH B 65 565 50 HOH HOH . H 6 HOH B 66 566 81 HOH HOH . H 6 HOH B 67 567 179 HOH HOH . H 6 HOH B 68 568 86 HOH HOH . H 6 HOH B 69 569 186 HOH HOH . H 6 HOH B 70 570 121 HOH HOH . H 6 HOH B 71 571 71 HOH HOH . H 6 HOH B 72 572 99 HOH HOH . H 6 HOH B 73 573 172 HOH HOH . H 6 HOH B 74 574 182 HOH HOH . H 6 HOH B 75 575 192 HOH HOH . H 6 HOH B 76 576 90 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 ACP . . . F 3 -45.472 19.035 59.646 0.8 85.62 ? PG ACP 401 B 1 HETATM 2 O O1G ACP . . . F 3 -46.246 20.316 59.387 0.8 85.68 ? O1G ACP 401 B 1 HETATM 3 O O2G ACP . . . F 3 -44.129 19.293 60.32 0.8 85.62 ? O2G ACP 401 B 1 HETATM 4 O O3G ACP . . . F 3 -45.344 18.165 58.4 0.8 85.65 ? O3G ACP 401 B 1 HETATM 5 P PB ACP . . . F 3 -46.233 16.653 61.94 0.8 85.16 ? PB ACP 401 B 1 HETATM 6 O O1B ACP . . . F 3 -44.809 16.613 62.397 0.8 85.22 ? O1B ACP 401 B 1 HETATM 7 O O2B ACP . . . F 3 -46.797 15.428 61.284 0.8 85.18 ? O2B ACP 401 B 1 HETATM 8 C C3B ACP . . . F 3 -46.468 18.061 60.832 0.8 85.4 ? C3B ACP 401 B 1 HETATM 9 P PA ACP . . . F 3 -48.874 17.007 63.271 0.8 84.53 ? PA ACP 401 B 1 HETATM 10 O O1A ACP . . . F 3 -49.238 15.604 63.558 0.8 84.54 ? O1A ACP 401 B 1 HETATM 11 O O2A ACP . . . F 3 -49.537 17.712 62.148 0.8 84.52 ? O2A ACP 401 B 1 HETATM 12 O O3A ACP . . . F 3 -47.287 17.118 63.094 0.8 84.85 ? O3A ACP 401 B 1 HETATM 13 O O5' ACP . . . F 3 -49.099 17.849 64.606 0.8 84.2 ? O5' ACP 401 B 1 HETATM 14 C C5' ACP . . . F 3 -48.427 17.502 65.835 0.8 83.96 ? C5' ACP 401 B 1 HETATM 15 C C4' ACP . . . F 3 -48.959 18.394 66.927 0.8 83.8 ? C4' ACP 401 B 1 HETATM 16 O O4' ACP . . . F 3 -48.793 19.774 66.53 0.8 83.75 ? O4' ACP 401 B 1 HETATM 17 C C3' ACP . . . F 3 -50.451 18.25 67.213 0.8 83.74 ? C3' ACP 401 B 1 HETATM 18 O O3' ACP . . . F 3 -50.694 17.186 68.133 0.8 83.75 ? O3' ACP 401 B 1 HETATM 19 C C2' ACP . . . F 3 -50.803 19.627 67.783 0.8 83.67 ? C2' ACP 401 B 1 HETATM 20 O O2' ACP . . . F 3 -50.504 19.722 69.173 0.8 83.64 ? O2' ACP 401 B 1 HETATM 21 C C1' ACP . . . F 3 -49.914 20.547 66.933 0.8 83.65 ? C1' ACP 401 B 1 HETATM 22 N N9 ACP . . . F 3 -50.57 21.088 65.743 0.8 83.57 ? N9 ACP 401 B 1 HETATM 23 C C8 ACP . . . F 3 -50.409 20.685 64.442 0.8 83.53 ? C8 ACP 401 B 1 HETATM 24 N N7 ACP . . . F 3 -51.134 21.356 63.581 0.8 83.55 ? N7 ACP 401 B 1 HETATM 25 C C5 ACP . . . F 3 -51.823 22.266 64.369 0.8 83.62 ? C5 ACP 401 B 1 HETATM 26 C C6 ACP . . . F 3 -52.751 23.278 64.06 0.8 83.67 ? C6 ACP 401 B 1 HETATM 27 N N6 ACP . . . F 3 -53.178 23.545 62.821 0.8 83.73 ? N6 ACP 401 B 1 HETATM 28 N N1 ACP . . . F 3 -53.236 24.018 65.081 0.8 83.67 ? N1 ACP 401 B 1 HETATM 29 C C2 ACP . . . F 3 -52.815 23.756 66.322 0.8 83.67 ? C2 ACP 401 B 1 HETATM 30 N N3 ACP . . . F 3 -51.948 22.827 66.734 0.8 83.68 ? N3 ACP 401 B 1 HETATM 31 C C4 ACP . . . F 3 -51.484 22.112 65.704 0.8 83.63 ? C4 ACP 401 B 1 HETATM 32 H H3B1 ACP . . . F 3 -47.299 17.742 60.199 0.8 85.39 ? H3B1 ACP 401 B 1 HETATM 33 H H3B2 ACP . . . F 3 -46.874 18.835 61.489 0.8 85.39 ? H3B2 ACP 401 B 1 HETATM 34 H "H5'1" ACP . . . F 3 -47.341 17.561 65.739 0.8 83.95 ? "H5'1" ACP 401 B 1 HETATM 35 H "H5'2" ACP . . . F 3 -48.657 16.458 66.058 0.8 83.95 ? "H5'2" ACP 401 B 1 HETATM 36 H H4' ACP . . . F 3 -48.36 18.264 67.83 0.8 83.8 ? H4' ACP 401 B 1 HETATM 37 H H3' ACP . . . F 3 -51.067 18.06 66.328 0.8 83.74 ? H3' ACP 401 B 1 HETATM 38 H HO3' ACP . . . F 3 -51.653 17.244 68.299 0.8 83.75 ? HO3' ACP 401 B 1 HETATM 39 H H2' ACP . . . F 3 -51.864 19.844 67.627 0.8 83.67 ? H2' ACP 401 B 1 HETATM 40 H HO2' ACP . . . F 3 -51.138 19.108 69.584 0.8 83.64 ? HO2' ACP 401 B 1 HETATM 41 H H1' ACP . . . F 3 -49.537 21.411 67.489 0.8 83.65 ? H1' ACP 401 B 1 HETATM 42 H H8 ACP . . . F 3 -49.741 19.878 64.176 0.8 83.53 ? H8 ACP 401 B 1 HETATM 43 H HN61 ACP . . . F 3 -52.816 22.988 62.05 0.8 83.72 ? HN61 ACP 401 B 1 HETATM 44 H HN62 ACP . . . F 3 -53.852 24.299 62.705 0.8 83.72 ? HN62 ACP 401 B 1 HETATM 45 H H2 ACP . . . F 3 -53.215 24.39 67.103 0.8 83.67 ? H2 ACP 401 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 45 #