data_3RSG # _model_server_result.job_id YPsKx7bcy9s9ASLcKMvwog _model_server_result.datetime_utc '2024-11-22 09:24:17' _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 3rsg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":494}' # _entry.id 3RSG # _exptl.entry_id 3RSG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 559.316 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description ADENOSINE-5-DIPHOSPHORIBOSE _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 3RSG _cell.length_a 122.168 _cell.length_b 122.168 _cell.length_c 155.108 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3RSG _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 4 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexadecameric _pdbx_struct_assembly.oligomeric_count 16 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4,5,6,7,8 # 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_555 -x,-y,z -1 0 0 0 -1 0 0 0 1 0 0 0 3 'crystal symmetry operation' 3_555 -y,x,z 0 -1 0 1 0 0 0 0 1 0 0 0 4 'crystal symmetry operation' 4_555 y,-x,z 0 1 0 -1 0 0 0 0 1 0 0 0 5 'crystal symmetry operation' 5_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 6 'crystal symmetry operation' 6_555 x,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 8_555 -y,-x,-z 0 -1 0 -1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 ASN 64 A ASN 52 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.916 ? metalc ? metalc2 A O ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.955 ? metalc ? metalc3 A OD2 ASP 126 A ASP 114 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.392 ? metalc ? metalc4 A O PHE 129 A PHE 117 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.818 ? metalc ? metalc5 A O VAL 158 A VAL 146 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc6 A O VAL 160 A VAL 148 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.829 ? metalc ? metalc7 A OG SER 162 A SER 150 1_555 C K K . A K 491 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.91 ? metalc ? metalc8 D MG MG . A MG 492 1_555 F O2A APR . A APR 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.978 ? metalc ? metalc9 D MG MG . A MG 492 1_555 F O1D APR . A APR 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.393 ? metalc ? metalc10 D MG MG . A MG 492 1_555 F O5D APR . A APR 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc11 D MG MG . A MG 492 1_555 F O4D APR . A APR 494 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.869 ? metalc ? metalc12 D MG MG . A MG 492 1_555 H O HOH . A HOH 536 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.371 ? metalc ? metalc13 D MG MG . A MG 492 1_555 H O HOH . A HOH 547 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? # _chem_comp.formula 'C15 H23 N5 O14 P2' _chem_comp.formula_weight 559.316 _chem_comp.id APR _chem_comp.mon_nstd_flag . _chem_comp.name ADENOSINE-5-DIPHOSPHORIBOSE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N1 C2 APR sing 13 n y N1 C6 APR doub 14 n y C2 N3 APR doub 15 n y C2 H2 APR sing 16 n n N3 C4 APR sing 17 n y C4 C5 APR doub 18 n y C4 N9 APR sing 19 n y C5 C6 APR sing 20 n y C5 N7 APR sing 21 n y C6 N6 APR sing 22 n n N6 H61 APR sing 23 n n N6 H62 APR sing 24 n n N7 C8 APR doub 25 n y C8 N9 APR sing 26 n y C8 H8 APR sing 27 n n N9 C1' APR sing 28 n n C1' C2' APR sing 29 n n C1' O4' APR sing 30 n n C1' "H'1" APR sing 31 n n C2' O2' APR sing 32 n n C2' C3' APR sing 33 n n C2' "H'2" APR sing 34 n n O2' "HO'2" APR sing 35 n n C3' O3' APR sing 36 n n C3' C4' APR sing 37 n n C3' "H'3" APR sing 38 n n O3' "HO'3" APR sing 39 n n O4' C4' APR sing 40 n n C4' C5' APR sing 41 n n C4' "H'4" APR sing 42 n n C5' O5' APR sing 43 n n C5' "H5'1" APR sing 44 n n C5' "H5'2" APR sing 45 n n O5' PA APR sing 46 n n PA O1A APR doub 47 n n PA O2A APR sing 48 n n PA O3A APR sing 49 n n O2A HOA2 APR sing 50 n n O3A PB APR sing 51 n n PB O1B APR doub 52 n n PB O2B APR sing 53 n n PB O5D APR sing 54 n n O2B HOB2 APR sing 55 n n O5D C5D APR sing 56 n n C5D C4D APR sing 57 n n C5D H5R1 APR sing 58 n n C5D H5R2 APR sing 59 n n O4D C1D APR sing 60 n n O4D C4D APR sing 61 n n O1D C1D APR sing 62 n n O1D HOR1 APR sing 63 n n C1D C2D APR sing 64 n n C1D "HR'1" APR sing 65 n n O2D C2D APR sing 66 n n O2D HOR2 APR sing 67 n n C2D C3D APR sing 68 n n C2D "HR'2" APR sing 69 n n O3D C3D APR sing 70 n n O3D HOR3 APR sing 71 n n C3D C4D APR sing 72 n n C3D "HR'3" APR sing 73 n n C4D "HR'4" APR sing 74 n n # _atom_sites.entry_id 3RSG _atom_sites.fract_transf_matrix[1][1] 0.008185 _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] 0.008185 _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] 0.006447 _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 C 3 K A 1 491 1 K K . D 4 MG A 1 492 2 MG MG . E 5 NAD A 1 493 3 NAD NAD . F 6 APR A 1 494 4 APR APR . G 5 NAD A 1 495 5 NAD NAD . H 7 HOH A 1 496 1 HOH HOH . H 7 HOH A 2 497 2 HOH HOH . H 7 HOH A 3 498 3 HOH HOH . H 7 HOH A 4 499 4 HOH HOH . H 7 HOH A 5 500 5 HOH HOH . H 7 HOH A 6 501 6 HOH HOH . H 7 HOH A 7 502 7 HOH HOH . H 7 HOH A 8 503 8 HOH HOH . H 7 HOH A 9 504 9 HOH HOH . H 7 HOH A 10 505 10 HOH HOH . H 7 HOH A 11 506 11 HOH HOH . H 7 HOH A 12 507 12 HOH HOH . H 7 HOH A 13 508 13 HOH HOH . H 7 HOH A 14 509 14 HOH HOH . H 7 HOH A 15 510 15 HOH HOH . H 7 HOH A 16 511 16 HOH HOH . H 7 HOH A 17 512 17 HOH HOH . H 7 HOH A 18 513 18 HOH HOH . H 7 HOH A 19 514 19 HOH HOH . H 7 HOH A 20 515 20 HOH HOH . H 7 HOH A 21 516 21 HOH HOH . H 7 HOH A 22 517 22 HOH HOH . H 7 HOH A 23 518 23 HOH HOH . H 7 HOH A 24 519 24 HOH HOH . H 7 HOH A 25 520 25 HOH HOH . H 7 HOH A 26 521 26 HOH HOH . H 7 HOH A 27 522 27 HOH HOH . H 7 HOH A 28 523 28 HOH HOH . H 7 HOH A 29 524 29 HOH HOH . H 7 HOH A 30 525 30 HOH HOH . H 7 HOH A 31 526 31 HOH HOH . H 7 HOH A 32 527 32 HOH HOH . H 7 HOH A 33 528 33 HOH HOH . H 7 HOH A 34 529 34 HOH HOH . H 7 HOH A 35 530 35 HOH HOH . H 7 HOH A 36 531 36 HOH HOH . H 7 HOH A 37 532 37 HOH HOH . H 7 HOH A 38 533 38 HOH HOH . H 7 HOH A 39 534 39 HOH HOH . H 7 HOH A 40 535 40 HOH HOH . H 7 HOH A 41 536 41 HOH HOH . H 7 HOH A 42 537 42 HOH HOH . H 7 HOH A 43 538 43 HOH HOH . H 7 HOH A 44 539 44 HOH HOH . H 7 HOH A 45 540 45 HOH HOH . H 7 HOH A 46 541 46 HOH HOH . H 7 HOH A 47 542 47 HOH HOH . H 7 HOH A 48 543 48 HOH HOH . H 7 HOH A 49 544 49 HOH HOH . H 7 HOH A 50 545 50 HOH HOH . H 7 HOH A 51 546 51 HOH HOH . H 7 HOH A 52 547 52 HOH HOH . H 7 HOH A 53 548 53 HOH HOH . H 7 HOH A 54 549 54 HOH HOH . H 7 HOH A 55 550 56 HOH HOH . H 7 HOH A 56 551 57 HOH HOH . H 7 HOH A 57 552 58 HOH HOH . H 7 HOH A 58 553 59 HOH HOH . H 7 HOH A 59 554 60 HOH HOH . H 7 HOH A 60 555 61 HOH HOH . H 7 HOH A 61 556 62 HOH HOH . H 7 HOH A 62 557 63 HOH HOH . H 7 HOH A 63 558 64 HOH HOH . H 7 HOH A 64 559 65 HOH HOH . H 7 HOH A 65 560 66 HOH HOH . H 7 HOH A 66 561 67 HOH HOH . H 7 HOH A 67 562 68 HOH HOH . H 7 HOH A 68 563 69 HOH HOH . H 7 HOH A 69 564 70 HOH HOH . H 7 HOH A 70 565 71 HOH HOH . H 7 HOH A 71 566 72 HOH HOH . H 7 HOH A 72 567 73 HOH HOH . H 7 HOH A 73 568 74 HOH HOH . H 7 HOH A 74 569 75 HOH HOH . H 7 HOH A 75 570 76 HOH HOH . H 7 HOH A 76 571 77 HOH HOH . H 7 HOH A 77 572 78 HOH HOH . H 7 HOH A 78 573 79 HOH HOH . H 7 HOH A 79 574 80 HOH HOH . H 7 HOH A 80 575 81 HOH HOH . H 7 HOH A 81 576 82 HOH HOH . H 7 HOH A 82 577 83 HOH HOH . H 7 HOH A 83 578 84 HOH HOH . H 7 HOH A 84 579 85 HOH HOH . H 7 HOH A 85 580 86 HOH HOH . H 7 HOH A 86 581 87 HOH HOH . H 7 HOH A 87 582 89 HOH HOH . H 7 HOH A 88 583 90 HOH HOH . H 7 HOH A 89 584 91 HOH HOH . H 7 HOH A 90 585 92 HOH HOH . H 7 HOH A 91 586 93 HOH HOH . H 7 HOH A 92 587 94 HOH HOH . H 7 HOH A 93 588 95 HOH HOH . H 7 HOH A 94 589 96 HOH HOH . H 7 HOH A 95 590 97 HOH HOH . H 7 HOH A 96 591 98 HOH HOH . H 7 HOH A 97 592 99 HOH HOH . H 7 HOH A 98 593 100 HOH HOH . H 7 HOH A 99 594 101 HOH HOH . H 7 HOH A 100 595 102 HOH HOH . H 7 HOH A 101 596 103 HOH HOH . H 7 HOH A 102 597 104 HOH HOH . H 7 HOH A 103 598 105 HOH HOH . H 7 HOH A 104 599 106 HOH HOH . H 7 HOH A 105 600 107 HOH HOH . H 7 HOH A 106 601 108 HOH HOH . H 7 HOH A 107 602 109 HOH HOH . H 7 HOH A 108 603 110 HOH HOH . H 7 HOH A 109 604 111 HOH HOH . H 7 HOH A 110 605 112 HOH HOH . H 7 HOH A 111 606 113 HOH HOH . H 7 HOH A 112 607 114 HOH HOH . H 7 HOH A 113 608 115 HOH HOH . H 7 HOH A 114 609 116 HOH HOH . H 7 HOH A 115 610 117 HOH HOH . H 7 HOH A 116 611 118 HOH HOH . H 7 HOH A 117 612 119 HOH HOH . H 7 HOH A 118 613 120 HOH HOH . H 7 HOH A 119 614 121 HOH HOH . I 7 HOH B 1 55 55 HOH HOH . I 7 HOH B 2 88 88 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 N N1 APR . . . F 6 24.695 7.493 30.137 1 76.21 ? N1 APR 494 A 1 HETATM 2 C C2 APR . . . F 6 24.718 6.16 30.306 1 76.5 ? C2 APR 494 A 1 HETATM 3 N N3 APR . . . F 6 24.508 5.58 31.5 1 77.71 ? N3 APR 494 A 1 HETATM 4 C C4 APR . . . F 6 24.252 6.334 32.597 1 78.29 ? C4 APR 494 A 1 HETATM 5 C C5 APR . . . F 6 24.208 7.794 32.479 1 77.24 ? C5 APR 494 A 1 HETATM 6 C C6 APR . . . F 6 24.452 8.357 31.142 1 76.43 ? C6 APR 494 A 1 HETATM 7 N N6 APR . . . F 6 24.438 9.691 30.947 1 76.62 ? N6 APR 494 A 1 HETATM 8 N N7 APR . . . F 6 23.939 8.278 33.693 1 76.84 ? N7 APR 494 A 1 HETATM 9 C C8 APR . . . F 6 23.813 7.228 34.529 1 78.47 ? C8 APR 494 A 1 HETATM 10 N N9 APR . . . F 6 24.007 6.075 33.872 1 78.87 ? N9 APR 494 A 1 HETATM 11 C C1' APR . . . F 6 23.924 4.72 34.448 1 79.36 ? C1' APR 494 A 1 HETATM 12 C C2' APR . . . F 6 25.155 4.347 35.235 1 79.77 ? C2' APR 494 A 1 HETATM 13 O O2' APR . . . F 6 26.193 3.781 34.442 1 78.06 ? O2' APR 494 A 1 HETATM 14 C C3' APR . . . F 6 24.562 3.356 36.197 1 79.28 ? C3' APR 494 A 1 HETATM 15 O O3' APR . . . F 6 24.504 2.096 35.552 1 78.75 ? O3' APR 494 A 1 HETATM 16 O O4' APR . . . F 6 22.829 4.639 35.364 1 78.29 ? O4' APR 494 A 1 HETATM 17 C C4' APR . . . F 6 23.173 3.882 36.504 1 78.64 ? C4' APR 494 A 1 HETATM 18 C C5' APR . . . F 6 23.158 4.811 37.715 1 77.6 ? C5' APR 494 A 1 HETATM 19 O O5' APR . . . F 6 23.564 4.116 38.888 1 75.56 ? O5' APR 494 A 1 HETATM 20 P PA APR . . . F 6 23.835 4.899 40.25 1 70.92 ? PA APR 494 A 1 HETATM 21 O O1A APR . . . F 6 24.867 5.92 39.983 1 78 ? O1A APR 494 A 1 HETATM 22 O O2A APR . . . F 6 24.032 3.928 41.345 1 73.25 ? O2A APR 494 A 1 HETATM 23 O O3A APR . . . F 6 22.554 5.839 40.409 1 76.62 ? O3A APR 494 A 1 HETATM 24 P PB APR . . . F 6 21.208 5.649 41.256 1 72.68 ? PB APR 494 A 1 HETATM 25 O O1B APR . . . F 6 20.707 7.022 41.435 1 74.23 ? O1B APR 494 A 1 HETATM 26 O O2B APR . . . F 6 20.297 4.647 40.665 1 73.3 ? O2B APR 494 A 1 HETATM 27 O O5D APR . . . F 6 21.618 5.121 42.704 1 77.88 ? O5D APR 494 A 1 HETATM 28 C C5D APR . . . F 6 20.585 4.902 43.665 1 82.12 ? C5D APR 494 A 1 HETATM 29 O O4D APR . . . F 6 21.985 4.166 45.532 1 84.89 ? O4D APR 494 A 1 HETATM 30 O O1D APR . . . F 6 24.186 4.819 45.02 1 82.72 ? O1D APR 494 A 1 HETATM 31 C C1D APR . . . F 6 23.179 4.775 46.025 1 85.61 ? C1D APR 494 A 1 HETATM 32 O O2D APR . . . F 6 22.232 6.177 47.675 1 84.49 ? O2D APR 494 A 1 HETATM 33 C C2D APR . . . F 6 22.797 6.192 46.365 1 86.57 ? C2D APR 494 A 1 HETATM 34 O O3D APR . . . F 6 20.881 7.543 45.678 1 88.88 ? O3D APR 494 A 1 HETATM 35 C C3D APR . . . F 6 21.781 6.508 45.285 1 86.81 ? C3D APR 494 A 1 HETATM 36 C C4D APR . . . F 6 21.065 5.173 45.092 1 85.17 ? C4D APR 494 A 1 # _model_server_stats.io_time_ms 91 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 36 #