data_4O1G # _model_server_result.job_id potf7_DDan-2DzBR9av3lQ _model_server_result.datetime_utc '2024-12-02 11:06:32' _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 4o1g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 4O1G # _exptl.entry_id 4O1G _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 3 _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 99.44 _cell.angle_gamma 90 _cell.entry_id 4O1G _cell.length_a 54.843 _cell.length_b 72.41 _cell.length_c 82.43 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4O1G _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_454 -x-1,y,-z-1 -1 0 0 0 1 0 0 0 -1 -41.32327 0 -81.313725 # _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 O ASP 251 A ASP 251 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? metalc ? metalc2 A O THR 253 A THR 253 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.878 ? metalc ? metalc3 A O VAL 287 A VAL 287 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? metalc ? metalc4 A O SER 290 A SER 290 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc5 A O GLY 292 A GLY 292 1_555 B NA NA . A NA 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? # _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 4O1G _atom_sites.fract_transf_matrix[1][1] 0.018234 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00303 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01381 _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] 0.012298 _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 NA A 1 401 1 NA NA . C 3 AGS A 1 402 1 AGS AGS . D 4 HOH A 1 501 1 HOH HOH . D 4 HOH A 2 502 2 HOH HOH . D 4 HOH A 3 503 3 HOH HOH . D 4 HOH A 4 504 4 HOH HOH . D 4 HOH A 5 505 5 HOH HOH . D 4 HOH A 6 506 6 HOH HOH . D 4 HOH A 7 507 7 HOH HOH . D 4 HOH A 8 508 8 HOH HOH . D 4 HOH A 9 509 9 HOH HOH . D 4 HOH A 10 510 10 HOH HOH . D 4 HOH A 11 511 11 HOH HOH . D 4 HOH A 12 512 12 HOH HOH . D 4 HOH A 13 513 13 HOH HOH . D 4 HOH A 14 514 14 HOH HOH . D 4 HOH A 15 515 15 HOH HOH . D 4 HOH A 16 516 16 HOH HOH . D 4 HOH A 17 517 17 HOH HOH . D 4 HOH A 18 518 18 HOH HOH . D 4 HOH A 19 519 19 HOH HOH . D 4 HOH A 20 520 20 HOH HOH . D 4 HOH A 21 521 21 HOH HOH . D 4 HOH A 22 522 22 HOH HOH . D 4 HOH A 23 523 23 HOH HOH . D 4 HOH A 24 524 24 HOH HOH . D 4 HOH A 25 525 25 HOH HOH . D 4 HOH A 26 526 26 HOH HOH . D 4 HOH A 27 527 28 HOH HOH . D 4 HOH A 28 528 29 HOH HOH . D 4 HOH A 29 529 30 HOH HOH . D 4 HOH A 30 530 31 HOH HOH . D 4 HOH A 31 531 32 HOH HOH . D 4 HOH A 32 532 33 HOH HOH . D 4 HOH A 33 533 34 HOH HOH . D 4 HOH A 34 534 35 HOH HOH . D 4 HOH A 35 535 36 HOH HOH . D 4 HOH A 36 536 37 HOH HOH . D 4 HOH A 37 537 38 HOH HOH . D 4 HOH A 38 538 39 HOH HOH . D 4 HOH A 39 539 40 HOH HOH . D 4 HOH A 40 540 41 HOH HOH . D 4 HOH A 41 541 42 HOH HOH . D 4 HOH A 42 542 43 HOH HOH . D 4 HOH A 43 543 44 HOH HOH . D 4 HOH A 44 544 45 HOH HOH . D 4 HOH A 45 545 46 HOH HOH . D 4 HOH A 46 546 47 HOH HOH . D 4 HOH A 47 547 48 HOH HOH . D 4 HOH A 48 548 49 HOH HOH . D 4 HOH A 49 549 50 HOH HOH . D 4 HOH A 50 550 51 HOH HOH . D 4 HOH A 51 551 52 HOH HOH . D 4 HOH A 52 552 53 HOH HOH . D 4 HOH A 53 553 54 HOH HOH . D 4 HOH A 54 554 55 HOH HOH . D 4 HOH A 55 555 56 HOH HOH . D 4 HOH A 56 556 57 HOH HOH . D 4 HOH A 57 557 58 HOH HOH . D 4 HOH A 58 558 59 HOH HOH . D 4 HOH A 59 559 60 HOH HOH . D 4 HOH A 60 560 61 HOH HOH . D 4 HOH A 61 561 62 HOH HOH . D 4 HOH A 62 562 63 HOH HOH . D 4 HOH A 63 563 64 HOH HOH . D 4 HOH A 64 564 65 HOH HOH . D 4 HOH A 65 565 66 HOH HOH . D 4 HOH A 66 566 67 HOH HOH . D 4 HOH A 67 567 68 HOH HOH . D 4 HOH A 68 568 69 HOH HOH . D 4 HOH A 69 569 70 HOH HOH . D 4 HOH A 70 570 71 HOH HOH . D 4 HOH A 71 571 72 HOH HOH . D 4 HOH A 72 572 73 HOH HOH . D 4 HOH A 73 573 74 HOH HOH . D 4 HOH A 74 574 75 HOH HOH . D 4 HOH A 75 575 76 HOH HOH . D 4 HOH A 76 576 77 HOH HOH . D 4 HOH A 77 577 78 HOH HOH . D 4 HOH A 78 578 79 HOH HOH . D 4 HOH A 79 579 80 HOH HOH . D 4 HOH A 80 580 81 HOH HOH . D 4 HOH A 81 581 82 HOH HOH . D 4 HOH A 82 582 83 HOH HOH . D 4 HOH A 83 583 84 HOH HOH . D 4 HOH A 84 584 85 HOH HOH . D 4 HOH A 85 585 86 HOH HOH . D 4 HOH A 86 586 87 HOH HOH . D 4 HOH A 87 587 88 HOH HOH . D 4 HOH A 88 588 89 HOH HOH . D 4 HOH A 89 589 90 HOH HOH . D 4 HOH A 90 590 91 HOH HOH . D 4 HOH A 91 591 92 HOH HOH . D 4 HOH A 92 592 93 HOH HOH . D 4 HOH A 93 593 96 HOH HOH . D 4 HOH A 94 594 97 HOH HOH . D 4 HOH A 95 595 98 HOH HOH . D 4 HOH A 96 596 99 HOH HOH . D 4 HOH A 97 597 100 HOH HOH . D 4 HOH A 98 598 101 HOH HOH . D 4 HOH A 99 599 102 HOH HOH . D 4 HOH A 100 600 103 HOH HOH . D 4 HOH A 101 601 104 HOH HOH . D 4 HOH A 102 602 105 HOH HOH . D 4 HOH A 103 603 106 HOH HOH . D 4 HOH A 104 604 107 HOH HOH . D 4 HOH A 105 605 108 HOH HOH . D 4 HOH A 106 606 109 HOH HOH . D 4 HOH A 107 607 110 HOH HOH . D 4 HOH A 108 608 111 HOH HOH . D 4 HOH A 109 609 112 HOH HOH . D 4 HOH A 110 610 113 HOH HOH . D 4 HOH A 111 611 114 HOH HOH . D 4 HOH A 112 612 115 HOH HOH . D 4 HOH A 113 613 116 HOH HOH . D 4 HOH A 114 614 117 HOH HOH . D 4 HOH A 115 615 118 HOH HOH . D 4 HOH A 116 616 119 HOH HOH . D 4 HOH A 117 617 120 HOH HOH . D 4 HOH A 118 618 121 HOH HOH . D 4 HOH A 119 619 122 HOH HOH . D 4 HOH A 120 620 123 HOH HOH . D 4 HOH A 121 621 124 HOH HOH . D 4 HOH A 122 622 125 HOH HOH . D 4 HOH A 123 623 126 HOH HOH . D 4 HOH A 124 624 127 HOH HOH . D 4 HOH A 125 625 128 HOH HOH . D 4 HOH A 126 626 129 HOH HOH . D 4 HOH A 127 627 130 HOH HOH . D 4 HOH A 128 628 131 HOH HOH . D 4 HOH A 129 629 132 HOH HOH . D 4 HOH A 130 630 133 HOH HOH . D 4 HOH A 131 631 134 HOH HOH . D 4 HOH A 132 632 135 HOH HOH . D 4 HOH A 133 633 136 HOH HOH . D 4 HOH A 134 634 137 HOH HOH . D 4 HOH A 135 635 138 HOH HOH . D 4 HOH A 136 636 139 HOH HOH . D 4 HOH A 137 637 140 HOH HOH . D 4 HOH A 138 638 141 HOH HOH . D 4 HOH A 139 639 142 HOH HOH . D 4 HOH A 140 640 143 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 . . . C 3 -9.347 7.424 -20.724 0.8 25.71 ? PG AGS 402 A 1 HETATM 2 S S1G AGS . . . C 3 -8.02 7.545 -22.278 0.8 32.72 ? S1G AGS 402 A 1 HETATM 3 O O2G AGS . . . C 3 -9.84 5.947 -20.511 0.8 24.11 ? O2G AGS 402 A 1 HETATM 4 O O3G AGS . . . C 3 -10.437 8.446 -20.822 0.8 27.18 ? O3G AGS 402 A 1 HETATM 5 P PB AGS . . . C 3 -8.918 8.071 -17.918 0.8 23.71 ? PB AGS 402 A 1 HETATM 6 O O1B AGS . . . C 3 -8.998 9.547 -17.739 0.8 21.15 ? O1B AGS 402 A 1 HETATM 7 O O2B AGS . . . C 3 -10.096 7.23 -17.543 0.8 23.58 ? O2B AGS 402 A 1 HETATM 8 O O3B AGS . . . C 3 -8.427 7.758 -19.423 0.8 25.93 ? O3B AGS 402 A 1 HETATM 9 P PA AGS . . . C 3 -6.246 8.135 -16.755 0.8 21.14 ? PA AGS 402 A 1 HETATM 10 O O1A AGS . . . C 3 -5.75 9.116 -17.786 0.8 22.91 ? O1A AGS 402 A 1 HETATM 11 O O2A AGS . . . C 3 -6.333 8.651 -15.318 0.8 16.24 ? O2A AGS 402 A 1 HETATM 12 O O3A AGS . . . C 3 -7.651 7.427 -17.168 0.8 22.41 ? O3A AGS 402 A 1 HETATM 13 O O5' AGS . . . C 3 -5.335 6.862 -16.94 0.8 19.54 ? O5' AGS 402 A 1 HETATM 14 C C5' AGS . . . C 3 -5.58 5.619 -16.258 0.8 19.62 ? C5' AGS 402 A 1 HETATM 15 C C4' AGS . . . C 3 -4.263 4.918 -15.905 0.8 20.54 ? C4' AGS 402 A 1 HETATM 16 O O4' AGS . . . C 3 -3.483 4.795 -17.073 0.8 21.07 ? O4' AGS 402 A 1 HETATM 17 C C3' AGS . . . C 3 -3.325 5.614 -14.916 0.8 20.71 ? C3' AGS 402 A 1 HETATM 18 O O3' AGS . . . C 3 -3.757 5.422 -13.566 0.8 21.18 ? O3' AGS 402 A 1 HETATM 19 C C2' AGS . . . C 3 -1.967 4.999 -15.285 0.8 21.24 ? C2' AGS 402 A 1 HETATM 20 O O2' AGS . . . C 3 -1.715 3.709 -14.691 0.8 19.4 ? O2' AGS 402 A 1 HETATM 21 C C1' AGS . . . C 3 -2.089 4.816 -16.792 0.8 20.93 ? C1' AGS 402 A 1 HETATM 22 N N9 AGS . . . C 3 -1.58 5.981 -17.537 0.8 22.44 ? N9 AGS 402 A 1 HETATM 23 C C8 AGS . . . C 3 -2.263 7.072 -17.906 0.8 22.81 ? C8 AGS 402 A 1 HETATM 24 N N7 AGS . . . C 3 -1.485 7.974 -18.551 0.8 22.68 ? N7 AGS 402 A 1 HETATM 25 C C5 AGS . . . C 3 -0.262 7.404 -18.608 0.8 23.26 ? C5 AGS 402 A 1 HETATM 26 C C6 AGS . . . C 3 1.043 7.798 -19.132 0.8 24.38 ? C6 AGS 402 A 1 HETATM 27 N N6 AGS . . . C 3 1.168 8.98 -19.775 0.8 26.07 ? N6 AGS 402 A 1 HETATM 28 N N1 AGS . . . C 3 2.063 6.94 -18.982 0.8 25.03 ? N1 AGS 402 A 1 HETATM 29 C C2 AGS . . . C 3 1.922 5.741 -18.395 0.8 23.37 ? C2 AGS 402 A 1 HETATM 30 N N3 AGS . . . C 3 0.76 5.324 -17.842 0.8 23.04 ? N3 AGS 402 A 1 HETATM 31 C C4 AGS . . . C 3 -0.33 6.101 -17.946 0.8 23.31 ? C4 AGS 402 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #