data_6E0L # _model_server_result.job_id 5mSXJctEPbrq0Yw1KK5yvw _model_server_result.datetime_utc '2024-10-18 16:22:47' _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 6e0l # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 6E0L # _exptl.entry_id 6E0L _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 '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 90 _cell.angle_gamma 90 _cell.entry_id 6E0L _cell.length_a 51.647 _cell.length_b 65.652 _cell.length_c 88.855 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6E0L _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,E _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 3 _struct_asym.id C _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 OD2 ASP 62 A ASP 62 1_555 B MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? metalc ? metalc2 B MG MG . A MG 301 1_555 C O3G APC . A APC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc3 B MG MG . A MG 301 1_555 C O1B APC . A APC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.889 ? metalc ? metalc4 B MG MG . A MG 301 1_555 C O1A APC . A APC 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 B MG MG . A MG 301 1_555 E O HOH . A HOH 453 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc6 B MG MG . A MG 301 1_555 E O HOH . A HOH 462 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? # _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 59 n n PG O2G APC sing 60 n n PG O3G APC sing 61 n n PG O3B APC sing 62 n n O2G HOG2 APC sing 63 n n O3G HOG3 APC sing 64 n n PB O1B APC doub 65 n n PB O2B APC sing 66 n n PB O3B APC sing 67 n n PB C3A APC sing 68 n n O2B HOB2 APC sing 69 n n PA O1A APC doub 70 n n PA O2A APC sing 71 n n PA C3A APC sing 72 n n PA O5' APC sing 73 n n O2A HOA2 APC sing 74 n n C3A H3A1 APC sing 75 n n C3A H3A2 APC sing 76 n n O5' C5' APC sing 77 n n C5' C4' APC sing 78 n n C5' "H5'1" APC sing 79 n n C5' "H5'2" APC sing 80 n n C4' O4' APC sing 81 n n C4' C3' APC sing 82 n n C4' H4' APC sing 83 n n O4' C1' APC sing 84 n n C3' O3' APC sing 85 n n C3' C2' APC sing 86 n n C3' H3' APC sing 87 n n O3' HO3' APC sing 88 n n C2' O2' APC sing 89 n n C2' C1' APC sing 90 n n C2' H2' APC sing 91 n n O2' HO2' APC sing 92 n n C1' N9 APC sing 93 n n C1' H1' APC sing 94 n n N9 C8 APC sing 95 n y N9 C4 APC sing 96 n y C8 N7 APC doub 97 n y C8 H8 APC sing 98 n n N7 C5 APC sing 99 n y C5 C6 APC sing 100 n y C5 C4 APC doub 101 n y C6 N6 APC sing 102 n n C6 N1 APC doub 103 n y N6 HN61 APC sing 104 n n N6 HN62 APC sing 105 n n N1 C2 APC sing 106 n y C2 N3 APC doub 107 n y C2 H2 APC sing 108 n n N3 C4 APC sing 109 n y # _atom_sites.entry_id 6E0L _atom_sites.fract_transf_matrix[1][1] 0.019362 _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] 0.015232 _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] 0.011254 _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 MG A 1 301 1 MG MG . C 3 APC A 1 302 1 APC APC . D 4 2KH A 1 303 1 2KH 2KH . E 5 HOH A 1 401 18 HOH HOH . E 5 HOH A 2 402 75 HOH HOH . E 5 HOH A 3 403 114 HOH HOH . E 5 HOH A 4 404 69 HOH HOH . E 5 HOH A 5 405 158 HOH HOH . E 5 HOH A 6 406 61 HOH HOH . E 5 HOH A 7 407 73 HOH HOH . E 5 HOH A 8 408 71 HOH HOH . E 5 HOH A 9 409 63 HOH HOH . E 5 HOH A 10 410 56 HOH HOH . E 5 HOH A 11 411 54 HOH HOH . E 5 HOH A 12 412 24 HOH HOH . E 5 HOH A 13 413 60 HOH HOH . E 5 HOH A 14 414 25 HOH HOH . E 5 HOH A 15 415 173 HOH HOH . E 5 HOH A 16 416 139 HOH HOH . E 5 HOH A 17 417 79 HOH HOH . E 5 HOH A 18 418 161 HOH HOH . E 5 HOH A 19 419 52 HOH HOH . E 5 HOH A 20 420 26 HOH HOH . E 5 HOH A 21 421 96 HOH HOH . E 5 HOH A 22 422 43 HOH HOH . E 5 HOH A 23 423 80 HOH HOH . E 5 HOH A 24 424 20 HOH HOH . E 5 HOH A 25 425 33 HOH HOH . E 5 HOH A 26 426 36 HOH HOH . E 5 HOH A 27 427 13 HOH HOH . E 5 HOH A 28 428 40 HOH HOH . E 5 HOH A 29 429 47 HOH HOH . E 5 HOH A 30 430 77 HOH HOH . E 5 HOH A 31 431 170 HOH HOH . E 5 HOH A 32 432 141 HOH HOH . E 5 HOH A 33 433 8 HOH HOH . E 5 HOH A 34 434 70 HOH HOH . E 5 HOH A 35 435 48 HOH HOH . E 5 HOH A 36 436 28 HOH HOH . E 5 HOH A 37 437 16 HOH HOH . E 5 HOH A 38 438 66 HOH HOH . E 5 HOH A 39 439 142 HOH HOH . E 5 HOH A 40 440 121 HOH HOH . E 5 HOH A 41 441 136 HOH HOH . E 5 HOH A 42 442 162 HOH HOH . E 5 HOH A 43 443 6 HOH HOH . E 5 HOH A 44 444 50 HOH HOH . E 5 HOH A 45 445 58 HOH HOH . E 5 HOH A 46 446 21 HOH HOH . E 5 HOH A 47 447 116 HOH HOH . E 5 HOH A 48 448 2 HOH HOH . E 5 HOH A 49 449 102 HOH HOH . E 5 HOH A 50 450 35 HOH HOH . E 5 HOH A 51 451 97 HOH HOH . E 5 HOH A 52 452 12 HOH HOH . E 5 HOH A 53 453 49 HOH HOH . E 5 HOH A 54 454 34 HOH HOH . E 5 HOH A 55 455 124 HOH HOH . E 5 HOH A 56 456 81 HOH HOH . E 5 HOH A 57 457 32 HOH HOH . E 5 HOH A 58 458 84 HOH HOH . E 5 HOH A 59 459 10 HOH HOH . E 5 HOH A 60 460 38 HOH HOH . E 5 HOH A 61 461 14 HOH HOH . E 5 HOH A 62 462 57 HOH HOH . E 5 HOH A 63 463 128 HOH HOH . E 5 HOH A 64 464 94 HOH HOH . E 5 HOH A 65 465 151 HOH HOH . E 5 HOH A 66 466 78 HOH HOH . E 5 HOH A 67 467 65 HOH HOH . E 5 HOH A 68 468 68 HOH HOH . E 5 HOH A 69 469 23 HOH HOH . E 5 HOH A 70 470 109 HOH HOH . E 5 HOH A 71 471 67 HOH HOH . E 5 HOH A 72 472 55 HOH HOH . E 5 HOH A 73 473 7 HOH HOH . E 5 HOH A 74 474 174 HOH HOH . E 5 HOH A 75 475 27 HOH HOH . E 5 HOH A 76 476 29 HOH HOH . E 5 HOH A 77 477 45 HOH HOH . E 5 HOH A 78 478 5 HOH HOH . E 5 HOH A 79 479 76 HOH HOH . E 5 HOH A 80 480 53 HOH HOH . E 5 HOH A 81 481 11 HOH HOH . E 5 HOH A 82 482 99 HOH HOH . E 5 HOH A 83 483 19 HOH HOH . E 5 HOH A 84 484 17 HOH HOH . E 5 HOH A 85 485 46 HOH HOH . E 5 HOH A 86 486 37 HOH HOH . E 5 HOH A 87 487 85 HOH HOH . E 5 HOH A 88 488 39 HOH HOH . E 5 HOH A 89 489 168 HOH HOH . E 5 HOH A 90 490 15 HOH HOH . E 5 HOH A 91 491 41 HOH HOH . E 5 HOH A 92 492 1 HOH HOH . E 5 HOH A 93 493 4 HOH HOH . E 5 HOH A 94 494 165 HOH HOH . E 5 HOH A 95 495 44 HOH HOH . E 5 HOH A 96 496 176 HOH HOH . E 5 HOH A 97 497 103 HOH HOH . E 5 HOH A 98 498 105 HOH HOH . E 5 HOH A 99 499 123 HOH HOH . E 5 HOH A 100 500 86 HOH HOH . E 5 HOH A 101 501 138 HOH HOH . E 5 HOH A 102 502 92 HOH HOH . E 5 HOH A 103 503 95 HOH HOH . E 5 HOH A 104 504 82 HOH HOH . E 5 HOH A 105 505 42 HOH HOH . E 5 HOH A 106 506 51 HOH HOH . E 5 HOH A 107 507 129 HOH HOH . E 5 HOH A 108 508 137 HOH HOH . E 5 HOH A 109 509 108 HOH HOH . E 5 HOH A 110 510 149 HOH HOH . E 5 HOH A 111 511 119 HOH HOH . E 5 HOH A 112 512 3 HOH HOH . E 5 HOH A 113 513 122 HOH HOH . E 5 HOH A 114 514 30 HOH HOH . E 5 HOH A 115 515 22 HOH HOH . E 5 HOH A 116 516 120 HOH HOH . E 5 HOH A 117 517 111 HOH HOH . E 5 HOH A 118 518 83 HOH HOH . E 5 HOH A 119 519 9 HOH HOH . E 5 HOH A 120 520 110 HOH HOH . E 5 HOH A 121 521 134 HOH HOH . E 5 HOH A 122 522 175 HOH HOH . E 5 HOH A 123 523 131 HOH HOH . E 5 HOH A 124 524 157 HOH HOH . E 5 HOH A 125 525 115 HOH HOH . E 5 HOH A 126 526 90 HOH HOH . E 5 HOH A 127 527 59 HOH HOH . E 5 HOH A 128 528 118 HOH HOH . E 5 HOH A 129 529 135 HOH HOH . E 5 HOH A 130 530 93 HOH HOH . E 5 HOH A 131 531 148 HOH HOH . E 5 HOH A 132 532 166 HOH HOH . E 5 HOH A 133 533 100 HOH HOH . E 5 HOH A 134 534 163 HOH HOH . E 5 HOH A 135 535 64 HOH HOH . E 5 HOH A 136 536 153 HOH HOH . E 5 HOH A 137 537 117 HOH HOH . E 5 HOH A 138 538 62 HOH HOH . E 5 HOH A 139 539 125 HOH HOH . E 5 HOH A 140 540 144 HOH HOH . E 5 HOH A 141 541 155 HOH HOH . E 5 HOH A 142 542 88 HOH HOH . E 5 HOH A 143 543 98 HOH HOH . E 5 HOH A 144 544 113 HOH HOH . E 5 HOH A 145 545 91 HOH HOH . E 5 HOH A 146 546 101 HOH HOH . E 5 HOH A 147 547 154 HOH HOH . E 5 HOH A 148 548 143 HOH HOH . E 5 HOH A 149 549 146 HOH HOH . E 5 HOH A 150 550 172 HOH HOH . E 5 HOH A 151 551 140 HOH HOH . E 5 HOH A 152 552 31 HOH HOH . E 5 HOH A 153 553 164 HOH HOH . E 5 HOH A 154 554 72 HOH HOH . E 5 HOH A 155 555 132 HOH HOH . E 5 HOH A 156 556 87 HOH HOH . E 5 HOH A 157 557 126 HOH HOH . E 5 HOH A 158 558 89 HOH HOH . E 5 HOH A 159 559 156 HOH HOH . E 5 HOH A 160 560 127 HOH HOH . E 5 HOH A 161 561 112 HOH HOH . E 5 HOH A 162 562 130 HOH HOH . E 5 HOH A 163 563 159 HOH HOH . E 5 HOH A 164 564 150 HOH HOH . E 5 HOH A 165 565 133 HOH HOH . E 5 HOH A 166 566 145 HOH HOH . E 5 HOH A 167 567 169 HOH HOH . E 5 HOH A 168 568 104 HOH HOH . E 5 HOH A 169 569 106 HOH HOH . E 5 HOH A 170 570 74 HOH HOH . E 5 HOH A 171 571 167 HOH HOH . E 5 HOH A 172 572 107 HOH HOH . E 5 HOH A 173 573 160 HOH HOH . E 5 HOH A 174 574 177 HOH HOH . E 5 HOH A 175 575 171 HOH HOH . E 5 HOH A 176 576 147 HOH HOH . E 5 HOH A 177 577 152 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 . . . C 3 19.704 34.353 52.016 1 22.81 ? PG APC 302 A 1 HETATM 2 O O1G APC . . . C 3 20.126 33.499 50.857 1 23.88 -1 O1G APC 302 A 1 HETATM 3 O O2G APC . . . C 3 18.435 35.126 51.717 1 22.92 ? O2G APC 302 A 1 HETATM 4 O O3G APC . . . C 3 20.811 35.288 52.416 1 23.63 -1 O3G APC 302 A 1 HETATM 5 P PB APC . . . C 3 20.372 32.934 54.482 1 23.61 ? PB APC 302 A 1 HETATM 6 O O1B APC . . . C 3 21.761 33.443 54.161 1 24.34 -1 O1B APC 302 A 1 HETATM 7 O O2B APC . . . C 3 20.386 31.427 54.542 1 24.48 ? O2B APC 302 A 1 HETATM 8 O O3B APC . . . C 3 19.381 33.328 53.246 1 23.61 ? O3B APC 302 A 1 HETATM 9 P PA APC . . . C 3 20.464 35.275 56.466 1 26.92 ? PA APC 302 A 1 HETATM 10 O O1A APC . . . C 3 21.338 35.787 55.346 1 26.08 ? O1A APC 302 A 1 HETATM 11 O O2A APC . . . C 3 19.45 36.322 56.883 1 29.08 -1 O2A APC 302 A 1 HETATM 12 C C3A APC . . . C 3 19.662 33.667 56.019 1 26.79 ? C3A APC 302 A 1 HETATM 13 O O5' APC . . . C 3 21.426 34.964 57.769 1 31.01 ? O5' APC 302 A 1 HETATM 14 C C5' APC . . . C 3 22.525 34.138 57.512 1 31.09 ? C5' APC 302 A 1 HETATM 15 C C4' APC . . . C 3 22.834 33.265 58.752 1 29.73 ? C4' APC 302 A 1 HETATM 16 O O4' APC . . . C 3 22.818 34.004 59.839 1 29.63 ? O4' APC 302 A 1 HETATM 17 C C3' APC . . . C 3 21.741 32.19 58.968 1 30.27 ? C3' APC 302 A 1 HETATM 18 O O3' APC . . . C 3 21.919 31.064 58.192 1 31.03 ? O3' APC 302 A 1 HETATM 19 C C2' APC . . . C 3 21.978 31.89 60.47 1 29.84 ? C2' APC 302 A 1 HETATM 20 O O2' APC . . . C 3 23.169 30.967 60.558 1 29.31 ? O2' APC 302 A 1 HETATM 21 C C1' APC . . . C 3 22.206 33.073 61.01 1 28.94 ? C1' APC 302 A 1 HETATM 22 N N9 APC . . . C 3 20.952 33.685 61.334 1 28.08 ? N9 APC 302 A 1 HETATM 23 C C8 APC . . . C 3 20.232 34.608 60.683 1 27.54 ? C8 APC 302 A 1 HETATM 24 N N7 APC . . . C 3 19.119 34.84 61.373 1 27.63 ? N7 APC 302 A 1 HETATM 25 C C5 APC . . . C 3 19.156 34.066 62.473 1 28.8 ? C5 APC 302 A 1 HETATM 26 C C6 APC . . . C 3 18.263 33.93 63.504 1 26.89 ? C6 APC 302 A 1 HETATM 27 N N6 APC . . . C 3 16.984 34.554 63.776 1 27.7 ? N6 APC 302 A 1 HETATM 28 N N1 APC . . . C 3 18.518 33.089 64.489 1 27.11 ? N1 APC 302 A 1 HETATM 29 C C2 APC . . . C 3 19.663 32.354 64.471 1 26.76 ? C2 APC 302 A 1 HETATM 30 N N3 APC . . . C 3 20.552 32.478 63.451 1 26.91 ? N3 APC 302 A 1 HETATM 31 C C4 APC . . . C 3 20.287 33.343 62.449 1 26.44 ? C4 APC 302 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #