data_6GR1 # _model_server_result.job_id EE5r0fpkwfCnH7YlpDNozg _model_server_result.datetime_utc '2024-11-23 22:56:52' _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 6gr1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 6GR1 # _exptl.entry_id 6GR1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 116.35 _cell.angle_gamma 90 _cell.entry_id 6GR1 _cell.length_a 53.37 _cell.length_b 41.813 _cell.length_c 53.949 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6GR1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A OD1 ASN 71 A ASN 51 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc2 B O1B APC . A APC 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc3 B O1A APC . A APC 301 1_555 C MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc4 C MG MG . A MG 302 1_555 D O HOH . A HOH 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.428 ? metalc ? metalc5 C MG MG . A MG 302 1_555 D O HOH . A HOH 426 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.265 ? metalc ? metalc6 C MG MG . A MG 302 1_555 D O HOH . A HOH 445 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-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 APC doub 13 n n PG O2G APC sing 14 n n PG O3G APC sing 15 n n PG O3B APC sing 16 n n O2G HOG2 APC sing 17 n n O3G HOG3 APC sing 18 n n PB O1B APC doub 19 n n PB O2B APC sing 20 n n PB O3B APC sing 21 n n PB C3A APC sing 22 n n O2B HOB2 APC sing 23 n n PA O1A APC doub 24 n n PA O2A APC sing 25 n n PA C3A APC sing 26 n n PA O5' APC sing 27 n n O2A HOA2 APC sing 28 n n C3A H3A1 APC sing 29 n n C3A H3A2 APC sing 30 n n O5' C5' APC sing 31 n n C5' C4' APC sing 32 n n C5' "H5'1" APC sing 33 n n C5' "H5'2" APC sing 34 n n C4' O4' APC sing 35 n n C4' C3' APC sing 36 n n C4' H4' APC sing 37 n n O4' C1' APC sing 38 n n C3' O3' APC sing 39 n n C3' C2' APC sing 40 n n C3' H3' APC sing 41 n n O3' HO3' APC sing 42 n n C2' O2' APC sing 43 n n C2' C1' APC sing 44 n n C2' H2' APC sing 45 n n O2' HO2' APC sing 46 n n C1' N9 APC sing 47 n n C1' H1' APC sing 48 n n N9 C8 APC sing 49 n y N9 C4 APC sing 50 n y C8 N7 APC doub 51 n y C8 H8 APC sing 52 n n N7 C5 APC sing 53 n y C5 C6 APC sing 54 n y C5 C4 APC doub 55 n y C6 N6 APC sing 56 n n C6 N1 APC doub 57 n y N6 HN61 APC sing 58 n n N6 HN62 APC sing 59 n n N1 C2 APC sing 60 n y C2 N3 APC doub 61 n y C2 H2 APC sing 62 n n N3 C4 APC sing 63 n y # _atom_sites.entry_id 6GR1 _atom_sites.fract_transf_matrix[1][1] 0.018737 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.009281 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023916 _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] 0.020685 _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 B 2 APC A 1 301 1 APC APC . C 3 MG A 1 302 1 MG MG . D 4 HOH A 1 401 68 HOH HOH . D 4 HOH A 2 402 134 HOH HOH . D 4 HOH A 3 403 168 HOH HOH . D 4 HOH A 4 404 14 HOH HOH . D 4 HOH A 5 405 179 HOH HOH . D 4 HOH A 6 406 61 HOH HOH . D 4 HOH A 7 407 197 HOH HOH . D 4 HOH A 8 408 45 HOH HOH . D 4 HOH A 9 409 124 HOH HOH . D 4 HOH A 10 410 5 HOH HOH . D 4 HOH A 11 411 105 HOH HOH . D 4 HOH A 12 412 40 HOH HOH . D 4 HOH A 13 413 37 HOH HOH . D 4 HOH A 14 414 49 HOH HOH . D 4 HOH A 15 415 151 HOH HOH . D 4 HOH A 16 416 44 HOH HOH . D 4 HOH A 17 417 6 HOH HOH . D 4 HOH A 18 418 158 HOH HOH . D 4 HOH A 19 419 92 HOH HOH . D 4 HOH A 20 420 89 HOH HOH . D 4 HOH A 21 421 110 HOH HOH . D 4 HOH A 22 422 113 HOH HOH . D 4 HOH A 23 423 90 HOH HOH . D 4 HOH A 24 424 83 HOH HOH . D 4 HOH A 25 425 137 HOH HOH . D 4 HOH A 26 426 48 HOH HOH . D 4 HOH A 27 427 29 HOH HOH . D 4 HOH A 28 428 163 HOH HOH . D 4 HOH A 29 429 64 HOH HOH . D 4 HOH A 30 430 154 HOH HOH . D 4 HOH A 31 431 11 HOH HOH . D 4 HOH A 32 432 41 HOH HOH . D 4 HOH A 33 433 84 HOH HOH . D 4 HOH A 34 434 59 HOH HOH . D 4 HOH A 35 435 58 HOH HOH . D 4 HOH A 36 436 35 HOH HOH . D 4 HOH A 37 437 75 HOH HOH . D 4 HOH A 38 438 146 HOH HOH . D 4 HOH A 39 439 166 HOH HOH . D 4 HOH A 40 440 62 HOH HOH . D 4 HOH A 41 441 119 HOH HOH . D 4 HOH A 42 442 114 HOH HOH . D 4 HOH A 43 443 36 HOH HOH . D 4 HOH A 44 444 70 HOH HOH . D 4 HOH A 45 445 50 HOH HOH . D 4 HOH A 46 446 109 HOH HOH . D 4 HOH A 47 447 74 HOH HOH . D 4 HOH A 48 448 12 HOH HOH . D 4 HOH A 49 449 100 HOH HOH . D 4 HOH A 50 450 76 HOH HOH . D 4 HOH A 51 451 152 HOH HOH . D 4 HOH A 52 452 25 HOH HOH . D 4 HOH A 53 453 104 HOH HOH . D 4 HOH A 54 454 85 HOH HOH . D 4 HOH A 55 455 72 HOH HOH . D 4 HOH A 56 456 156 HOH HOH . D 4 HOH A 57 457 178 HOH HOH . D 4 HOH A 58 458 115 HOH HOH . D 4 HOH A 59 459 38 HOH HOH . D 4 HOH A 60 460 180 HOH HOH . D 4 HOH A 61 461 19 HOH HOH . D 4 HOH A 62 462 117 HOH HOH . D 4 HOH A 63 463 10 HOH HOH . D 4 HOH A 64 464 175 HOH HOH . D 4 HOH A 65 465 127 HOH HOH . D 4 HOH A 66 466 9 HOH HOH . D 4 HOH A 67 467 112 HOH HOH . D 4 HOH A 68 468 63 HOH HOH . D 4 HOH A 69 469 3 HOH HOH . D 4 HOH A 70 470 73 HOH HOH . D 4 HOH A 71 471 24 HOH HOH . D 4 HOH A 72 472 22 HOH HOH . D 4 HOH A 73 473 111 HOH HOH . D 4 HOH A 74 474 181 HOH HOH . D 4 HOH A 75 475 96 HOH HOH . D 4 HOH A 76 476 66 HOH HOH . D 4 HOH A 77 477 28 HOH HOH . D 4 HOH A 78 478 102 HOH HOH . D 4 HOH A 79 479 155 HOH HOH . D 4 HOH A 80 480 33 HOH HOH . D 4 HOH A 81 481 164 HOH HOH . D 4 HOH A 82 482 198 HOH HOH . D 4 HOH A 83 483 43 HOH HOH . D 4 HOH A 84 484 54 HOH HOH . D 4 HOH A 85 485 47 HOH HOH . D 4 HOH A 86 486 159 HOH HOH . D 4 HOH A 87 487 172 HOH HOH . D 4 HOH A 88 488 30 HOH HOH . D 4 HOH A 89 489 60 HOH HOH . D 4 HOH A 90 490 103 HOH HOH . D 4 HOH A 91 491 34 HOH HOH . D 4 HOH A 92 492 67 HOH HOH . D 4 HOH A 93 493 170 HOH HOH . D 4 HOH A 94 494 7 HOH HOH . D 4 HOH A 95 495 69 HOH HOH . D 4 HOH A 96 496 77 HOH HOH . D 4 HOH A 97 497 147 HOH HOH . D 4 HOH A 98 498 4 HOH HOH . D 4 HOH A 99 499 126 HOH HOH . D 4 HOH A 100 500 189 HOH HOH . D 4 HOH A 101 501 148 HOH HOH . D 4 HOH A 102 502 16 HOH HOH . D 4 HOH A 103 503 98 HOH HOH . D 4 HOH A 104 504 187 HOH HOH . D 4 HOH A 105 505 106 HOH HOH . D 4 HOH A 106 506 57 HOH HOH . D 4 HOH A 107 507 20 HOH HOH . D 4 HOH A 108 508 79 HOH HOH . D 4 HOH A 109 509 42 HOH HOH . D 4 HOH A 110 510 26 HOH HOH . D 4 HOH A 111 511 81 HOH HOH . D 4 HOH A 112 512 93 HOH HOH . D 4 HOH A 113 513 1 HOH HOH . D 4 HOH A 114 514 32 HOH HOH . D 4 HOH A 115 515 116 HOH HOH . D 4 HOH A 116 516 186 HOH HOH . D 4 HOH A 117 517 23 HOH HOH . D 4 HOH A 118 518 139 HOH HOH . D 4 HOH A 119 519 53 HOH HOH . D 4 HOH A 120 520 95 HOH HOH . D 4 HOH A 121 521 88 HOH HOH . D 4 HOH A 122 522 144 HOH HOH . D 4 HOH A 123 523 108 HOH HOH . D 4 HOH A 124 524 21 HOH HOH . D 4 HOH A 125 525 140 HOH HOH . D 4 HOH A 126 526 56 HOH HOH . D 4 HOH A 127 527 82 HOH HOH . D 4 HOH A 128 528 80 HOH HOH . D 4 HOH A 129 529 150 HOH HOH . D 4 HOH A 130 530 46 HOH HOH . D 4 HOH A 131 531 13 HOH HOH . D 4 HOH A 132 532 149 HOH HOH . D 4 HOH A 133 533 173 HOH HOH . D 4 HOH A 134 534 78 HOH HOH . D 4 HOH A 135 535 87 HOH HOH . D 4 HOH A 136 536 184 HOH HOH . D 4 HOH A 137 537 129 HOH HOH . D 4 HOH A 138 538 194 HOH HOH . D 4 HOH A 139 539 2 HOH HOH . D 4 HOH A 140 540 196 HOH HOH . D 4 HOH A 141 541 101 HOH HOH . D 4 HOH A 142 542 86 HOH HOH . D 4 HOH A 143 543 145 HOH HOH . D 4 HOH A 144 544 94 HOH HOH . D 4 HOH A 145 545 31 HOH HOH . D 4 HOH A 146 546 157 HOH HOH . D 4 HOH A 147 547 51 HOH HOH . D 4 HOH A 148 548 18 HOH HOH . D 4 HOH A 149 549 165 HOH HOH . D 4 HOH A 150 550 131 HOH HOH . D 4 HOH A 151 551 123 HOH HOH . D 4 HOH A 152 552 121 HOH HOH . D 4 HOH A 153 553 160 HOH HOH . D 4 HOH A 154 554 27 HOH HOH . D 4 HOH A 155 555 99 HOH HOH . D 4 HOH A 156 556 128 HOH HOH . D 4 HOH A 157 557 191 HOH HOH . D 4 HOH A 158 558 153 HOH HOH . D 4 HOH A 159 559 52 HOH HOH . D 4 HOH A 160 560 176 HOH HOH . D 4 HOH A 161 561 185 HOH HOH . D 4 HOH A 162 562 190 HOH HOH . D 4 HOH A 163 563 162 HOH HOH . D 4 HOH A 164 564 195 HOH HOH . D 4 HOH A 165 565 188 HOH HOH . D 4 HOH A 166 566 143 HOH HOH . D 4 HOH A 167 567 91 HOH HOH . D 4 HOH A 168 568 107 HOH HOH . D 4 HOH A 169 569 136 HOH HOH . D 4 HOH A 170 570 122 HOH HOH . D 4 HOH A 171 571 193 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 APC . . . B 2 -22.748 3.848 1.295 1 33.63 ? PG APC 301 A 1 HETATM 2 O O1G APC . . . B 2 -23.201 3.039 0.102 1 33.54 ? O1G APC 301 A 1 HETATM 3 O O2G APC . . . B 2 -23.497 5.147 1.503 1 36.57 ? O2G APC 301 A 1 HETATM 4 O O3G APC . . . B 2 -21.248 3.999 1.404 1 30.84 ? O3G APC 301 A 1 HETATM 5 P PB APC . . . B 2 -22.992 2.762 4.012 1 21.53 ? PB APC 301 A 1 HETATM 6 O O1B APC . . . B 2 -21.799 3.621 4.311 1 22.22 ? O1B APC 301 A 1 HETATM 7 O O2B APC . . . B 2 -24.219 3.011 4.834 1 19.68 ? O2B APC 301 A 1 HETATM 8 O O3B APC . . . B 2 -23.355 2.972 2.481 1 30.35 ? O3B APC 301 A 1 HETATM 9 P PA APC . . . B 2 -21.265 0.625 5.292 1 18.9 ? PA APC 301 A 1 HETATM 10 O O1A APC . . . B 2 -20.059 1.47 5.032 1 18.6 ? O1A APC 301 A 1 HETATM 11 O O2A APC . . . B 2 -21.076 -0.867 5.35 1 19.16 ? O2A APC 301 A 1 HETATM 12 C C3A APC . . . B 2 -22.549 1.001 4.044 1 20.37 ? C3A APC 301 A 1 HETATM 13 O O5' APC . . . B 2 -21.932 1.05 6.68 1 17.44 ? O5' APC 301 A 1 HETATM 14 C C5' APC . . . B 2 -23.138 0.457 7.15 1 16.19 ? C5' APC 301 A 1 HETATM 15 C C4' APC . . . B 2 -23.815 1.346 8.165 1 16.32 ? C4' APC 301 A 1 HETATM 16 O O4' APC . . . B 2 -23.064 1.314 9.404 1 14.57 ? O4' APC 301 A 1 HETATM 17 C C3' APC . . . B 2 -23.911 2.843 7.846 1 16.57 ? C3' APC 301 A 1 HETATM 18 O O3' APC . . . B 2 -25.034 3.1 7.017 1 17.32 ? O3' APC 301 A 1 HETATM 19 C C2' APC . . . B 2 -24.114 3.427 9.246 1 15.91 ? C2' APC 301 A 1 HETATM 20 O O2' APC . . . B 2 -25.461 3.287 9.634 1 16.68 ? O2' APC 301 A 1 HETATM 21 C C1' APC . . . B 2 -23.3 2.487 10.139 1 15.19 ? C1' APC 301 A 1 HETATM 22 N N9 APC . . . B 2 -22.005 3.021 10.535 1 14.96 ? N9 APC 301 A 1 HETATM 23 C C8 APC . . . B 2 -20.78 2.525 10.173 1 14.36 ? C8 APC 301 A 1 HETATM 24 N N7 APC . . . B 2 -19.788 3.242 10.646 1 16.12 ? N7 APC 301 A 1 HETATM 25 C C5 APC . . . B 2 -20.398 4.253 11.39 1 14.92 ? C5 APC 301 A 1 HETATM 26 C C6 APC . . . B 2 -19.89 5.328 12.148 1 13.49 ? C6 APC 301 A 1 HETATM 27 N N6 APC . . . B 2 -18.594 5.601 12.284 1 13.86 ? N6 APC 301 A 1 HETATM 28 N N1 APC . . . B 2 -20.773 6.144 12.751 1 13.7 ? N1 APC 301 A 1 HETATM 29 C C2 APC . . . B 2 -22.079 5.873 12.644 1 15.67 ? C2 APC 301 A 1 HETATM 30 N N3 APC . . . B 2 -22.672 4.926 11.92 1 15.61 ? N3 APC 301 A 1 HETATM 31 C C4 APC . . . B 2 -21.769 4.123 11.328 1 14.99 ? C4 APC 301 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 920 _model_server_stats.encode_time_ms 18 _model_server_stats.element_count 31 #