data_4M5G # _model_server_result.job_id LnK7_AttFkvQQcVBL-DYiQ _model_server_result.datetime_utc '2024-11-23 20:59:34' _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 4m5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 4M5G # _exptl.entry_id 4M5G _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 113.96 _cell.angle_gamma 90 _cell.entry_id 4M5G _cell.length_a 35.875 _cell.length_b 57.417 _cell.length_c 38.327 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M5G _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,E,F,G,H,I,J _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 ASP 99 A ASP 95 1_555 D CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc2 A OD2 ASP 99 A ASP 95 1_555 E CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc3 A OD1 ASP 101 A ASP 97 1_555 D CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A OD2 ASP 101 A ASP 97 1_555 E CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc5 B O1A APC . A APC 301 1_555 D CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc6 B O1B APC . A APC 301 1_555 D CA CA . A CA 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc7 B O2G APC . A APC 301 1_555 E CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc8 B O1B APC . A APC 301 1_555 E CA CA . A CA 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.383 ? metalc ? metalc9 D CA CA . A CA 303 1_555 J O HOH . A HOH 428 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc10 D CA CA . A CA 303 1_555 J O HOH . A HOH 429 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc11 E CA CA . A CA 304 1_555 J O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc12 E CA CA . A CA 304 1_555 J O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? # _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 4M5G _atom_sites.fract_transf_matrix[1][1] 0.027875 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.012385 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017416 _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] 0.028551 _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 1 301 301 APC APC . C 3 YH1 A 1 302 901 YH1 YH1 . D 4 CA A 1 303 201 CA CA . E 4 CA A 1 304 202 CA CA . F 5 CL A 1 305 401 CL CL . G 5 CL A 1 306 402 CL CL . H 5 CL A 1 307 403 CL CL . I 5 CL A 1 308 404 CL CL . J 6 HOH A 1 401 1 HOH HOH . J 6 HOH A 2 402 2 HOH HOH . J 6 HOH A 3 403 3 HOH HOH . J 6 HOH A 4 404 4 HOH HOH . J 6 HOH A 5 405 5 HOH HOH . J 6 HOH A 6 406 6 HOH HOH . J 6 HOH A 7 407 7 HOH HOH . J 6 HOH A 8 408 8 HOH HOH . J 6 HOH A 9 409 9 HOH HOH . J 6 HOH A 10 410 10 HOH HOH . J 6 HOH A 11 411 11 HOH HOH . J 6 HOH A 12 412 12 HOH HOH . J 6 HOH A 13 413 13 HOH HOH . J 6 HOH A 14 414 14 HOH HOH . J 6 HOH A 15 415 15 HOH HOH . J 6 HOH A 16 416 16 HOH HOH . J 6 HOH A 17 417 17 HOH HOH . J 6 HOH A 18 418 18 HOH HOH . J 6 HOH A 19 419 19 HOH HOH . J 6 HOH A 20 420 20 HOH HOH . J 6 HOH A 21 421 21 HOH HOH . J 6 HOH A 22 422 22 HOH HOH . J 6 HOH A 23 423 23 HOH HOH . J 6 HOH A 24 424 24 HOH HOH . J 6 HOH A 25 425 25 HOH HOH . J 6 HOH A 26 426 26 HOH HOH . J 6 HOH A 27 427 27 HOH HOH . J 6 HOH A 28 428 28 HOH HOH . J 6 HOH A 29 429 29 HOH HOH . J 6 HOH A 30 430 30 HOH HOH . J 6 HOH A 31 431 31 HOH HOH . J 6 HOH A 32 432 32 HOH HOH . J 6 HOH A 33 433 33 HOH HOH . J 6 HOH A 34 434 34 HOH HOH . J 6 HOH A 35 435 35 HOH HOH . J 6 HOH A 36 436 36 HOH HOH . J 6 HOH A 37 437 37 HOH HOH . J 6 HOH A 38 438 38 HOH HOH . J 6 HOH A 39 439 39 HOH HOH . J 6 HOH A 40 440 40 HOH HOH . J 6 HOH A 41 441 41 HOH HOH . J 6 HOH A 42 442 42 HOH HOH . J 6 HOH A 43 443 43 HOH HOH . J 6 HOH A 44 444 44 HOH HOH . J 6 HOH A 45 445 45 HOH HOH . J 6 HOH A 46 446 46 HOH HOH . J 6 HOH A 47 447 47 HOH HOH . J 6 HOH A 48 448 48 HOH HOH . J 6 HOH A 49 449 49 HOH HOH . J 6 HOH A 50 450 50 HOH HOH . J 6 HOH A 51 451 51 HOH HOH . J 6 HOH A 52 452 52 HOH HOH . J 6 HOH A 53 453 53 HOH HOH . J 6 HOH A 54 454 54 HOH HOH . J 6 HOH A 55 455 55 HOH HOH . J 6 HOH A 56 456 56 HOH HOH . J 6 HOH A 57 457 57 HOH HOH . J 6 HOH A 58 458 58 HOH HOH . J 6 HOH A 59 459 59 HOH HOH . J 6 HOH A 60 460 60 HOH HOH . J 6 HOH A 61 461 61 HOH HOH . J 6 HOH A 62 462 62 HOH HOH . J 6 HOH A 63 463 63 HOH HOH . J 6 HOH A 64 464 64 HOH HOH . J 6 HOH A 65 465 65 HOH HOH . J 6 HOH A 66 466 66 HOH HOH . J 6 HOH A 67 467 67 HOH HOH . J 6 HOH A 68 468 68 HOH HOH . J 6 HOH A 69 469 69 HOH HOH . J 6 HOH A 70 470 70 HOH HOH . J 6 HOH A 71 471 71 HOH HOH . J 6 HOH A 72 472 72 HOH HOH . J 6 HOH A 73 473 73 HOH HOH . J 6 HOH A 74 474 74 HOH HOH . J 6 HOH A 75 475 75 HOH HOH . J 6 HOH A 76 476 76 HOH HOH . J 6 HOH A 77 477 77 HOH HOH . J 6 HOH A 78 478 78 HOH HOH . J 6 HOH A 79 479 79 HOH HOH . J 6 HOH A 80 480 80 HOH HOH . J 6 HOH A 81 481 81 HOH HOH . J 6 HOH A 82 482 82 HOH HOH . J 6 HOH A 83 483 83 HOH HOH . J 6 HOH A 84 484 84 HOH HOH . J 6 HOH A 85 485 85 HOH HOH . J 6 HOH A 86 486 86 HOH HOH . J 6 HOH A 87 487 87 HOH HOH . J 6 HOH A 88 488 88 HOH HOH . J 6 HOH A 89 489 89 HOH HOH . J 6 HOH A 90 490 90 HOH HOH . J 6 HOH A 91 491 91 HOH HOH . J 6 HOH A 92 492 92 HOH HOH . J 6 HOH A 93 493 93 HOH HOH . J 6 HOH A 94 494 94 HOH HOH . J 6 HOH A 95 495 95 HOH HOH . J 6 HOH A 96 496 96 HOH HOH . J 6 HOH A 97 497 97 HOH HOH . J 6 HOH A 98 498 98 HOH HOH . J 6 HOH A 99 499 99 HOH HOH . J 6 HOH A 100 500 100 HOH HOH . J 6 HOH A 101 501 101 HOH HOH . J 6 HOH A 102 502 102 HOH HOH . J 6 HOH A 103 503 103 HOH HOH . J 6 HOH A 104 504 104 HOH HOH . J 6 HOH A 105 505 105 HOH HOH . J 6 HOH A 106 506 106 HOH HOH . J 6 HOH A 107 507 107 HOH HOH . J 6 HOH A 108 508 108 HOH HOH . J 6 HOH A 109 509 109 HOH HOH . J 6 HOH A 110 510 110 HOH HOH . J 6 HOH A 111 511 111 HOH HOH . J 6 HOH A 112 512 112 HOH HOH . J 6 HOH A 113 513 113 HOH HOH . J 6 HOH A 114 514 114 HOH HOH . J 6 HOH A 115 515 115 HOH HOH . J 6 HOH A 116 516 116 HOH HOH . J 6 HOH A 117 517 117 HOH HOH . J 6 HOH A 118 518 118 HOH HOH . J 6 HOH A 119 519 119 HOH HOH . J 6 HOH A 120 520 120 HOH HOH . J 6 HOH A 121 521 121 HOH HOH . J 6 HOH A 122 522 122 HOH HOH . J 6 HOH A 123 523 123 HOH HOH . J 6 HOH A 124 524 124 HOH HOH . J 6 HOH A 125 525 125 HOH HOH . J 6 HOH A 126 526 126 HOH HOH . J 6 HOH A 127 527 127 HOH HOH . J 6 HOH A 128 528 128 HOH HOH . J 6 HOH A 129 529 129 HOH HOH . J 6 HOH A 130 530 130 HOH HOH . J 6 HOH A 131 531 131 HOH HOH . J 6 HOH A 132 532 132 HOH HOH . J 6 HOH A 133 533 133 HOH HOH . J 6 HOH A 134 534 134 HOH HOH . J 6 HOH A 135 535 135 HOH HOH . J 6 HOH A 136 536 136 HOH HOH . J 6 HOH A 137 537 137 HOH HOH . J 6 HOH A 138 538 138 HOH HOH . J 6 HOH A 139 539 139 HOH HOH . J 6 HOH A 140 540 140 HOH HOH . J 6 HOH A 141 541 141 HOH HOH . J 6 HOH A 142 542 142 HOH HOH . J 6 HOH A 143 543 143 HOH HOH . J 6 HOH A 144 544 144 HOH HOH . J 6 HOH A 145 545 145 HOH HOH . J 6 HOH A 146 546 146 HOH HOH . J 6 HOH A 147 547 147 HOH HOH . J 6 HOH A 148 548 148 HOH HOH . J 6 HOH A 149 549 149 HOH HOH . J 6 HOH A 150 550 150 HOH HOH . J 6 HOH A 151 551 151 HOH HOH . J 6 HOH A 152 552 152 HOH HOH . J 6 HOH A 153 553 153 HOH HOH . J 6 HOH A 154 554 154 HOH HOH . J 6 HOH A 155 555 155 HOH HOH . J 6 HOH A 156 556 156 HOH HOH . J 6 HOH A 157 557 157 HOH HOH . J 6 HOH A 158 558 158 HOH HOH . J 6 HOH A 159 559 159 HOH HOH . J 6 HOH A 160 560 160 HOH HOH . J 6 HOH A 161 561 161 HOH HOH . J 6 HOH A 162 562 162 HOH HOH . J 6 HOH A 163 563 163 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 59.188 11.389 39.007 1 7.19 ? PG APC 301 A 1 HETATM 2 O O1G APC . . . B 2 58.511 12.681 38.638 1 7.89 ? O1G APC 301 A 1 HETATM 3 O O2G APC . . . B 2 58.395 10.151 38.691 1 8.77 ? O2G APC 301 A 1 HETATM 4 O O3G APC . . . B 2 59.731 11.397 40.41 1 10.2 ? O3G APC 301 A 1 HETATM 5 P PB APC . . . B 2 61.668 10.351 37.98 1 8.91 ? PB APC 301 A 1 HETATM 6 O O1B APC . . . B 2 61.171 9.019 38.384 1 8.27 ? O1B APC 301 A 1 HETATM 7 O O2B APC . . . B 2 62.236 10.371 36.491 1 11.29 ? O2B APC 301 A 1 HETATM 8 O O3B APC . . . B 2 60.46 11.4 38.02 1 8.89 ? O3B APC 301 A 1 HETATM 9 P PA APC . . . B 2 64.393 9.907 39.142 1 9.37 ? PA APC 301 A 1 HETATM 10 O O1A APC . . . B 2 64.068 8.506 38.802 1 7.92 ? O1A APC 301 A 1 HETATM 11 O O2A APC . . . B 2 65.495 10.537 38.189 1 11.45 ? O2A APC 301 A 1 HETATM 12 C C3A APC . . . B 2 62.923 10.954 39.125 1 8.64 ? C3A APC 301 A 1 HETATM 13 O O5' APC . . . B 2 64.881 9.841 40.679 1 11.49 ? O5' APC 301 A 1 HETATM 14 C C5' APC . . . B 2 65.588 10.871 41.347 1 13.1 ? C5' APC 301 A 1 HETATM 15 C C4' APC . . . B 2 65.607 10.551 42.843 1 11.88 ? C4' APC 301 A 1 HETATM 16 O O4' APC . . . B 2 64.294 10.405 43.378 1 11.39 ? O4' APC 301 A 1 HETATM 17 C C3' APC . . . B 2 66.275 9.246 43.276 1 11.7 ? C3' APC 301 A 1 HETATM 18 O O3' APC . . . B 2 67.698 9.367 43.336 1 15.39 ? O3' APC 301 A 1 HETATM 19 C C2' APC . . . B 2 65.661 8.985 44.648 1 10.5 ? C2' APC 301 A 1 HETATM 20 O O2' APC . . . B 2 66.594 9.301 45.689 1 11.16 ? O2' APC 301 A 1 HETATM 21 C C1' APC . . . B 2 64.515 9.983 44.726 1 9.73 ? C1' APC 301 A 1 HETATM 22 N N9 APC . . . B 2 63.218 9.499 45.234 1 8 ? N9 APC 301 A 1 HETATM 23 C C8 APC . . . B 2 62.466 10.242 46.069 1 8.9 ? C8 APC 301 A 1 HETATM 24 N N7 APC . . . B 2 61.315 9.61 46.371 1 8.54 ? N7 APC 301 A 1 HETATM 25 C C5 APC . . . B 2 61.343 8.443 45.707 1 7.37 ? C5 APC 301 A 1 HETATM 26 C C6 APC . . . B 2 60.414 7.324 45.604 1 6.48 ? C6 APC 301 A 1 HETATM 27 N N6 APC . . . B 2 59.248 7.367 46.274 1 6.43 ? N6 APC 301 A 1 HETATM 28 N N1 APC . . . B 2 60.784 6.29 44.828 1 6.06 ? N1 APC 301 A 1 HETATM 29 C C2 APC . . . B 2 61.953 6.281 44.152 1 6.4 ? C2 APC 301 A 1 HETATM 30 N N3 APC . . . B 2 62.862 7.266 44.199 1 6.84 ? N3 APC 301 A 1 HETATM 31 C C4 APC . . . B 2 62.593 8.356 44.951 1 7.28 ? C4 APC 301 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #