data_6R4B # _model_server_result.job_id 1Yu74McUHUt8Wte2-6MAdQ _model_server_result.datetime_utc '2024-10-10 09:26:43' _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 6r4b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":501}' # _entry.id 6R4B # _exptl.entry_id 6R4B _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 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 6R4B _cell.length_a 81.851 _cell.length_b 81.851 _cell.length_c 174.371 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6R4B _symmetry.cell_setting ? _symmetry.Int_Tables_number 178 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 61 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 _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 2 _struct_asym.id B _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 A C THR 169 A THR 287 1_555 A N TPO 170 A TPO 288 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A C TPO 170 A TPO 288 1_555 A N LEU 171 A LEU 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? metalc ? metalc1 A OD1 ASN 143 A ASN 261 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc2 A OD2 ASP 156 A ASP 274 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc3 A OD1 ASP 156 A ASP 274 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.594 ? metalc ? metalc4 B O3B ADP . A ADP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.973 ? metalc ? metalc5 B O2A ADP . A ADP 501 1_555 C MG MG . A MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.14 ? metalc ? metalc6 B O1B ADP . A ADP 501 1_555 D MG MG . A MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc7 C MG MG . A MG 502 1_555 J O HOH . A HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.813 ? metalc ? metalc8 C MG MG . A MG 502 1_555 J O HOH . A HOH 632 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.006 ? metalc ? metalc9 D MG MG . A MG 503 1_555 J O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.869 ? metalc ? metalc10 D MG MG . A MG 503 1_555 J O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.872 ? # _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 6R4B _atom_sites.fract_transf_matrix[1][1] 0.012217 _atom_sites.fract_transf_matrix[1][2] 0.007054 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014107 _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] 0.005735 _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 B 2 ADP A 1 501 1392 ADP ADP . C 3 MG A 1 502 1395 MG MG . D 3 MG A 1 503 1396 MG MG . E 4 CL A 1 504 1397 CL CL . F 4 CL A 1 505 1398 CL CL . G 4 CL A 1 506 1399 CL CL . H 4 CL A 1 507 1400 CL CL . I 5 JSN A 1 508 1 JSN LIG . J 6 HOH A 1 601 53 HOH HOH . J 6 HOH A 2 602 34 HOH HOH . J 6 HOH A 3 603 22 HOH HOH . J 6 HOH A 4 604 17 HOH HOH . J 6 HOH A 5 605 19 HOH HOH . J 6 HOH A 6 606 30 HOH HOH . J 6 HOH A 7 607 9 HOH HOH . J 6 HOH A 8 608 23 HOH HOH . J 6 HOH A 9 609 40 HOH HOH . J 6 HOH A 10 610 24 HOH HOH . J 6 HOH A 11 611 43 HOH HOH . J 6 HOH A 12 612 38 HOH HOH . J 6 HOH A 13 613 11 HOH HOH . J 6 HOH A 14 614 6 HOH HOH . J 6 HOH A 15 615 26 HOH HOH . J 6 HOH A 16 616 13 HOH HOH . J 6 HOH A 17 617 56 HOH HOH . J 6 HOH A 18 618 54 HOH HOH . J 6 HOH A 19 619 20 HOH HOH . J 6 HOH A 20 620 35 HOH HOH . J 6 HOH A 21 621 12 HOH HOH . J 6 HOH A 22 622 44 HOH HOH . J 6 HOH A 23 623 15 HOH HOH . J 6 HOH A 24 624 8 HOH HOH . J 6 HOH A 25 625 27 HOH HOH . J 6 HOH A 26 626 1 HOH HOH . J 6 HOH A 27 627 55 HOH HOH . J 6 HOH A 28 628 18 HOH HOH . J 6 HOH A 29 629 14 HOH HOH . J 6 HOH A 30 630 7 HOH HOH . J 6 HOH A 31 631 32 HOH HOH . J 6 HOH A 32 632 52 HOH HOH . J 6 HOH A 33 633 5 HOH HOH . J 6 HOH A 34 634 60 HOH HOH . J 6 HOH A 35 635 36 HOH HOH . J 6 HOH A 36 636 28 HOH HOH . J 6 HOH A 37 637 16 HOH HOH . J 6 HOH A 38 638 58 HOH HOH . J 6 HOH A 39 639 2 HOH HOH . J 6 HOH A 40 640 49 HOH HOH . J 6 HOH A 41 641 37 HOH HOH . J 6 HOH A 42 642 4 HOH HOH . J 6 HOH A 43 643 21 HOH HOH . J 6 HOH A 44 644 25 HOH HOH . J 6 HOH A 45 645 59 HOH HOH . J 6 HOH A 46 646 42 HOH HOH . J 6 HOH A 47 647 45 HOH HOH . J 6 HOH A 48 648 10 HOH HOH . J 6 HOH A 49 649 41 HOH HOH . J 6 HOH A 50 650 39 HOH HOH . J 6 HOH A 51 651 51 HOH HOH . J 6 HOH A 52 652 3 HOH HOH . J 6 HOH A 53 653 31 HOH HOH . J 6 HOH A 54 654 48 HOH HOH . J 6 HOH A 55 655 57 HOH HOH . J 6 HOH A 56 656 33 HOH HOH . J 6 HOH A 57 657 29 HOH HOH . J 6 HOH A 58 658 47 HOH HOH . J 6 HOH A 59 659 46 HOH HOH . J 6 HOH A 60 660 61 HOH HOH . J 6 HOH A 61 661 50 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 . . . B 2 -12.035 23.928 -6 1 44.37 ? PB ADP 501 A 1 HETATM 2 O O1B ADP . . . B 2 -12.649 23.563 -7.328 1 46.49 ? O1B ADP 501 A 1 HETATM 3 O O2B ADP . . . B 2 -11.501 22.723 -5.259 1 43.11 ? O2B ADP 501 A 1 HETATM 4 O O3B ADP . . . B 2 -12.847 24.905 -5.166 1 45.47 ? O3B ADP 501 A 1 HETATM 5 P PA ADP . . . B 2 -10.53 26.2 -7.025 1 38.06 ? PA ADP 501 A 1 HETATM 6 O O1A ADP . . . B 2 -10.219 26.175 -8.499 1 48.49 ? O1A ADP 501 A 1 HETATM 7 O O2A ADP . . . B 2 -11.604 27.141 -6.55 1 39.6 ? O2A ADP 501 A 1 HETATM 8 O O3A ADP . . . B 2 -10.686 24.758 -6.368 1 38.21 ? O3A ADP 501 A 1 HETATM 9 O O5' ADP . . . B 2 -9.136 26.682 -6.349 1 43.67 ? O5' ADP 501 A 1 HETATM 10 C C5' ADP . . . B 2 -8.896 26.537 -4.943 1 43.47 ? C5' ADP 501 A 1 HETATM 11 C C4' ADP . . . B 2 -8.164 27.783 -4.397 1 38.09 ? C4' ADP 501 A 1 HETATM 12 O O4' ADP . . . B 2 -6.853 27.959 -4.971 1 37.56 ? O4' ADP 501 A 1 HETATM 13 C C3' ADP . . . B 2 -8.895 29.093 -4.688 1 42.57 ? C3' ADP 501 A 1 HETATM 14 O O3' ADP . . . B 2 -9.851 29.395 -3.673 1 44.56 ? O3' ADP 501 A 1 HETATM 15 C C2' ADP . . . B 2 -7.769 30.115 -4.687 1 40.29 ? C2' ADP 501 A 1 HETATM 16 O O2' ADP . . . B 2 -7.406 30.412 -3.33 1 39.18 ? O2' ADP 501 A 1 HETATM 17 C C1' ADP . . . B 2 -6.599 29.336 -5.274 1 37.1 ? C1' ADP 501 A 1 HETATM 18 N N9 ADP . . . B 2 -6.551 29.504 -6.743 1 38.61 ? N9 ADP 501 A 1 HETATM 19 C C8 ADP . . . B 2 -7.265 28.788 -7.648 1 43.93 ? C8 ADP 501 A 1 HETATM 20 N N7 ADP . . . B 2 -6.993 29.184 -8.912 1 39.46 ? N7 ADP 501 A 1 HETATM 21 C C5 ADP . . . B 2 -6.082 30.186 -8.83 1 38.41 ? C5 ADP 501 A 1 HETATM 22 C C6 ADP . . . B 2 -5.349 31.045 -9.792 1 41.74 ? C6 ADP 501 A 1 HETATM 23 N N6 ADP . . . B 2 -5.549 30.929 -11.133 1 37.33 ? N6 ADP 501 A 1 HETATM 24 N N1 ADP . . . B 2 -4.481 31.958 -9.29 1 39.59 ? N1 ADP 501 A 1 HETATM 25 C C2 ADP . . . B 2 -4.278 32.099 -7.961 1 39.83 ? C2 ADP 501 A 1 HETATM 26 N N3 ADP . . . B 2 -4.902 31.347 -7.033 1 35.93 ? N3 ADP 501 A 1 HETATM 27 C C4 ADP . . . B 2 -5.798 30.387 -7.401 1 35.61 ? C4 ADP 501 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #