data_6B89 # _model_server_result.job_id I2WlikslvzrbglJJixOkNg _model_server_result.datetime_utc '2024-11-04 22:19:05' _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 6b89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":401}' # _entry.id 6B89 # _exptl.entry_id 6B89 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 91.52 _cell.angle_gamma 90 _cell.entry_id 6B89 _cell.length_a 190.319 _cell.length_b 35.1 _cell.length_c 63.05 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6B89 _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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 2 C N N ? 2 F 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 metalc ? metalc1 A OG1 THR 42 A THR 43 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 A OE1 GLN 84 A GLN 85 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc3 C O2B ADP . A ADP 401 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.053 ? metalc ? metalc4 D MG MG . A MG 402 1_555 I O HOH . A HOH 521 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc5 D MG MG . A MG 402 1_555 I O HOH . A HOH 523 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc6 D MG MG . A MG 402 1_555 I O HOH . A HOH 530 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.993 ? metalc ? metalc7 B OG1 THR 42 B THR 43 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc8 B OE1 GLN 84 B GLN 85 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc9 F O1B ADP . B ADP 401 1_555 G MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc10 G MG MG . B MG 402 1_555 J O HOH . B HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.161 ? metalc ? metalc11 G MG MG . B MG 402 1_555 J O HOH . B HOH 518 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc12 G MG MG . B MG 402 1_555 J O HOH . B HOH 520 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? # _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 6B89 _atom_sites.fract_transf_matrix[1][1] 0.005254 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000139 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.02849 _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] 0.015866 _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 ADP A 1 401 401 ADP ADP . D 3 MG A 1 402 403 MG MG . E 4 NOV A 1 403 2 NOV NOV . F 2 ADP B 1 401 401 ADP ADP . G 3 MG B 1 402 403 MG MG . H 4 NOV B 1 403 1 NOV NOV . I 5 HOH A 1 501 82 HOH HOH . I 5 HOH A 2 502 78 HOH HOH . I 5 HOH A 3 503 73 HOH HOH . I 5 HOH A 4 504 95 HOH HOH . I 5 HOH A 5 505 93 HOH HOH . I 5 HOH A 6 506 11 HOH HOH . I 5 HOH A 7 507 76 HOH HOH . I 5 HOH A 8 508 13 HOH HOH . I 5 HOH A 9 509 65 HOH HOH . I 5 HOH A 10 510 27 HOH HOH . I 5 HOH A 11 511 97 HOH HOH . I 5 HOH A 12 512 64 HOH HOH . I 5 HOH A 13 513 7 HOH HOH . I 5 HOH A 14 514 63 HOH HOH . I 5 HOH A 15 515 49 HOH HOH . I 5 HOH A 16 516 12 HOH HOH . I 5 HOH A 17 517 3 HOH HOH . I 5 HOH A 18 518 14 HOH HOH . I 5 HOH A 19 519 55 HOH HOH . I 5 HOH A 20 520 21 HOH HOH . I 5 HOH A 21 521 62 HOH HOH . I 5 HOH A 22 522 92 HOH HOH . I 5 HOH A 23 523 101 HOH HOH . I 5 HOH A 24 524 2 HOH HOH . I 5 HOH A 25 525 69 HOH HOH . I 5 HOH A 26 526 68 HOH HOH . I 5 HOH A 27 527 5 HOH HOH . I 5 HOH A 28 528 34 HOH HOH . I 5 HOH A 29 529 23 HOH HOH . I 5 HOH A 30 530 61 HOH HOH . I 5 HOH A 31 531 81 HOH HOH . I 5 HOH A 32 532 17 HOH HOH . I 5 HOH A 33 533 90 HOH HOH . I 5 HOH A 34 534 86 HOH HOH . I 5 HOH A 35 535 91 HOH HOH . I 5 HOH A 36 536 83 HOH HOH . I 5 HOH A 37 537 46 HOH HOH . I 5 HOH A 38 538 33 HOH HOH . I 5 HOH A 39 539 84 HOH HOH . I 5 HOH A 40 540 52 HOH HOH . I 5 HOH A 41 541 98 HOH HOH . I 5 HOH A 42 542 89 HOH HOH . I 5 HOH A 43 543 85 HOH HOH . I 5 HOH A 44 544 9 HOH HOH . I 5 HOH A 45 545 29 HOH HOH . I 5 HOH A 46 546 40 HOH HOH . I 5 HOH A 47 547 77 HOH HOH . I 5 HOH A 48 548 87 HOH HOH . I 5 HOH A 49 549 80 HOH HOH . I 5 HOH A 50 550 24 HOH HOH . I 5 HOH A 51 551 4 HOH HOH . I 5 HOH A 52 552 72 HOH HOH . I 5 HOH A 53 553 70 HOH HOH . I 5 HOH A 54 554 71 HOH HOH . I 5 HOH A 55 555 47 HOH HOH . I 5 HOH A 56 556 96 HOH HOH . I 5 HOH A 57 557 67 HOH HOH . I 5 HOH A 58 558 32 HOH HOH . J 5 HOH B 1 501 16 HOH HOH . J 5 HOH B 2 502 38 HOH HOH . J 5 HOH B 3 503 99 HOH HOH . J 5 HOH B 4 504 20 HOH HOH . J 5 HOH B 5 505 18 HOH HOH . J 5 HOH B 6 506 42 HOH HOH . J 5 HOH B 7 507 8 HOH HOH . J 5 HOH B 8 508 28 HOH HOH . J 5 HOH B 9 509 58 HOH HOH . J 5 HOH B 10 510 43 HOH HOH . J 5 HOH B 11 511 54 HOH HOH . J 5 HOH B 12 512 19 HOH HOH . J 5 HOH B 13 513 31 HOH HOH . J 5 HOH B 14 514 88 HOH HOH . J 5 HOH B 15 515 37 HOH HOH . J 5 HOH B 16 516 15 HOH HOH . J 5 HOH B 17 517 94 HOH HOH . J 5 HOH B 18 518 59 HOH HOH . J 5 HOH B 19 519 10 HOH HOH . J 5 HOH B 20 520 60 HOH HOH . J 5 HOH B 21 521 6 HOH HOH . J 5 HOH B 22 522 26 HOH HOH . J 5 HOH B 23 523 41 HOH HOH . J 5 HOH B 24 524 74 HOH HOH . J 5 HOH B 25 525 50 HOH HOH . J 5 HOH B 26 526 100 HOH HOH . J 5 HOH B 27 527 48 HOH HOH . J 5 HOH B 28 528 36 HOH HOH . J 5 HOH B 29 529 56 HOH HOH . J 5 HOH B 30 530 51 HOH HOH . J 5 HOH B 31 531 35 HOH HOH . J 5 HOH B 32 532 22 HOH HOH . J 5 HOH B 33 533 25 HOH HOH . J 5 HOH B 34 534 30 HOH HOH . J 5 HOH B 35 535 1 HOH HOH . J 5 HOH B 36 536 39 HOH HOH . J 5 HOH B 37 537 44 HOH HOH . J 5 HOH B 38 538 75 HOH HOH . J 5 HOH B 39 539 45 HOH HOH . J 5 HOH B 40 540 57 HOH HOH . J 5 HOH B 41 541 53 HOH HOH . J 5 HOH B 42 542 79 HOH HOH . J 5 HOH B 43 543 66 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 2 -38.366 8.856 15.169 1 10.16 ? PB ADP 401 A 1 HETATM 2 O O1B ADP . . . C 2 -39.204 8.551 13.948 1 9.82 ? O1B ADP 401 A 1 HETATM 3 O O2B ADP . . . C 2 -37.448 7.731 15.593 1 7.43 ? O2B ADP 401 A 1 HETATM 4 O O3B ADP . . . C 2 -37.72 10.246 15.013 1 7.72 ? O3B ADP 401 A 1 HETATM 5 P PA ADP . . . C 2 -39.728 8.35 17.691 1 11.77 ? PA ADP 401 A 1 HETATM 6 O O1A ADP . . . C 2 -40.2 6.965 17.456 1 8.89 ? O1A ADP 401 A 1 HETATM 7 O O2A ADP . . . C 2 -38.451 8.44 18.536 1 11.67 ? O2A ADP 401 A 1 HETATM 8 O O3A ADP . . . C 2 -39.397 9.021 16.334 1 7.65 ? O3A ADP 401 A 1 HETATM 9 O O5' ADP . . . C 2 -40.804 9.293 18.356 1 12.9 ? O5' ADP 401 A 1 HETATM 10 C C5' ADP . . . C 2 -42.162 9.343 17.869 1 12.61 ? C5' ADP 401 A 1 HETATM 11 C C4' ADP . . . C 2 -42.911 10.394 18.65 1 13.59 ? C4' ADP 401 A 1 HETATM 12 O O4' ADP . . . C 2 -43.189 9.905 19.987 1 15.01 ? O4' ADP 401 A 1 HETATM 13 C C3' ADP . . . C 2 -42.171 11.712 18.846 1 15.74 ? C3' ADP 401 A 1 HETATM 14 O O3' ADP . . . C 2 -43.133 12.758 18.878 1 16.68 ? O3' ADP 401 A 1 HETATM 15 C C2' ADP . . . C 2 -41.505 11.508 20.21 1 17.35 ? C2' ADP 401 A 1 HETATM 16 O O2' ADP . . . C 2 -41.176 12.717 20.885 1 19.48 ? O2' ADP 401 A 1 HETATM 17 C C1' ADP . . . C 2 -42.628 10.786 20.94 1 15.55 ? C1' ADP 401 A 1 HETATM 18 N N9 ADP . . . C 2 -42.201 10.004 22.09 1 16.11 ? N9 ADP 401 A 1 HETATM 19 C C8 ADP . . . C 2 -41.212 9.059 22.132 1 15.75 ? C8 ADP 401 A 1 HETATM 20 N N7 ADP . . . C 2 -41.051 8.505 23.311 1 16.68 ? N7 ADP 401 A 1 HETATM 21 C C5 ADP . . . C 2 -42.002 9.135 24.1 1 17.07 ? C5 ADP 401 A 1 HETATM 22 C C6 ADP . . . C 2 -42.358 8.993 25.455 1 18.02 ? C6 ADP 401 A 1 HETATM 23 N N6 ADP . . . C 2 -41.764 8.143 26.297 1 18.32 ? N6 ADP 401 A 1 HETATM 24 N N1 ADP . . . C 2 -43.36 9.77 25.924 1 17.77 ? N1 ADP 401 A 1 HETATM 25 C C2 ADP . . . C 2 -43.961 10.623 25.091 1 17.17 ? C2 ADP 401 A 1 HETATM 26 N N3 ADP . . . C 2 -43.717 10.836 23.797 1 17.61 ? N3 ADP 401 A 1 HETATM 27 C C4 ADP . . . C 2 -42.72 10.058 23.359 1 16.43 ? C4 ADP 401 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 16 _model_server_stats.element_count 27 #