data_8BR9 # _model_server_result.job_id j2egmminF-Vjm0oUGrpzjg _model_server_result.datetime_utc '2024-10-25 20:27:30' _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 8br9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 8BR9 # _exptl.entry_id 8BR9 _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 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 8BR9 _cell.length_a 140.464 _cell.length_b 38.642 _cell.length_c 43.528 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8BR9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall 'P 2 2ab' _symmetry.space_group_name_H-M 'P 21 21 2' # _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 _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 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 covale ? covale1 B N LYS 1 B LYS 1226 1_555 B C LYS 38 B LYS 2064 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 B SG CYS 6 B CYS 1231 1_555 D C7 RF6 . B RF6 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.875 ? covale ? covale3 B SG CYS 13 B CYS 1238 1_555 D C RF6 . B RF6 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.852 ? # _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 8BR9 _atom_sites.fract_transf_matrix[1][1] 0.007119 _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] 0.025879 _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] 0.022974 _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 ADP A 1 401 401 ADP ADP . D 4 RF6 B 1 2101 3262 RF6 DVP . E 5 HOH A 1 501 55 HOH HOH . E 5 HOH A 2 502 75 HOH HOH . E 5 HOH A 3 503 5 HOH HOH . E 5 HOH A 4 504 58 HOH HOH . E 5 HOH A 5 505 35 HOH HOH . E 5 HOH A 6 506 48 HOH HOH . E 5 HOH A 7 507 21 HOH HOH . E 5 HOH A 8 508 27 HOH HOH . E 5 HOH A 9 509 36 HOH HOH . E 5 HOH A 10 510 60 HOH HOH . E 5 HOH A 11 511 61 HOH HOH . E 5 HOH A 12 512 2 HOH HOH . E 5 HOH A 13 513 13 HOH HOH . E 5 HOH A 14 514 40 HOH HOH . E 5 HOH A 15 515 17 HOH HOH . E 5 HOH A 16 516 1 HOH HOH . E 5 HOH A 17 517 74 HOH HOH . E 5 HOH A 18 518 28 HOH HOH . E 5 HOH A 19 519 66 HOH HOH . E 5 HOH A 20 520 43 HOH HOH . E 5 HOH A 21 521 56 HOH HOH . E 5 HOH A 22 522 54 HOH HOH . E 5 HOH A 23 523 7 HOH HOH . E 5 HOH A 24 524 26 HOH HOH . E 5 HOH A 25 525 3 HOH HOH . E 5 HOH A 26 526 32 HOH HOH . E 5 HOH A 27 527 73 HOH HOH . E 5 HOH A 28 528 63 HOH HOH . E 5 HOH A 29 529 9 HOH HOH . E 5 HOH A 30 530 49 HOH HOH . E 5 HOH A 31 531 79 HOH HOH . E 5 HOH A 32 532 64 HOH HOH . E 5 HOH A 33 533 6 HOH HOH . E 5 HOH A 34 534 25 HOH HOH . E 5 HOH A 35 535 16 HOH HOH . E 5 HOH A 36 536 42 HOH HOH . E 5 HOH A 37 537 69 HOH HOH . E 5 HOH A 38 538 22 HOH HOH . E 5 HOH A 39 539 65 HOH HOH . E 5 HOH A 40 540 80 HOH HOH . E 5 HOH A 41 541 59 HOH HOH . E 5 HOH A 42 542 12 HOH HOH . E 5 HOH A 43 543 34 HOH HOH . E 5 HOH A 44 544 39 HOH HOH . E 5 HOH A 45 545 10 HOH HOH . E 5 HOH A 46 546 53 HOH HOH . E 5 HOH A 47 547 29 HOH HOH . E 5 HOH A 48 548 62 HOH HOH . E 5 HOH A 49 549 31 HOH HOH . E 5 HOH A 50 550 11 HOH HOH . E 5 HOH A 51 551 30 HOH HOH . E 5 HOH A 52 552 44 HOH HOH . E 5 HOH A 53 553 14 HOH HOH . E 5 HOH A 54 554 78 HOH HOH . E 5 HOH A 55 555 33 HOH HOH . E 5 HOH A 56 556 77 HOH HOH . E 5 HOH A 57 557 20 HOH HOH . E 5 HOH A 58 558 23 HOH HOH . E 5 HOH A 59 559 46 HOH HOH . E 5 HOH A 60 560 38 HOH HOH . E 5 HOH A 61 561 68 HOH HOH . E 5 HOH A 62 562 41 HOH HOH . E 5 HOH A 63 563 83 HOH HOH . E 5 HOH A 64 564 72 HOH HOH . E 5 HOH A 65 565 47 HOH HOH . E 5 HOH A 66 566 50 HOH HOH . E 5 HOH A 67 567 37 HOH HOH . E 5 HOH A 68 568 15 HOH HOH . E 5 HOH A 69 569 76 HOH HOH . F 5 HOH B 1 2201 4 HOH HOH . F 5 HOH B 2 2202 45 HOH HOH . F 5 HOH B 3 2203 18 HOH HOH . F 5 HOH B 4 2204 52 HOH HOH . F 5 HOH B 5 2205 8 HOH HOH . F 5 HOH B 6 2206 84 HOH HOH . F 5 HOH B 7 2207 81 HOH HOH . F 5 HOH B 8 2208 67 HOH HOH . F 5 HOH B 9 2209 51 HOH HOH . F 5 HOH B 10 2210 57 HOH HOH . F 5 HOH B 11 2211 70 HOH HOH . F 5 HOH B 12 2212 19 HOH HOH . F 5 HOH B 13 2213 82 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 . . . C 3 19.921 -37.981 -3.993 1 128.96 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 3 19.014 -36.796 -3.672 1 85.54 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 3 19.172 -39.21 -3.525 1 94.56 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 3 21.32 -37.818 -3.359 1 90.29 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 3 20.246 -36.867 -6.633 1 67.44 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 3 19.223 -35.82 -6.465 1 46.67 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 3 21.657 -36.325 -6.371 1 77.22 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 3 19.984 -38.041 -5.585 1 91.51 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 3 20.203 -37.38 -8.171 1 95.94 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 3 21.162 -38.26 -8.788 1 91.51 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 3 20.927 -38.239 -10.278 1 92.6 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 3 21.236 -36.927 -10.789 1 88.34 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 3 21.806 -39.199 -11.068 1 104.43 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 3 21.17 -40.473 -11.125 1 105.6 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 3 21.926 -38.517 -12.438 1 99.92 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 3 20.931 -38.945 -13.363 1 100.03 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 3 21.744 -37.024 -12.109 1 92.67 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 3 22.963 -36.221 -12.204 1 87.48 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 3 23.916 -36.04 -11.235 1 82.2 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 3 24.92 -35.282 -11.605 1 78.08 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 3 24.607 -34.937 -12.912 1 81.35 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 3 25.27 -34.137 -13.869 1 77.35 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 3 26.462 -33.568 -13.667 1 77.26 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 3 24.666 -33.963 -15.069 1 73.18 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 3 23.492 -34.566 -15.293 1 75.92 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 3 22.786 -35.355 -14.476 1 80.62 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 3 23.4 -35.501 -13.292 1 82.82 ? C4 ADP 401 A 1 HETATM 28 H "H5'1" ADP . . . C 3 21.086 -39.263 -8.371 1 109.93 ? "H5'1" ADP 401 A 1 HETATM 29 H "H5'2" ADP . . . C 3 22.125 -37.844 -8.496 1 109.93 ? "H5'2" ADP 401 A 1 HETATM 30 H H4' ADP . . . C 3 19.866 -38.361 -10.492 1 111.23 ? H4' ADP 401 A 1 HETATM 31 H H3' ADP . . . C 3 22.777 -39.32 -10.59 1 125.44 ? H3' ADP 401 A 1 HETATM 32 H HO3' ADP . . . C 3 21.888 -41.154 -11.036 1 126.83 ? HO3' ADP 401 A 1 HETATM 33 H H2' ADP . . . C 3 22.914 -38.703 -12.858 1 120.02 ? H2' ADP 401 A 1 HETATM 34 H HO2' ADP . . . C 3 21.091 -39.918 -13.479 1 120.15 ? HO2' ADP 401 A 1 HETATM 35 H H1' ADP . . . C 3 21.009 -36.571 -12.771 1 111.32 ? H1' ADP 401 A 1 HETATM 36 H H8 ADP . . . C 3 23.846 -36.485 -10.243 1 98.75 ? H8 ADP 401 A 1 HETATM 37 H HN61 ADP . . . C 3 26.899 -33 -14.386 1 92.82 ? HN61 ADP 401 A 1 HETATM 38 H HN62 ADP . . . C 3 26.94 -33.708 -12.782 1 92.82 ? HN62 ADP 401 A 1 HETATM 39 H H2 ADP . . . C 3 23.075 -34.374 -16.28 1 91.21 ? H2 ADP 401 A 1 # _model_server_stats.io_time_ms 73 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 354 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 39 #