data_6J7E # _model_server_result.job_id 88p6R0Dgbu3G1pzvYw6fWg _model_server_result.datetime_utc '2024-10-18 15:24:28' _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 6j7e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 6J7E # _exptl.entry_id 6J7E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE 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 120 _cell.entry_id 6J7E _cell.length_a 104.549 _cell.length_b 104.549 _cell.length_c 42.762 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6J7E _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 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 109 A ASP 245 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.842 ? metalc ? metalc2 B O2G AGS . A AGS 401 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.372 ? metalc ? metalc3 C MG MG . A MG 402 1_555 E O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.859 ? metalc ? metalc4 C MG MG . A MG 402 1_555 E O HOH . A HOH 508 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.618 ? metalc ? metalc5 C MG MG . A MG 402 1_555 E O HOH . A HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc6 C MG MG . A MG 402 1_555 E O HOH . A HOH 534 6_664 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 6J7E _atom_sites.fract_transf_matrix[1][1] 0.009565 _atom_sites.fract_transf_matrix[1][2] 0.005522 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011045 _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] 0.023385 _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 AGS A 1 401 401 AGS AGS . C 3 MG A 1 402 1 MG MG . D 4 GOL A 1 403 600 GOL GOL . E 5 HOH A 1 501 5 HOH HOH . E 5 HOH A 2 502 27 HOH HOH . E 5 HOH A 3 503 8 HOH HOH . E 5 HOH A 4 504 29 HOH HOH . E 5 HOH A 5 505 20 HOH HOH . E 5 HOH A 6 506 44 HOH HOH . E 5 HOH A 7 507 58 HOH HOH . E 5 HOH A 8 508 46 HOH HOH . E 5 HOH A 9 509 22 HOH HOH . E 5 HOH A 10 510 13 HOH HOH . E 5 HOH A 11 511 57 HOH HOH . E 5 HOH A 12 512 72 HOH HOH . E 5 HOH A 13 513 9 HOH HOH . E 5 HOH A 14 514 39 HOH HOH . E 5 HOH A 15 515 59 HOH HOH . E 5 HOH A 16 516 37 HOH HOH . E 5 HOH A 17 517 28 HOH HOH . E 5 HOH A 18 518 6 HOH HOH . E 5 HOH A 19 519 17 HOH HOH . E 5 HOH A 20 520 52 HOH HOH . E 5 HOH A 21 521 24 HOH HOH . E 5 HOH A 22 522 15 HOH HOH . E 5 HOH A 23 523 32 HOH HOH . E 5 HOH A 24 524 51 HOH HOH . E 5 HOH A 25 525 4 HOH HOH . E 5 HOH A 26 526 18 HOH HOH . E 5 HOH A 27 527 65 HOH HOH . E 5 HOH A 28 528 50 HOH HOH . E 5 HOH A 29 529 1 HOH HOH . E 5 HOH A 30 530 43 HOH HOH . E 5 HOH A 31 531 69 HOH HOH . E 5 HOH A 32 532 10 HOH HOH . E 5 HOH A 33 533 68 HOH HOH . E 5 HOH A 34 534 48 HOH HOH . E 5 HOH A 35 535 56 HOH HOH . E 5 HOH A 36 536 41 HOH HOH . E 5 HOH A 37 537 36 HOH HOH . E 5 HOH A 38 538 31 HOH HOH . E 5 HOH A 39 539 14 HOH HOH . E 5 HOH A 40 540 40 HOH HOH . E 5 HOH A 41 541 25 HOH HOH . E 5 HOH A 42 542 63 HOH HOH . E 5 HOH A 43 543 45 HOH HOH . E 5 HOH A 44 544 60 HOH HOH . E 5 HOH A 45 545 70 HOH HOH . E 5 HOH A 46 546 35 HOH HOH . E 5 HOH A 47 547 38 HOH HOH . E 5 HOH A 48 548 19 HOH HOH . E 5 HOH A 49 549 16 HOH HOH . E 5 HOH A 50 550 23 HOH HOH . E 5 HOH A 51 551 12 HOH HOH . E 5 HOH A 52 552 7 HOH HOH . E 5 HOH A 53 553 21 HOH HOH . E 5 HOH A 54 554 33 HOH HOH . E 5 HOH A 55 555 62 HOH HOH . E 5 HOH A 56 556 66 HOH HOH . E 5 HOH A 57 557 30 HOH HOH . E 5 HOH A 58 558 67 HOH HOH . E 5 HOH A 59 559 34 HOH HOH . E 5 HOH A 60 560 61 HOH HOH . E 5 HOH A 61 561 64 HOH HOH . E 5 HOH A 62 562 49 HOH HOH . E 5 HOH A 63 563 42 HOH HOH . E 5 HOH A 64 564 47 HOH HOH . E 5 HOH A 65 565 55 HOH HOH . E 5 HOH A 66 566 53 HOH HOH . E 5 HOH A 67 567 26 HOH HOH . E 5 HOH A 68 568 54 HOH HOH . E 5 HOH A 69 569 71 HOH HOH . E 5 HOH A 70 570 11 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 AGS . . . B 2 -76.816 74.085 0.756 1 66.77 ? PG AGS 401 A 1 HETATM 2 S S1G AGS . . . B 2 -75.147 73.434 1.556 1 64.65 ? S1G AGS 401 A 1 HETATM 3 O O2G AGS . . . B 2 -76.7 74.1 -0.812 1 51.49 ? O2G AGS 401 A 1 HETATM 4 O O3G AGS . . . B 2 -77.126 75.533 1.256 1 57.94 ? O3G AGS 401 A 1 HETATM 5 P PB AGS . . . B 2 -79.485 73.433 1.036 1 35.86 ? PB AGS 401 A 1 HETATM 6 O O1B AGS . . . B 2 -80.098 74.033 2.233 1 38.14 ? O1B AGS 401 A 1 HETATM 7 O O2B AGS . . . B 2 -79.7 74.308 -0.197 1 41.6 ? O2B AGS 401 A 1 HETATM 8 O O3B AGS . . . B 2 -77.956 73.147 1.267 1 36.38 ? O3B AGS 401 A 1 HETATM 9 P PA AGS . . . B 2 -80.567 71.402 -0.638 1 58.59 ? PA AGS 401 A 1 HETATM 10 O O1A AGS . . . B 2 -82.033 71.595 -0.739 1 45.72 ? O1A AGS 401 A 1 HETATM 11 O O2A AGS . . . B 2 -79.812 72.097 -1.782 1 58.57 ? O2A AGS 401 A 1 HETATM 12 O O3A AGS . . . B 2 -80.074 71.961 0.773 1 43.21 ? O3A AGS 401 A 1 HETATM 13 O O5' AGS . . . B 2 -80.176 69.843 -0.685 1 61.86 ? O5' AGS 401 A 1 HETATM 14 C C5' AGS . . . B 2 -80.864 68.779 0.014 1 56.71 ? C5' AGS 401 A 1 HETATM 15 C C4' AGS . . . B 2 -81.008 67.586 -0.91 1 57.21 ? C4' AGS 401 A 1 HETATM 16 O O4' AGS . . . B 2 -82.041 66.706 -0.421 1 54.85 ? O4' AGS 401 A 1 HETATM 17 C C3' AGS . . . B 2 -81.427 67.907 -2.336 1 60.42 ? C3' AGS 401 A 1 HETATM 18 O O3' AGS . . . B 2 -80.928 66.92 -3.23 1 64.35 ? O3' AGS 401 A 1 HETATM 19 C C2' AGS . . . B 2 -82.962 67.938 -2.243 1 63.2 ? C2' AGS 401 A 1 HETATM 20 O O2' AGS . . . B 2 -83.595 67.493 -3.439 1 70.61 ? O2' AGS 401 A 1 HETATM 21 C C1' AGS . . . B 2 -83.263 66.967 -1.092 1 61.51 ? C1' AGS 401 A 1 HETATM 22 N N9 AGS . . . B 2 -84.244 67.44 -0.102 1 64.74 ? N9 AGS 401 A 1 HETATM 23 C C8 AGS . . . B 2 -84.036 68.381 0.875 1 55.99 ? C8 AGS 401 A 1 HETATM 24 N N7 AGS . . . B 2 -85.076 68.588 1.647 1 56.16 ? N7 AGS 401 A 1 HETATM 25 C C5 AGS . . . B 2 -86.034 67.711 1.155 1 55.75 ? C5 AGS 401 A 1 HETATM 26 C C6 AGS . . . B 2 -87.361 67.436 1.545 1 55.83 ? C6 AGS 401 A 1 HETATM 27 N N6 AGS . . . B 2 -87.981 68.04 2.562 1 54.6 ? N6 AGS 401 A 1 HETATM 28 N N1 AGS . . . B 2 -88.042 66.512 0.84 1 57.63 ? N1 AGS 401 A 1 HETATM 29 C C2 AGS . . . B 2 -87.428 65.897 -0.175 1 61.26 ? C2 AGS 401 A 1 HETATM 30 N N3 AGS . . . B 2 -86.186 66.069 -0.633 1 58.89 ? N3 AGS 401 A 1 HETATM 31 C C4 AGS . . . B 2 -85.536 66.997 0.078 1 55.12 ? C4 AGS 401 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 31 #