data_6RU6 # _model_server_result.job_id XJz59opA8NCuXBVuT3W4ug _model_server_result.datetime_utc '2025-07-15 12:31:32' _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 6ru6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":301}' # _entry.id 6RU6 # _exptl.entry_id 6RU6 _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 109.72 _cell.angle_gamma 90 _cell.entry_id 6RU6 _cell.length_a 171.937 _cell.length_b 48.924 _cell.length_c 85.199 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RU6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 monomeric 1 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,J,K,L,P,R 1 1 B,M,N,O,Q 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 D N N ? 3 M 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 C C PRO 3 C PRO 581 1_555 C N SEP 4 C SEP 582 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale2 C C SEP 4 C SEP 582 1_555 C N SER 5 C SER 583 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.35 ? metalc ? metalc1 A OD1 ASN 145 A ASN 143 1_555 E NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc2 A O TYR 288 A TYR 286 1_555 E NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc3 A OD1 ASN 293 A ASN 291 1_555 E NA NA . A NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc4 E NA NA . A NA 302 1_555 P O HOH . A HOH 415 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.649 ? metalc ? metalc5 E NA NA . A NA 302 1_555 P O HOH . A HOH 475 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? # _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 6RU6 _atom_sites.fract_transf_matrix[1][1] 0.005816 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002085 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02044 _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] 0.012468 _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 D 3 ACP A 1 301 1 ACP ACP . E 4 NA A 1 302 5 NA NA . F 5 EDO A 1 303 11 EDO EDO . G 5 EDO A 1 304 12 EDO EDO . H 5 EDO A 1 305 13 EDO EDO . I 5 EDO A 1 306 14 EDO EDO . J 5 EDO A 1 307 15 EDO EDO . K 5 EDO A 1 308 16 EDO EDO . L 5 EDO A 1 309 17 EDO EDO . M 3 ACP B 1 301 2 ACP ACP . N 6 SO4 B 1 302 8 SO4 SO4 . O 5 EDO B 1 303 19 EDO EDO . P 7 HOH A 1 401 124 HOH HOH . P 7 HOH A 2 402 134 HOH HOH . P 7 HOH A 3 403 105 HOH HOH . P 7 HOH A 4 404 128 HOH HOH . P 7 HOH A 5 405 45 HOH HOH . P 7 HOH A 6 406 135 HOH HOH . P 7 HOH A 7 407 123 HOH HOH . P 7 HOH A 8 408 131 HOH HOH . P 7 HOH A 9 409 37 HOH HOH . P 7 HOH A 10 410 116 HOH HOH . P 7 HOH A 11 411 141 HOH HOH . P 7 HOH A 12 412 132 HOH HOH . P 7 HOH A 13 413 69 HOH HOH . P 7 HOH A 14 414 75 HOH HOH . P 7 HOH A 15 415 72 HOH HOH . P 7 HOH A 16 416 50 HOH HOH . P 7 HOH A 17 417 7 HOH HOH . P 7 HOH A 18 418 25 HOH HOH . P 7 HOH A 19 419 66 HOH HOH . P 7 HOH A 20 420 121 HOH HOH . P 7 HOH A 21 421 144 HOH HOH . P 7 HOH A 22 422 60 HOH HOH . P 7 HOH A 23 423 106 HOH HOH . P 7 HOH A 24 424 126 HOH HOH . P 7 HOH A 25 425 12 HOH HOH . P 7 HOH A 26 426 108 HOH HOH . P 7 HOH A 27 427 11 HOH HOH . P 7 HOH A 28 428 160 HOH HOH . P 7 HOH A 29 429 125 HOH HOH . P 7 HOH A 30 430 19 HOH HOH . P 7 HOH A 31 431 51 HOH HOH . P 7 HOH A 32 432 40 HOH HOH . P 7 HOH A 33 433 52 HOH HOH . P 7 HOH A 34 434 91 HOH HOH . P 7 HOH A 35 435 39 HOH HOH . P 7 HOH A 36 436 87 HOH HOH . P 7 HOH A 37 437 78 HOH HOH . P 7 HOH A 38 438 57 HOH HOH . P 7 HOH A 39 439 28 HOH HOH . P 7 HOH A 40 440 35 HOH HOH . P 7 HOH A 41 441 64 HOH HOH . P 7 HOH A 42 442 120 HOH HOH . P 7 HOH A 43 443 74 HOH HOH . P 7 HOH A 44 444 24 HOH HOH . P 7 HOH A 45 445 67 HOH HOH . P 7 HOH A 46 446 86 HOH HOH . P 7 HOH A 47 447 109 HOH HOH . P 7 HOH A 48 448 14 HOH HOH . P 7 HOH A 49 449 133 HOH HOH . P 7 HOH A 50 450 54 HOH HOH . P 7 HOH A 51 451 76 HOH HOH . P 7 HOH A 52 452 4 HOH HOH . P 7 HOH A 53 453 98 HOH HOH . P 7 HOH A 54 454 23 HOH HOH . P 7 HOH A 55 455 6 HOH HOH . P 7 HOH A 56 456 158 HOH HOH . P 7 HOH A 57 457 32 HOH HOH . P 7 HOH A 58 458 143 HOH HOH . P 7 HOH A 59 459 3 HOH HOH . P 7 HOH A 60 460 122 HOH HOH . P 7 HOH A 61 461 1 HOH HOH . P 7 HOH A 62 462 15 HOH HOH . P 7 HOH A 63 463 88 HOH HOH . P 7 HOH A 64 464 142 HOH HOH . P 7 HOH A 65 465 114 HOH HOH . P 7 HOH A 66 466 33 HOH HOH . P 7 HOH A 67 467 56 HOH HOH . P 7 HOH A 68 468 61 HOH HOH . P 7 HOH A 69 469 117 HOH HOH . P 7 HOH A 70 470 139 HOH HOH . P 7 HOH A 71 471 44 HOH HOH . P 7 HOH A 72 472 55 HOH HOH . P 7 HOH A 73 473 127 HOH HOH . P 7 HOH A 74 474 140 HOH HOH . P 7 HOH A 75 475 119 HOH HOH . P 7 HOH A 76 476 145 HOH HOH . Q 7 HOH B 1 401 149 HOH HOH . Q 7 HOH B 2 402 153 HOH HOH . Q 7 HOH B 3 403 136 HOH HOH . Q 7 HOH B 4 404 34 HOH HOH . Q 7 HOH B 5 405 152 HOH HOH . Q 7 HOH B 6 406 30 HOH HOH . Q 7 HOH B 7 407 159 HOH HOH . Q 7 HOH B 8 408 20 HOH HOH . Q 7 HOH B 9 409 95 HOH HOH . Q 7 HOH B 10 410 59 HOH HOH . Q 7 HOH B 11 411 68 HOH HOH . Q 7 HOH B 12 412 161 HOH HOH . Q 7 HOH B 13 413 83 HOH HOH . Q 7 HOH B 14 414 102 HOH HOH . Q 7 HOH B 15 415 41 HOH HOH . Q 7 HOH B 16 416 138 HOH HOH . Q 7 HOH B 17 417 81 HOH HOH . Q 7 HOH B 18 418 29 HOH HOH . Q 7 HOH B 19 419 147 HOH HOH . Q 7 HOH B 20 420 26 HOH HOH . Q 7 HOH B 21 421 62 HOH HOH . Q 7 HOH B 22 422 93 HOH HOH . Q 7 HOH B 23 423 48 HOH HOH . Q 7 HOH B 24 424 97 HOH HOH . Q 7 HOH B 25 425 22 HOH HOH . Q 7 HOH B 26 426 155 HOH HOH . Q 7 HOH B 27 427 70 HOH HOH . Q 7 HOH B 28 428 49 HOH HOH . Q 7 HOH B 29 429 43 HOH HOH . Q 7 HOH B 30 430 58 HOH HOH . Q 7 HOH B 31 431 84 HOH HOH . Q 7 HOH B 32 432 2 HOH HOH . Q 7 HOH B 33 433 80 HOH HOH . Q 7 HOH B 34 434 103 HOH HOH . Q 7 HOH B 35 435 77 HOH HOH . Q 7 HOH B 36 436 148 HOH HOH . Q 7 HOH B 37 437 151 HOH HOH . Q 7 HOH B 38 438 113 HOH HOH . Q 7 HOH B 39 439 157 HOH HOH . Q 7 HOH B 40 440 85 HOH HOH . Q 7 HOH B 41 441 96 HOH HOH . Q 7 HOH B 42 442 110 HOH HOH . Q 7 HOH B 43 443 27 HOH HOH . Q 7 HOH B 44 444 47 HOH HOH . Q 7 HOH B 45 445 38 HOH HOH . Q 7 HOH B 46 446 42 HOH HOH . Q 7 HOH B 47 447 71 HOH HOH . Q 7 HOH B 48 448 46 HOH HOH . Q 7 HOH B 49 449 73 HOH HOH . Q 7 HOH B 50 450 82 HOH HOH . Q 7 HOH B 51 451 94 HOH HOH . Q 7 HOH B 52 452 36 HOH HOH . Q 7 HOH B 53 453 100 HOH HOH . Q 7 HOH B 54 454 154 HOH HOH . Q 7 HOH B 55 455 18 HOH HOH . Q 7 HOH B 56 456 146 HOH HOH . Q 7 HOH B 57 457 63 HOH HOH . Q 7 HOH B 58 458 150 HOH HOH . Q 7 HOH B 59 459 156 HOH HOH . Q 7 HOH B 60 460 53 HOH HOH . Q 7 HOH B 61 461 9 HOH HOH . Q 7 HOH B 62 462 112 HOH HOH . R 7 HOH C 1 601 130 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 . . . M 3 19.278 -3.574 25.906 1 133.43 ? PG ACP 301 B 1 HETATM 2 O O1G ACP . . . M 3 20.729 -3.355 26.114 1 131.65 ? O1G ACP 301 B 1 HETATM 3 O O2G ACP . . . M 3 18.86 -3.144 24.407 1 127.48 ? O2G ACP 301 B 1 HETATM 4 O O3G ACP . . . M 3 18.458 -2.646 26.938 1 123.53 ? O3G ACP 301 B 1 HETATM 5 P PB ACP . . . M 3 19.841 -6.552 25.228 1 139.4 ? PB ACP 301 B 1 HETATM 6 O O1B ACP . . . M 3 18.968 -7.139 24.178 1 132.26 ? O1B ACP 301 B 1 HETATM 7 O O2B ACP . . . M 3 20.309 -7.735 26.219 1 141.28 ? O2B ACP 301 B 1 HETATM 8 C C3B ACP . . . M 3 18.875 -5.333 26.215 1 133.96 ? C3B ACP 301 B 1 HETATM 9 P PA ACP . . . M 3 22.334 -6.827 23.835 1 122.86 ? PA ACP 301 B 1 HETATM 10 O O1A ACP . . . M 3 21.884 -7.24 22.443 1 107.53 ? O1A ACP 301 B 1 HETATM 11 O O2A ACP . . . M 3 22.749 -7.884 24.832 1 126.47 ? O2A ACP 301 B 1 HETATM 12 O O3A ACP . . . M 3 21.161 -5.908 24.52 1 138.4 ? O3A ACP 301 B 1 HETATM 13 O O5' ACP . . . M 3 23.583 -5.79 23.684 1 108.9 ? O5' ACP 301 B 1 HETATM 14 C C5' ACP . . . M 3 24.369 -5.375 24.817 1 88.39 ? C5' ACP 301 B 1 HETATM 15 C C4' ACP . . . M 3 25.226 -4.129 24.492 1 80.43 ? C4' ACP 301 B 1 HETATM 16 O O4' ACP . . . M 3 26.083 -4.354 23.357 1 68.79 ? O4' ACP 301 B 1 HETATM 17 C C3' ACP . . . M 3 24.405 -2.877 24.172 1 74.14 ? C3' ACP 301 B 1 HETATM 18 O O3' ACP . . . M 3 24.618 -1.906 25.193 1 84.4 ? O3' ACP 301 B 1 HETATM 19 C C2' ACP . . . M 3 24.903 -2.348 22.835 1 67.48 ? C2' ACP 301 B 1 HETATM 20 O O2' ACP . . . M 3 25.24 -0.942 22.9 1 61.33 ? O2' ACP 301 B 1 HETATM 21 C C1' ACP . . . M 3 26.133 -3.195 22.515 1 59.6 ? C1' ACP 301 B 1 HETATM 22 N N9 ACP . . . M 3 26.17 -3.626 21.104 1 51.6 ? N9 ACP 301 B 1 HETATM 23 C C8 ACP . . . M 3 25.303 -4.457 20.52 1 46.35 ? C8 ACP 301 B 1 HETATM 24 N N7 ACP . . . M 3 25.626 -4.635 19.206 1 47 ? N7 ACP 301 B 1 HETATM 25 C C5 ACP . . . M 3 26.741 -3.942 18.954 1 46.22 ? C5 ACP 301 B 1 HETATM 26 C C6 ACP . . . M 3 27.606 -3.729 17.769 1 43.83 ? C6 ACP 301 B 1 HETATM 27 N N6 ACP . . . M 3 27.332 -4.331 16.585 1 38.43 ? N6 ACP 301 B 1 HETATM 28 N N1 ACP . . . M 3 28.671 -2.9 17.909 1 45.94 ? N1 ACP 301 B 1 HETATM 29 C C2 ACP . . . M 3 28.963 -2.315 19.109 1 46.38 ? C2 ACP 301 B 1 HETATM 30 N N3 ACP . . . M 3 28.188 -2.487 20.222 1 45.04 ? N3 ACP 301 B 1 HETATM 31 C C4 ACP . . . M 3 27.095 -3.273 20.197 1 47.88 ? C4 ACP 301 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 283 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #