data_7OHG # _model_server_result.job_id iBfhL3uq5OnX77xqeZjZTw _model_server_result.datetime_utc '2024-10-20 05:32:16' _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 7ohg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 7OHG # _exptl.entry_id 7OHG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 682.155 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'Non-hydrolasable alarmone analogue' _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 7OHG _cell.length_a 88.121 _cell.length_b 88.121 _cell.length_c 182.889 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OHG _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _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,K,L _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 NE2 HIS 52 A HIS 52 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.433 ? metalc ? metalc2 A NE2 HIS 76 A HIS 76 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc3 A OD2 ASP 77 A ASP 77 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.584 ? metalc ? metalc4 A OD1 ASP 146 A ASP 146 1_555 E MN MN . A MN 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc5 B O17 VE8 . A VE8 401 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.568 ? metalc ? metalc6 B O15 VE8 . A VE8 401 1_555 F MG MG . A MG 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? # _chem_comp.formula 'C10 H19 N6 O19 P5' _chem_comp.formula_weight 682.155 _chem_comp.id VE8 _chem_comp.mon_nstd_flag . _chem_comp.name 'Non-hydrolasable alarmone analogue' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '~{N}-[(2~{S},3~{S},4~{R},5~{R})-5-(2-azanyl-6-oxidanylidene-1~{H}-purin-9-yl)-4-oxidanyl-2-[[oxidanyl-[oxidanyl(phosphonooxy)phosphoryl]oxy-phosphoryl]oxymethyl]oxolan-3-yl]-phosphonooxy-phosphonamidic acid' # 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 O13 P4 VE8 doub 393 n n O14 P4 VE8 sing 394 n n P4 O12 VE8 sing 395 n n P4 O11 VE8 sing 396 n n O16 P3 VE8 doub 397 n n O15 P3 VE8 sing 398 n n P3 O11 VE8 sing 399 n n P3 O10 VE8 sing 400 n n O10 P2 VE8 sing 401 n n O17 P2 VE8 doub 402 n n P2 O9 VE8 sing 403 n n P2 O8 VE8 sing 404 n n C8 N2 VE8 doub 405 n y C8 N VE8 sing 406 n y O8 C7 VE8 sing 407 n n O18 C6 VE8 sing 408 n n O18 C3 VE8 sing 409 n n C6 C7 VE8 sing 410 n n C6 C5 VE8 sing 411 n n C3 N VE8 sing 412 n n C3 C4 VE8 sing 413 n n N2 C1 VE8 sing 414 n y N C2 VE8 sing 415 n y N1 C5 VE8 sing 416 n n N1 P VE8 sing 417 n n O1 C4 VE8 sing 418 n n C5 C4 VE8 sing 419 n n O4 P1 VE8 doub 420 n n O7 P VE8 doub 421 n n C1 C2 VE8 doub 422 n y C1 C VE8 sing 423 n n C2 N3 VE8 sing 424 n n P O2 VE8 sing 425 n n P O6 VE8 sing 426 n n C O VE8 doub 427 n n C N5 VE8 sing 428 n n N3 C9 VE8 doub 429 n n P1 O2 VE8 sing 430 n n P1 O5 VE8 sing 431 n n P1 O3 VE8 sing 432 n n N5 C9 VE8 sing 433 n n C9 N4 VE8 sing 434 n n O9 H1 VE8 sing 435 n n O15 H2 VE8 sing 436 n n O14 H3 VE8 sing 437 n n O12 H4 VE8 sing 438 n n C7 H5 VE8 sing 439 n n C7 H6 VE8 sing 440 n n C6 H7 VE8 sing 441 n n C5 H8 VE8 sing 442 n n N1 H9 VE8 sing 443 n n O6 H10 VE8 sing 444 n n O5 H11 VE8 sing 445 n n O3 H12 VE8 sing 446 n n C4 H13 VE8 sing 447 n n O1 H14 VE8 sing 448 n n C3 H15 VE8 sing 449 n n C8 H16 VE8 sing 450 n n N4 H17 VE8 sing 451 n n N4 H18 VE8 sing 452 n n N5 H19 VE8 sing 453 n n # _atom_sites.entry_id 7OHG _atom_sites.fract_transf_matrix[1][1] 0.011348 _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] 0.011348 _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] 0.005468 _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 VE8 A 1 401 401 VE8 GN5 . C 3 GOL A 1 402 402 GOL GOL . D 4 FMT A 1 403 403 FMT FMT . E 5 MN A 1 404 1 MN MN . F 6 MG A 1 405 1 MG MG . G 7 CL A 1 406 2 CL CL . H 7 CL A 1 407 3 CL CL . I 7 CL A 1 408 4 CL CL . J 7 CL A 1 409 5 CL CL . K 7 CL A 1 410 6 CL CL . L 8 HOH A 1 501 25 HOH HOH . L 8 HOH A 2 502 1 HOH HOH . L 8 HOH A 3 503 89 HOH HOH . L 8 HOH A 4 504 23 HOH HOH . L 8 HOH A 5 505 13 HOH HOH . L 8 HOH A 6 506 98 HOH HOH . L 8 HOH A 7 507 9 HOH HOH . L 8 HOH A 8 508 90 HOH HOH . L 8 HOH A 9 509 57 HOH HOH . L 8 HOH A 10 510 44 HOH HOH . L 8 HOH A 11 511 79 HOH HOH . L 8 HOH A 12 512 12 HOH HOH . L 8 HOH A 13 513 17 HOH HOH . L 8 HOH A 14 514 100 HOH HOH . L 8 HOH A 15 515 11 HOH HOH . L 8 HOH A 16 516 54 HOH HOH . L 8 HOH A 17 517 26 HOH HOH . L 8 HOH A 18 518 95 HOH HOH . L 8 HOH A 19 519 47 HOH HOH . L 8 HOH A 20 520 102 HOH HOH . L 8 HOH A 21 521 87 HOH HOH . L 8 HOH A 22 522 8 HOH HOH . L 8 HOH A 23 523 45 HOH HOH . L 8 HOH A 24 524 78 HOH HOH . L 8 HOH A 25 525 81 HOH HOH . L 8 HOH A 26 526 50 HOH HOH . L 8 HOH A 27 527 16 HOH HOH . L 8 HOH A 28 528 21 HOH HOH . L 8 HOH A 29 529 24 HOH HOH . L 8 HOH A 30 530 75 HOH HOH . L 8 HOH A 31 531 18 HOH HOH . L 8 HOH A 32 532 43 HOH HOH . L 8 HOH A 33 533 14 HOH HOH . L 8 HOH A 34 534 38 HOH HOH . L 8 HOH A 35 535 94 HOH HOH . L 8 HOH A 36 536 70 HOH HOH . L 8 HOH A 37 537 58 HOH HOH . L 8 HOH A 38 538 76 HOH HOH . L 8 HOH A 39 539 51 HOH HOH . L 8 HOH A 40 540 27 HOH HOH . L 8 HOH A 41 541 39 HOH HOH . L 8 HOH A 42 542 35 HOH HOH . L 8 HOH A 43 543 42 HOH HOH . L 8 HOH A 44 544 66 HOH HOH . L 8 HOH A 45 545 63 HOH HOH . L 8 HOH A 46 546 28 HOH HOH . L 8 HOH A 47 547 60 HOH HOH . L 8 HOH A 48 548 10 HOH HOH . L 8 HOH A 49 549 68 HOH HOH . L 8 HOH A 50 550 37 HOH HOH . L 8 HOH A 51 551 84 HOH HOH . L 8 HOH A 52 552 33 HOH HOH . L 8 HOH A 53 553 69 HOH HOH . L 8 HOH A 54 554 71 HOH HOH . L 8 HOH A 55 555 22 HOH HOH . L 8 HOH A 56 556 56 HOH HOH . L 8 HOH A 57 557 6 HOH HOH . L 8 HOH A 58 558 61 HOH HOH . L 8 HOH A 59 559 31 HOH HOH . L 8 HOH A 60 560 34 HOH HOH . L 8 HOH A 61 561 77 HOH HOH . L 8 HOH A 62 562 85 HOH HOH . L 8 HOH A 63 563 3 HOH HOH . L 8 HOH A 64 564 20 HOH HOH . L 8 HOH A 65 565 74 HOH HOH . L 8 HOH A 66 566 73 HOH HOH . L 8 HOH A 67 567 88 HOH HOH . L 8 HOH A 68 568 48 HOH HOH . L 8 HOH A 69 569 5 HOH HOH . L 8 HOH A 70 570 7 HOH HOH . L 8 HOH A 71 571 15 HOH HOH . L 8 HOH A 72 572 80 HOH HOH . L 8 HOH A 73 573 46 HOH HOH . L 8 HOH A 74 574 40 HOH HOH . L 8 HOH A 75 575 103 HOH HOH . L 8 HOH A 76 576 32 HOH HOH . L 8 HOH A 77 577 30 HOH HOH . L 8 HOH A 78 578 2 HOH HOH . L 8 HOH A 79 579 83 HOH HOH . L 8 HOH A 80 580 99 HOH HOH . L 8 HOH A 81 581 53 HOH HOH . L 8 HOH A 82 582 36 HOH HOH . L 8 HOH A 83 583 82 HOH HOH . L 8 HOH A 84 584 59 HOH HOH . L 8 HOH A 85 585 4 HOH HOH . L 8 HOH A 86 586 91 HOH HOH . L 8 HOH A 87 587 96 HOH HOH . L 8 HOH A 88 588 86 HOH HOH . L 8 HOH A 89 589 64 HOH HOH . L 8 HOH A 90 590 41 HOH HOH . L 8 HOH A 91 591 19 HOH HOH . L 8 HOH A 92 592 93 HOH HOH . L 8 HOH A 93 593 92 HOH HOH . L 8 HOH A 94 594 29 HOH HOH . L 8 HOH A 95 595 55 HOH HOH . L 8 HOH A 96 596 49 HOH HOH . L 8 HOH A 97 597 101 HOH HOH . L 8 HOH A 98 598 65 HOH HOH . L 8 HOH A 99 599 52 HOH HOH . L 8 HOH A 100 600 62 HOH HOH . L 8 HOH A 101 601 72 HOH HOH . L 8 HOH A 102 602 67 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 O O17 VE8 . . . B 2 58.857 51.008 -2.98 1 144.22 ? O17 VE8 401 A 1 HETATM 2 P P2 VE8 . . . B 2 59.911 50.069 -2.539 1 144.29 ? P2 VE8 401 A 1 HETATM 3 O O9 VE8 . . . B 2 59.474 48.606 -2.421 1 144.17 ? O9 VE8 401 A 1 HETATM 4 O O10 VE8 . . . B 2 61.178 50.1 -3.509 1 145.85 ? O10 VE8 401 A 1 HETATM 5 P P3 VE8 . . . B 2 61.434 50.42 -5.051 1 147.26 ? P3 VE8 401 A 1 HETATM 6 O O16 VE8 . . . B 2 61.604 49.169 -5.831 1 147.41 ? O16 VE8 401 A 1 HETATM 7 O O15 VE8 . . . B 2 60.288 51.351 -5.516 1 147.45 ? O15 VE8 401 A 1 HETATM 8 O O11 VE8 . . . B 2 62.779 51.287 -5.023 1 147.57 ? O11 VE8 401 A 1 HETATM 9 P P4 VE8 . . . B 2 63.63 52.183 -6.046 1 147.53 ? P4 VE8 401 A 1 HETATM 10 O O14 VE8 . . . B 2 62.854 53.385 -6.501 1 147.4 ? O14 VE8 401 A 1 HETATM 11 O O13 VE8 . . . B 2 64.008 51.221 -7.192 1 147.44 ? O13 VE8 401 A 1 HETATM 12 O O12 VE8 . . . B 2 64.91 52.549 -5.271 1 147.4 ? O12 VE8 401 A 1 HETATM 13 O O8 VE8 . . . B 2 60.474 50.487 -1.093 1 142.93 ? O8 VE8 401 A 1 HETATM 14 C C7 VE8 . . . B 2 61.022 51.776 -0.74 1 141.64 ? C7 VE8 401 A 1 HETATM 15 C C6 VE8 . . . B 2 62.504 51.789 -1.025 1 140.44 ? C6 VE8 401 A 1 HETATM 16 C C5 VE8 . . . B 2 63.401 51.128 0.032 1 140.29 ? C5 VE8 401 A 1 HETATM 17 N N1 VE8 . . . B 2 63.68 49.694 -0.213 1 140.96 ? N1 VE8 401 A 1 HETATM 18 P P VE8 . . . B 2 64.146 48.563 0.895 1 141.54 ? P VE8 401 A 1 HETATM 19 O O7 VE8 . . . B 2 64.798 47.393 0.307 1 141.56 ? O7 VE8 401 A 1 HETATM 20 O O6 VE8 . . . B 2 65.232 49.235 1.845 1 141.46 ? O6 VE8 401 A 1 HETATM 21 O O2 VE8 . . . B 2 62.886 48.108 1.835 1 141.98 ? O2 VE8 401 A 1 HETATM 22 P P1 VE8 . . . B 2 61.366 47.627 1.665 1 142.18 ? P1 VE8 401 A 1 HETATM 23 O O5 VE8 . . . B 2 60.387 48.709 2.051 1 142.1 ? O5 VE8 401 A 1 HETATM 24 O O4 VE8 . . . B 2 61.257 47.189 0.184 1 142.31 ? O4 VE8 401 A 1 HETATM 25 O O3 VE8 . . . B 2 61.249 46.377 2.56 1 142.15 ? O3 VE8 401 A 1 HETATM 26 C C4 VE8 . . . B 2 64.616 52.081 0.205 1 139.38 ? C4 VE8 401 A 1 HETATM 27 O O1 VE8 . . . B 2 65.863 51.414 0.023 1 139.33 ? O1 VE8 401 A 1 HETATM 28 O O18 VE8 . . . B 2 62.968 53.152 -1.084 1 139.4 ? O18 VE8 401 A 1 HETATM 29 C C3 VE8 . . . B 2 64.363 53.137 -0.875 1 138.51 ? C3 VE8 401 A 1 HETATM 30 N N VE8 . . . B 2 64.799 54.5 -0.517 1 136.82 ? N VE8 401 A 1 HETATM 31 C C8 VE8 . . . B 2 65.665 55.288 -1.226 1 136.24 ? C8 VE8 401 A 1 HETATM 32 N N2 VE8 . . . B 2 65.857 56.467 -0.685 1 135.79 ? N2 VE8 401 A 1 HETATM 33 C C1 VE8 . . . B 2 65.071 56.453 0.454 1 135.5 ? C1 VE8 401 A 1 HETATM 34 C C2 VE8 . . . B 2 64.412 55.249 0.57 1 135.89 ? C2 VE8 401 A 1 HETATM 35 N N3 VE8 . . . B 2 63.566 54.857 1.538 1 135.49 ? N3 VE8 401 A 1 HETATM 36 C C9 VE8 . . . B 2 63.389 55.787 2.475 1 135.15 ? C9 VE8 401 A 1 HETATM 37 N N4 VE8 . . . B 2 62.559 55.548 3.488 1 135.07 ? N4 VE8 401 A 1 HETATM 38 N N5 VE8 . . . B 2 64.005 57.011 2.452 1 135 ? N5 VE8 401 A 1 HETATM 39 C C VE8 . . . B 2 64.87 57.443 1.468 1 135.02 ? C VE8 401 A 1 HETATM 40 O O VE8 . . . B 2 65.366 58.565 1.524 1 134.81 ? O VE8 401 A 1 # _model_server_stats.io_time_ms 26 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #