data_6S4F # _model_server_result.job_id AGIPUpxf5_YT-0DqzQnnmQ _model_server_result.datetime_utc '2024-11-06 22:34:54' _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 6s4f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":407}' # _entry.id 6S4F # _exptl.entry_id 6S4F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _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 6S4F _cell.length_a 116.895 _cell.length_b 116.895 _cell.length_c 112.965 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S4F _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 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,E,F,G,H,I,J,K,L,M,N,O,P,Q _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 4 _struct_asym.id I _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H15 N5 O10 P2' _chem_comp.formula_weight 427.201 _chem_comp.id ADP _chem_comp.mon_nstd_flag n _chem_comp.name "ADENOSINE-5'-DIPHOSPHATE" _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 PB O1B ADP doub 1 n n PB O2B ADP sing 2 n n PB O3B ADP sing 3 n n PB O3A ADP sing 4 n n O2B HOB2 ADP sing 5 n n O3B HOB3 ADP sing 6 n n PA O1A ADP doub 7 n n PA O2A ADP sing 8 n n PA O3A ADP sing 9 n n PA O5' ADP sing 10 n n O2A HOA2 ADP sing 11 n n O5' C5' ADP sing 12 n n C5' C4' ADP sing 13 n n C5' "H5'1" ADP sing 14 n n C5' "H5'2" ADP sing 15 n n C4' O4' ADP sing 16 n n C4' C3' ADP sing 17 n n C4' H4' ADP sing 18 n n O4' C1' ADP sing 19 n n C3' O3' ADP sing 20 n n C3' C2' ADP sing 21 n n C3' H3' ADP sing 22 n n O3' HO3' ADP sing 23 n n C2' O2' ADP sing 24 n n C2' C1' ADP sing 25 n n C2' H2' ADP sing 26 n n O2' HO2' ADP sing 27 n n C1' N9 ADP sing 28 n n C1' H1' ADP sing 29 n n N9 C8 ADP sing 30 n y N9 C4 ADP sing 31 n y C8 N7 ADP doub 32 n y C8 H8 ADP sing 33 n n N7 C5 ADP sing 34 n y C5 C6 ADP sing 35 n y C5 C4 ADP doub 36 n y C6 N6 ADP sing 37 n n C6 N1 ADP doub 38 n y N6 HN61 ADP sing 39 n n N6 HN62 ADP sing 40 n n N1 C2 ADP sing 41 n y C2 N3 ADP doub 42 n y C2 H2 ADP sing 43 n n N3 C4 ADP sing 44 n y # _atom_sites.entry_id 6S4F _atom_sites.fract_transf_matrix[1][1] 0.008555 _atom_sites.fract_transf_matrix[1][2] 0.004939 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009878 _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] 0.008852 _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 2 KUN A 1 401 2 KUN LIG . D 3 PO4 A 1 402 2 PO4 PO4 . E 3 PO4 A 1 403 3 PO4 PO4 . F 3 PO4 A 1 404 4 PO4 PO4 . G 3 PO4 A 1 405 7 PO4 PO4 . H 3 PO4 A 1 406 9 PO4 PO4 . I 4 ADP A 1 407 1 ADP ADP . J 5 GOL A 1 408 1 GOL GOL . K 2 KUN B 1 401 1 KUN LIG . L 3 PO4 B 1 402 5 PO4 PO4 . M 3 PO4 B 1 403 6 PO4 PO4 . N 3 PO4 B 1 404 8 PO4 PO4 . O 5 GOL B 1 405 2 GOL GOL . P 6 HOH A 1 501 6 HOH HOH . P 6 HOH A 2 502 38 HOH HOH . P 6 HOH A 3 503 79 HOH HOH . P 6 HOH A 4 504 77 HOH HOH . P 6 HOH A 5 505 58 HOH HOH . P 6 HOH A 6 506 34 HOH HOH . P 6 HOH A 7 507 24 HOH HOH . P 6 HOH A 8 508 69 HOH HOH . P 6 HOH A 9 509 10 HOH HOH . P 6 HOH A 10 510 28 HOH HOH . P 6 HOH A 11 511 20 HOH HOH . P 6 HOH A 12 512 129 HOH HOH . P 6 HOH A 13 513 19 HOH HOH . P 6 HOH A 14 514 124 HOH HOH . P 6 HOH A 15 515 122 HOH HOH . P 6 HOH A 16 516 135 HOH HOH . P 6 HOH A 17 517 162 HOH HOH . P 6 HOH A 18 518 133 HOH HOH . P 6 HOH A 19 519 53 HOH HOH . P 6 HOH A 20 520 130 HOH HOH . P 6 HOH A 21 521 18 HOH HOH . P 6 HOH A 22 522 22 HOH HOH . P 6 HOH A 23 523 107 HOH HOH . P 6 HOH A 24 524 16 HOH HOH . P 6 HOH A 25 525 42 HOH HOH . P 6 HOH A 26 526 105 HOH HOH . P 6 HOH A 27 527 131 HOH HOH . P 6 HOH A 28 528 123 HOH HOH . P 6 HOH A 29 529 27 HOH HOH . P 6 HOH A 30 530 7 HOH HOH . P 6 HOH A 31 531 17 HOH HOH . P 6 HOH A 32 532 47 HOH HOH . P 6 HOH A 33 533 5 HOH HOH . P 6 HOH A 34 534 102 HOH HOH . P 6 HOH A 35 535 147 HOH HOH . P 6 HOH A 36 536 45 HOH HOH . P 6 HOH A 37 537 91 HOH HOH . P 6 HOH A 38 538 13 HOH HOH . P 6 HOH A 39 539 90 HOH HOH . P 6 HOH A 40 540 8 HOH HOH . P 6 HOH A 41 541 80 HOH HOH . P 6 HOH A 42 542 60 HOH HOH . P 6 HOH A 43 543 43 HOH HOH . P 6 HOH A 44 544 125 HOH HOH . P 6 HOH A 45 545 108 HOH HOH . P 6 HOH A 46 546 142 HOH HOH . P 6 HOH A 47 547 96 HOH HOH . P 6 HOH A 48 548 136 HOH HOH . P 6 HOH A 49 549 71 HOH HOH . P 6 HOH A 50 550 85 HOH HOH . P 6 HOH A 51 551 138 HOH HOH . P 6 HOH A 52 552 82 HOH HOH . P 6 HOH A 53 553 132 HOH HOH . P 6 HOH A 54 554 145 HOH HOH . P 6 HOH A 55 555 83 HOH HOH . P 6 HOH A 56 556 35 HOH HOH . P 6 HOH A 57 557 59 HOH HOH . P 6 HOH A 58 558 140 HOH HOH . P 6 HOH A 59 559 106 HOH HOH . P 6 HOH A 60 560 139 HOH HOH . P 6 HOH A 61 561 87 HOH HOH . P 6 HOH A 62 562 50 HOH HOH . P 6 HOH A 63 563 21 HOH HOH . P 6 HOH A 64 564 81 HOH HOH . P 6 HOH A 65 565 36 HOH HOH . P 6 HOH A 66 566 93 HOH HOH . P 6 HOH A 67 567 23 HOH HOH . P 6 HOH A 68 568 103 HOH HOH . P 6 HOH A 69 569 52 HOH HOH . P 6 HOH A 70 570 134 HOH HOH . P 6 HOH A 71 571 48 HOH HOH . P 6 HOH A 72 572 149 HOH HOH . P 6 HOH A 73 573 141 HOH HOH . P 6 HOH A 74 574 86 HOH HOH . P 6 HOH A 75 575 150 HOH HOH . P 6 HOH A 76 576 39 HOH HOH . P 6 HOH A 77 577 37 HOH HOH . P 6 HOH A 78 578 114 HOH HOH . P 6 HOH A 79 579 143 HOH HOH . P 6 HOH A 80 580 46 HOH HOH . P 6 HOH A 81 581 92 HOH HOH . P 6 HOH A 82 582 137 HOH HOH . P 6 HOH A 83 583 84 HOH HOH . Q 6 HOH B 1 501 127 HOH HOH . Q 6 HOH B 2 502 119 HOH HOH . Q 6 HOH B 3 503 56 HOH HOH . Q 6 HOH B 4 504 65 HOH HOH . Q 6 HOH B 5 505 9 HOH HOH . Q 6 HOH B 6 506 75 HOH HOH . Q 6 HOH B 7 507 26 HOH HOH . Q 6 HOH B 8 508 70 HOH HOH . Q 6 HOH B 9 509 109 HOH HOH . Q 6 HOH B 10 510 76 HOH HOH . Q 6 HOH B 11 511 67 HOH HOH . Q 6 HOH B 12 512 51 HOH HOH . Q 6 HOH B 13 513 3 HOH HOH . Q 6 HOH B 14 514 11 HOH HOH . Q 6 HOH B 15 515 12 HOH HOH . Q 6 HOH B 16 516 66 HOH HOH . Q 6 HOH B 17 517 1 HOH HOH . Q 6 HOH B 18 518 73 HOH HOH . Q 6 HOH B 19 519 41 HOH HOH . Q 6 HOH B 20 520 155 HOH HOH . Q 6 HOH B 21 521 126 HOH HOH . Q 6 HOH B 22 522 57 HOH HOH . Q 6 HOH B 23 523 113 HOH HOH . Q 6 HOH B 24 524 89 HOH HOH . Q 6 HOH B 25 525 153 HOH HOH . Q 6 HOH B 26 526 55 HOH HOH . Q 6 HOH B 27 527 121 HOH HOH . Q 6 HOH B 28 528 148 HOH HOH . Q 6 HOH B 29 529 68 HOH HOH . Q 6 HOH B 30 530 2 HOH HOH . Q 6 HOH B 31 531 4 HOH HOH . Q 6 HOH B 32 532 25 HOH HOH . Q 6 HOH B 33 533 40 HOH HOH . Q 6 HOH B 34 534 44 HOH HOH . Q 6 HOH B 35 535 62 HOH HOH . Q 6 HOH B 36 536 29 HOH HOH . Q 6 HOH B 37 537 152 HOH HOH . Q 6 HOH B 38 538 63 HOH HOH . Q 6 HOH B 39 539 128 HOH HOH . Q 6 HOH B 40 540 104 HOH HOH . Q 6 HOH B 41 541 156 HOH HOH . Q 6 HOH B 42 542 159 HOH HOH . Q 6 HOH B 43 543 120 HOH HOH . Q 6 HOH B 44 544 158 HOH HOH . Q 6 HOH B 45 545 101 HOH HOH . Q 6 HOH B 46 546 30 HOH HOH . Q 6 HOH B 47 547 33 HOH HOH . Q 6 HOH B 48 548 72 HOH HOH . Q 6 HOH B 49 549 98 HOH HOH . Q 6 HOH B 50 550 151 HOH HOH . Q 6 HOH B 51 551 15 HOH HOH . Q 6 HOH B 52 552 100 HOH HOH . Q 6 HOH B 53 553 117 HOH HOH . Q 6 HOH B 54 554 144 HOH HOH . Q 6 HOH B 55 555 61 HOH HOH . Q 6 HOH B 56 556 146 HOH HOH . Q 6 HOH B 57 557 64 HOH HOH . Q 6 HOH B 58 558 111 HOH HOH . Q 6 HOH B 59 559 49 HOH HOH . Q 6 HOH B 60 560 161 HOH HOH . Q 6 HOH B 61 561 160 HOH HOH . Q 6 HOH B 62 562 32 HOH HOH . Q 6 HOH B 63 563 115 HOH HOH . Q 6 HOH B 64 564 110 HOH HOH . Q 6 HOH B 65 565 99 HOH HOH . Q 6 HOH B 66 566 88 HOH HOH . Q 6 HOH B 67 567 157 HOH HOH . Q 6 HOH B 68 568 74 HOH HOH . Q 6 HOH B 69 569 118 HOH HOH . Q 6 HOH B 70 570 154 HOH HOH . Q 6 HOH B 71 571 78 HOH HOH . Q 6 HOH B 72 572 116 HOH HOH . Q 6 HOH B 73 573 31 HOH HOH . Q 6 HOH B 74 574 95 HOH HOH . Q 6 HOH B 75 575 97 HOH HOH . Q 6 HOH B 76 576 54 HOH HOH . Q 6 HOH B 77 577 94 HOH HOH . Q 6 HOH B 78 578 112 HOH HOH . Q 6 HOH B 79 579 14 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 PB ADP . . . I 4 45.291 -6.546 13.075 1 160.02 ? PB ADP 407 A 1 HETATM 2 O O1B ADP . . . I 4 45.988 -5.572 12.162 1 154.04 ? O1B ADP 407 A 1 HETATM 3 O O2B ADP . . . I 4 43.785 -6.444 13.032 1 156.2 ? O2B ADP 407 A 1 HETATM 4 O O3B ADP . . . I 4 45.796 -7.964 12.962 1 169.68 ? O3B ADP 407 A 1 HETATM 5 P PA ADP . . . I 4 45.768 -6.907 15.918 1 183.23 ? PA ADP 407 A 1 HETATM 6 O O1A ADP . . . I 4 44.847 -8.101 15.784 1 182.46 ? O1A ADP 407 A 1 HETATM 7 O O2A ADP . . . I 4 47.213 -7.155 16.296 1 192.07 ? O2A ADP 407 A 1 HETATM 8 O O3A ADP . . . I 4 45.73 -6.022 14.551 1 174.55 ? O3A ADP 407 A 1 HETATM 9 O O5' ADP . . . I 4 45.178 -5.891 17.037 1 151.04 ? O5' ADP 407 A 1 HETATM 10 C C5' ADP . . . I 4 43.782 -5.758 17.318 1 122.1 ? C5' ADP 407 A 1 HETATM 11 C C4' ADP . . . I 4 43.356 -4.311 17.094 1 104.92 ? C4' ADP 407 A 1 HETATM 12 O O4' ADP . . . I 4 41.934 -4.275 16.897 1 111.58 ? O4' ADP 407 A 1 HETATM 13 C C3' ADP . . . I 4 43.654 -3.43 18.296 1 95.86 ? C3' ADP 407 A 1 HETATM 14 O O3' ADP . . . I 4 44.278 -2.208 17.886 1 75.29 ? O3' ADP 407 A 1 HETATM 15 C C2' ADP . . . I 4 42.28 -3.243 18.929 1 96.1 ? C2' ADP 407 A 1 HETATM 16 O O2' ADP . . . I 4 42.18 -2.083 19.775 1 69.44 ? O2' ADP 407 A 1 HETATM 17 C C1' ADP . . . I 4 41.335 -3.268 17.713 1 98.04 ? C1' ADP 407 A 1 HETATM 18 N N9 ADP . . . I 4 39.879 -3.459 18.082 1 108.49 ? N9 ADP 407 A 1 HETATM 19 C C8 ADP . . . I 4 39.38 -4.388 18.935 1 108.65 ? C8 ADP 407 A 1 HETATM 20 N N7 ADP . . . I 4 38.026 -4.246 19.073 1 107.52 ? N7 ADP 407 A 1 HETATM 21 C C5 ADP . . . I 4 37.61 -3.21 18.315 1 101.49 ? C5 ADP 407 A 1 HETATM 22 C C6 ADP . . . I 4 36.313 -2.519 18.024 1 107.09 ? C6 ADP 407 A 1 HETATM 23 N N6 ADP . . . I 4 35.145 -2.923 18.577 1 107.82 ? N6 ADP 407 A 1 HETATM 24 N N1 ADP . . . I 4 36.313 -1.463 17.175 1 105.29 ? N1 ADP 407 A 1 HETATM 25 C C2 ADP . . . I 4 37.457 -1.038 16.606 1 108.58 ? C2 ADP 407 A 1 HETATM 26 N N3 ADP . . . I 4 38.661 -1.628 16.832 1 106.18 ? N3 ADP 407 A 1 HETATM 27 C C4 ADP . . . I 4 38.83 -2.694 17.665 1 100.16 ? C4 ADP 407 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #