data_4N09 # _model_server_result.job_id hHCeV-DhFnCiAuIYWMNRoQ _model_server_result.datetime_utc '2024-11-04 22:34:24' _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 4n09 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":402}' # _entry.id 4N09 # _exptl.entry_id 4N09 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.78 _cell.angle_gamma 90 _cell.entry_id 4N09 _cell.length_a 184.53 _cell.length_b 90.22 _cell.length_c 98.04 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4N09 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,F,G,O 1 1 B,H,I,J,P 2 1 C,K,L,Q 3 1 D,M,N,R 4 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 I N N ? 3 L N N ? 3 N N 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 disulf ? disulf1 A SG CYS 242 A CYS 239 1_555 D SG CYS 242 D CYS 239 4_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? disulf ? disulf2 B SG CYS 242 B CYS 239 1_555 C SG CYS 242 C CYS 239 2_556 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? # _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 ? # _atom_sites.entry_id 4N09 _atom_sites.fract_transf_matrix[1][1] 0.005419 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001329 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011084 _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] 0.010502 _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 E 2 ADN A 1 401 1 ADN ADN . F 3 ADP A 1 402 2 ADP ADP . G 4 EDO A 1 403 2 EDO EDO . H 2 ADN B 1 401 3 ADN ADN . I 3 ADP B 1 402 4 ADP ADP . J 4 EDO B 1 403 1 EDO EDO . K 2 ADN C 1 401 5 ADN ADN . L 3 ADP C 1 402 6 ADP ADP . M 2 ADN D 1 401 7 ADN ADN . N 3 ADP D 1 402 8 ADP ADP . O 5 HOH A 1 501 23 HOH HOH . O 5 HOH A 2 502 24 HOH HOH . O 5 HOH A 3 503 25 HOH HOH . O 5 HOH A 4 504 26 HOH HOH . O 5 HOH A 5 505 27 HOH HOH . O 5 HOH A 6 506 28 HOH HOH . O 5 HOH A 7 507 29 HOH HOH . O 5 HOH A 8 508 30 HOH HOH . O 5 HOH A 9 509 31 HOH HOH . O 5 HOH A 10 510 32 HOH HOH . O 5 HOH A 11 511 33 HOH HOH . O 5 HOH A 12 512 34 HOH HOH . O 5 HOH A 13 513 35 HOH HOH . O 5 HOH A 14 514 37 HOH HOH . O 5 HOH A 15 515 72 HOH HOH . O 5 HOH A 16 516 73 HOH HOH . O 5 HOH A 17 517 81 HOH HOH . O 5 HOH A 18 518 96 HOH HOH . O 5 HOH A 19 519 104 HOH HOH . O 5 HOH A 20 520 106 HOH HOH . O 5 HOH A 21 521 110 HOH HOH . O 5 HOH A 22 522 111 HOH HOH . O 5 HOH A 23 523 112 HOH HOH . O 5 HOH A 24 524 113 HOH HOH . O 5 HOH A 25 525 123 HOH HOH . O 5 HOH A 26 526 126 HOH HOH . O 5 HOH A 27 527 130 HOH HOH . O 5 HOH A 28 528 136 HOH HOH . O 5 HOH A 29 529 137 HOH HOH . O 5 HOH A 30 530 141 HOH HOH . P 5 HOH B 1 501 1 HOH HOH . P 5 HOH B 2 502 2 HOH HOH . P 5 HOH B 3 503 3 HOH HOH . P 5 HOH B 4 504 4 HOH HOH . P 5 HOH B 5 505 5 HOH HOH . P 5 HOH B 6 506 6 HOH HOH . P 5 HOH B 7 507 7 HOH HOH . P 5 HOH B 8 508 8 HOH HOH . P 5 HOH B 9 509 9 HOH HOH . P 5 HOH B 10 510 10 HOH HOH . P 5 HOH B 11 511 11 HOH HOH . P 5 HOH B 12 512 12 HOH HOH . P 5 HOH B 13 513 13 HOH HOH . P 5 HOH B 14 514 14 HOH HOH . P 5 HOH B 15 515 15 HOH HOH . P 5 HOH B 16 516 16 HOH HOH . P 5 HOH B 17 517 17 HOH HOH . P 5 HOH B 18 518 18 HOH HOH . P 5 HOH B 19 519 19 HOH HOH . P 5 HOH B 20 520 20 HOH HOH . P 5 HOH B 21 521 21 HOH HOH . P 5 HOH B 22 522 22 HOH HOH . P 5 HOH B 23 523 38 HOH HOH . P 5 HOH B 24 524 39 HOH HOH . P 5 HOH B 25 525 40 HOH HOH . P 5 HOH B 26 526 41 HOH HOH . P 5 HOH B 27 527 42 HOH HOH . P 5 HOH B 28 528 43 HOH HOH . P 5 HOH B 29 529 44 HOH HOH . P 5 HOH B 30 530 45 HOH HOH . P 5 HOH B 31 531 46 HOH HOH . P 5 HOH B 32 532 47 HOH HOH . P 5 HOH B 33 533 48 HOH HOH . P 5 HOH B 34 534 49 HOH HOH . P 5 HOH B 35 535 71 HOH HOH . P 5 HOH B 36 536 76 HOH HOH . P 5 HOH B 37 537 78 HOH HOH . P 5 HOH B 38 538 80 HOH HOH . P 5 HOH B 39 539 87 HOH HOH . P 5 HOH B 40 540 88 HOH HOH . P 5 HOH B 41 541 90 HOH HOH . P 5 HOH B 42 542 92 HOH HOH . P 5 HOH B 43 543 93 HOH HOH . P 5 HOH B 44 544 95 HOH HOH . P 5 HOH B 45 545 97 HOH HOH . P 5 HOH B 46 546 98 HOH HOH . P 5 HOH B 47 547 101 HOH HOH . P 5 HOH B 48 548 102 HOH HOH . P 5 HOH B 49 549 103 HOH HOH . P 5 HOH B 50 550 116 HOH HOH . P 5 HOH B 51 551 118 HOH HOH . P 5 HOH B 52 552 122 HOH HOH . P 5 HOH B 53 553 125 HOH HOH . P 5 HOH B 54 554 127 HOH HOH . P 5 HOH B 55 555 128 HOH HOH . P 5 HOH B 56 556 129 HOH HOH . P 5 HOH B 57 557 131 HOH HOH . P 5 HOH B 58 558 132 HOH HOH . P 5 HOH B 59 559 134 HOH HOH . P 5 HOH B 60 560 135 HOH HOH . P 5 HOH B 61 561 138 HOH HOH . P 5 HOH B 62 562 139 HOH HOH . P 5 HOH B 63 563 142 HOH HOH . P 5 HOH B 64 564 143 HOH HOH . Q 5 HOH C 1 501 50 HOH HOH . Q 5 HOH C 2 502 51 HOH HOH . Q 5 HOH C 3 503 52 HOH HOH . Q 5 HOH C 4 504 53 HOH HOH . Q 5 HOH C 5 505 54 HOH HOH . Q 5 HOH C 6 506 55 HOH HOH . Q 5 HOH C 7 507 57 HOH HOH . Q 5 HOH C 8 508 58 HOH HOH . Q 5 HOH C 9 509 59 HOH HOH . Q 5 HOH C 10 510 60 HOH HOH . Q 5 HOH C 11 511 61 HOH HOH . Q 5 HOH C 12 512 62 HOH HOH . Q 5 HOH C 13 513 63 HOH HOH . Q 5 HOH C 14 514 64 HOH HOH . Q 5 HOH C 15 515 65 HOH HOH . Q 5 HOH C 16 516 75 HOH HOH . Q 5 HOH C 17 517 77 HOH HOH . Q 5 HOH C 18 518 79 HOH HOH . Q 5 HOH C 19 519 82 HOH HOH . Q 5 HOH C 20 520 84 HOH HOH . Q 5 HOH C 21 521 85 HOH HOH . Q 5 HOH C 22 522 86 HOH HOH . Q 5 HOH C 23 523 91 HOH HOH . Q 5 HOH C 24 524 94 HOH HOH . Q 5 HOH C 25 525 99 HOH HOH . Q 5 HOH C 26 526 108 HOH HOH . Q 5 HOH C 27 527 109 HOH HOH . Q 5 HOH C 28 528 117 HOH HOH . Q 5 HOH C 29 529 119 HOH HOH . Q 5 HOH C 30 530 120 HOH HOH . Q 5 HOH C 31 531 121 HOH HOH . Q 5 HOH C 32 532 124 HOH HOH . Q 5 HOH C 33 533 133 HOH HOH . Q 5 HOH C 34 534 145 HOH HOH . Q 5 HOH C 35 535 146 HOH HOH . Q 5 HOH C 36 536 147 HOH HOH . Q 5 HOH C 37 537 148 HOH HOH . Q 5 HOH C 38 538 149 HOH HOH . Q 5 HOH C 39 539 150 HOH HOH . Q 5 HOH C 40 540 151 HOH HOH . R 5 HOH D 1 501 66 HOH HOH . R 5 HOH D 2 502 67 HOH HOH . R 5 HOH D 3 503 68 HOH HOH . R 5 HOH D 4 504 69 HOH HOH . R 5 HOH D 5 505 70 HOH HOH . R 5 HOH D 6 506 83 HOH HOH . R 5 HOH D 7 507 89 HOH HOH . R 5 HOH D 8 508 100 HOH HOH . R 5 HOH D 9 509 105 HOH HOH . R 5 HOH D 10 510 107 HOH HOH . R 5 HOH D 11 511 114 HOH HOH . R 5 HOH D 12 512 115 HOH HOH . R 5 HOH D 13 513 140 HOH HOH . R 5 HOH D 14 514 144 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 . . . F 3 49.82 13.626 30.647 1 79.85 ? PB ADP 402 A 1 HETATM 2 O O1B ADP . . . F 3 51.22 13.735 30.018 1 72.53 ? O1B ADP 402 A 1 HETATM 3 O O2B ADP . . . F 3 48.64 13.843 29.699 1 66.59 ? O2B ADP 402 A 1 HETATM 4 O O3B ADP . . . F 3 49.58 12.417 31.542 1 76.61 ? O3B ADP 402 A 1 HETATM 5 P PA ADP . . . F 3 49.327 14.945 33.138 1 52.59 ? PA ADP 402 A 1 HETATM 6 O O1A ADP . . . F 3 48.361 13.766 33.264 1 60.01 ? O1A ADP 402 A 1 HETATM 7 O O2A ADP . . . F 3 50.459 15.146 34.147 1 54.79 ? O2A ADP 402 A 1 HETATM 8 O O3A ADP . . . F 3 49.907 14.914 31.637 1 61.22 ? O3A ADP 402 A 1 HETATM 9 O O5' ADP . . . F 3 48.411 16.276 33.156 1 48.86 ? O5' ADP 402 A 1 HETATM 10 C C5' ADP . . . F 3 48.785 17.487 32.542 1 39.35 ? C5' ADP 402 A 1 HETATM 11 C C4' ADP . . . F 3 47.984 18.522 33.253 1 36.05 ? C4' ADP 402 A 1 HETATM 12 O O4' ADP . . . F 3 46.615 18.294 32.965 1 33.44 ? O4' ADP 402 A 1 HETATM 13 C C3' ADP . . . F 3 48.142 18.466 34.769 1 35.36 ? C3' ADP 402 A 1 HETATM 14 O O3' ADP . . . F 3 49.284 19.201 35.229 1 34.25 ? O3' ADP 402 A 1 HETATM 15 C C2' ADP . . . F 3 46.818 19.049 35.188 1 32.67 ? C2' ADP 402 A 1 HETATM 16 O O2' ADP . . . F 3 46.867 20.444 35.083 1 29.36 ? O2' ADP 402 A 1 HETATM 17 C C1' ADP . . . F 3 45.845 18.59 34.129 1 34.29 ? C1' ADP 402 A 1 HETATM 18 N N9 ADP . . . F 3 45.138 17.355 34.583 1 38.69 ? N9 ADP 402 A 1 HETATM 19 C C8 ADP . . . F 3 45.448 16.111 34.188 1 38.08 ? C8 ADP 402 A 1 HETATM 20 N N7 ADP . . . F 3 44.623 15.226 34.772 1 41.69 ? N7 ADP 402 A 1 HETATM 21 C C5 ADP . . . F 3 43.768 15.898 35.544 1 38.1 ? C5 ADP 402 A 1 HETATM 22 C C6 ADP . . . F 3 42.643 15.553 36.419 1 40.61 ? C6 ADP 402 A 1 HETATM 23 N N6 ADP . . . F 3 42.278 14.265 36.556 1 40.73 ? N6 ADP 402 A 1 HETATM 24 N N1 ADP . . . F 3 42 16.545 37.077 1 42.53 ? N1 ADP 402 A 1 HETATM 25 C C2 ADP . . . F 3 42.36 17.826 36.932 1 38.71 ? C2 ADP 402 A 1 HETATM 26 N N3 ADP . . . F 3 43.367 18.182 36.131 1 39.46 ? N3 ADP 402 A 1 HETATM 27 C C4 ADP . . . F 3 44.102 17.293 35.426 1 37.15 ? C4 ADP 402 A 1 # _model_server_stats.io_time_ms 62 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 239 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #