data_6QEL # _model_server_result.job_id yRrDigOjB3LHkO8T2XV3-Q _model_server_result.datetime_utc '2025-03-09 02:36:50' _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 6qel # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"W","auth_seq_id":1001}' # _entry.id 6QEL # _exptl.entry_id 6QEL _exptl.method 'ELECTRON MICROSCOPY' # _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 7 _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 6QEL _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QEL _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall 'P 1' _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,R,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA _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 ? _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 M N N ? 3 O N N ? 3 Q N N ? 3 S N N ? 3 U N N ? 3 W N N ? 3 Y 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 238 A THR 238 1_555 N MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc2 A OE2 GLU 262 A GLU 262 1_555 N MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc3 M O2B ADP . A ADP 1001 1_555 N MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc4 B OG1 THR 238 B THR 238 1_555 P MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc5 B OE1 GLU 262 B GLU 262 1_555 P MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc6 B OE2 GLU 262 B GLU 262 1_555 P MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? metalc ? metalc7 O O2B ADP . B ADP 1001 1_555 P MG MG . B MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.13 ? metalc ? metalc8 C OG1 THR 238 C THR 238 1_555 R MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc9 C OE1 GLU 262 C GLU 262 1_555 R MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc10 C OE2 GLU 262 C GLU 262 1_555 R MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc11 Q O2B ADP . C ADP 1001 1_555 R MG MG . C MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc12 D OG1 THR 238 D THR 238 1_555 T MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc13 D OE1 GLU 262 D GLU 262 1_555 T MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? metalc ? metalc14 D OE2 GLU 262 D GLU 262 1_555 T MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc15 S O2B ADP . D ADP 1001 1_555 T MG MG . D MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc16 E OG1 THR 238 E THR 238 1_555 V MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.928 ? metalc ? metalc17 E OE1 GLU 262 E GLU 262 1_555 V MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc18 E OE2 GLU 262 E GLU 262 1_555 V MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc19 U O2B ADP . E ADP 1001 1_555 V MG MG . E MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc20 F OG1 THR 238 F THR 238 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? metalc ? metalc21 F OE1 GLU 262 F GLU 262 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc22 F OE2 GLU 262 F GLU 262 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc23 W O2B ADP . F ADP 1001 1_555 X MG MG . F MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? metalc ? metalc24 G OD1 ASN 113 G ASN 113 1_555 Z MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc25 Y O2B ADP . G ADP 301 1_555 Z MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.848 ? metalc ? metalc26 Y O3B ADP . G ADP 301 1_555 Z MG MG . G MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc27 H OD1 ASN 113 H ASN 113 1_555 BA MG MG . H MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.841 ? metalc ? metalc28 I OD1 ASN 113 I ASN 113 1_555 DA MG MG . I MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? metalc ? metalc29 I OD1 ASP 169 I ASP 169 1_555 DA MG MG . I MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.903 ? metalc ? metalc30 J OD1 ASN 113 J ASN 113 1_555 FA MG MG . J MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.821 ? metalc ? metalc31 J OD1 ASP 169 J ASP 169 1_555 FA MG MG . J MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.861 ? metalc ? metalc32 K OD1 ASN 113 K ASN 113 1_555 HA MG MG . K MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.912 ? metalc ? metalc33 K OD1 ASP 169 K ASP 169 1_555 HA MG MG . K MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.915 ? metalc ? metalc34 L OD1 ASN 113 L ASN 113 1_555 JA MG MG . L MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc35 L OD1 ASP 169 L ASP 169 1_555 JA MG MG . L MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.469 ? metalc ? metalc36 IA O2B 08T . L 08T 301 1_555 JA MG MG . L MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.948 ? # _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 48 n n PB O2B ADP sing 49 n n PB O3B ADP sing 50 n n PB O3A ADP sing 51 n n O2B HOB2 ADP sing 52 n n O3B HOB3 ADP sing 53 n n PA O1A ADP doub 54 n n PA O2A ADP sing 55 n n PA O3A ADP sing 56 n n PA O5' ADP sing 57 n n O2A HOA2 ADP sing 58 n n O5' C5' ADP sing 59 n n C5' C4' ADP sing 60 n n C5' "H5'1" ADP sing 61 n n C5' "H5'2" ADP sing 62 n n C4' O4' ADP sing 63 n n C4' C3' ADP sing 64 n n C4' H4' ADP sing 65 n n O4' C1' ADP sing 66 n n C3' O3' ADP sing 67 n n C3' C2' ADP sing 68 n n C3' H3' ADP sing 69 n n O3' HO3' ADP sing 70 n n C2' O2' ADP sing 71 n n C2' C1' ADP sing 72 n n C2' H2' ADP sing 73 n n O2' HO2' ADP sing 74 n n C1' N9 ADP sing 75 n n C1' H1' ADP sing 76 n n N9 C8 ADP sing 77 n y N9 C4 ADP sing 78 n y C8 N7 ADP doub 79 n y C8 H8 ADP sing 80 n n N7 C5 ADP sing 81 n y C5 C6 ADP sing 82 n y C5 C4 ADP doub 83 n y C6 N6 ADP sing 84 n n C6 N1 ADP doub 85 n y N6 HN61 ADP sing 86 n n N6 HN62 ADP sing 87 n n N1 C2 ADP sing 88 n y C2 N3 ADP doub 89 n y C2 H2 ADP sing 90 n n N3 C4 ADP sing 91 n y # _atom_sites.entry_id 6QEL _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 M 3 ADP A 1 1001 1001 ADP ADP . N 4 MG A 1 1002 1002 MG MG . O 3 ADP B 1 1001 1001 ADP ADP . P 4 MG B 1 1002 1002 MG MG . Q 3 ADP C 1 1001 1001 ADP ADP . R 4 MG C 1 1002 1002 MG MG . S 3 ADP D 1 1001 1001 ADP ADP . T 4 MG D 1 1002 1002 MG MG . U 3 ADP E 1 1001 1001 ADP ADP . V 4 MG E 1 1002 1002 MG MG . W 3 ADP F 1 1001 1001 ADP ADP . X 4 MG F 1 1002 1002 MG MG . Y 3 ADP G 1 301 301 ADP ADP . Z 4 MG G 1 302 302 MG MG . AA 5 08T H 1 301 301 08T 08T . BA 4 MG H 1 302 302 MG MG . CA 5 08T I 1 301 301 08T 08T . DA 4 MG I 1 302 302 MG MG . EA 5 08T J 1 301 301 08T 08T . FA 4 MG J 1 302 302 MG MG . GA 5 08T K 1 301 301 08T 08T . HA 4 MG K 1 302 302 MG MG . IA 5 08T L 1 301 301 08T 08T . JA 4 MG L 1 302 302 MG MG . # 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 . . . W 3 128.097 133.656 171.148 1 22.43 ? PB ADP 1001 F 1 HETATM 2 O O1B ADP . . . W 3 128.108 134.952 170.383 1 22.43 ? O1B ADP 1001 F 1 HETATM 3 O O2B ADP . . . W 3 127.571 133.746 172.558 1 22.43 ? O2B ADP 1001 F 1 HETATM 4 O O3B ADP . . . W 3 129.378 132.889 171.029 1 22.43 ? O3B ADP 1001 F 1 HETATM 5 P PA ADP . . . W 3 125.483 132.811 170.573 1 22.43 ? PA ADP 1001 F 1 HETATM 6 O O1A ADP . . . W 3 124.949 131.44 170.876 1 22.43 ? O1A ADP 1001 F 1 HETATM 7 O O2A ADP . . . W 3 125.171 133.937 171.516 1 22.43 ? O2A ADP 1001 F 1 HETATM 8 O O3A ADP . . . W 3 127.068 132.701 170.359 1 22.43 ? O3A ADP 1001 F 1 HETATM 9 O O5' ADP . . . W 3 124.955 133.227 169.12 1 22.43 ? O5' ADP 1001 F 1 HETATM 10 C C5' ADP . . . W 3 124.378 132.187 168.355 1 22.43 ? C5' ADP 1001 F 1 HETATM 11 C C4' ADP . . . W 3 124.048 132.561 166.915 1 22.43 ? C4' ADP 1001 F 1 HETATM 12 O O4' ADP . . . W 3 122.903 131.826 166.493 1 22.43 ? O4' ADP 1001 F 1 HETATM 13 C C3' ADP . . . W 3 123.742 134.025 166.689 1 22.43 ? C3' ADP 1001 F 1 HETATM 14 O O3' ADP . . . W 3 124.866 134.675 166.092 1 22.43 ? O3' ADP 1001 F 1 HETATM 15 C C2' ADP . . . W 3 122.554 134.056 165.762 1 22.43 ? C2' ADP 1001 F 1 HETATM 16 O O2' ADP . . . W 3 122.93 134.494 164.46 1 22.43 ? O2' ADP 1001 F 1 HETATM 17 C C1' ADP . . . W 3 122.042 132.646 165.713 1 22.43 ? C1' ADP 1001 F 1 HETATM 18 N N9 ADP . . . W 3 120.714 132.638 166.332 1 22.43 ? N9 ADP 1001 F 1 HETATM 19 C C8 ADP . . . W 3 120.538 132.594 167.651 1 22.43 ? C8 ADP 1001 F 1 HETATM 20 N N7 ADP . . . W 3 119.225 132.594 167.961 1 22.43 ? N7 ADP 1001 F 1 HETATM 21 C C5 ADP . . . W 3 118.552 132.64 166.806 1 22.43 ? C5 ADP 1001 F 1 HETATM 22 C C6 ADP . . . W 3 117.134 132.666 166.422 1 22.43 ? C6 ADP 1001 F 1 HETATM 23 N N6 ADP . . . W 3 116.185 132.639 167.376 1 22.43 ? N6 ADP 1001 F 1 HETATM 24 N N1 ADP . . . W 3 116.827 132.719 165.113 1 22.43 ? N1 ADP 1001 F 1 HETATM 25 C C2 ADP . . . W 3 117.781 132.742 164.169 1 22.43 ? C2 ADP 1001 F 1 HETATM 26 N N3 ADP . . . W 3 119.094 132.723 164.454 1 22.43 ? N3 ADP 1001 F 1 HETATM 27 C C4 ADP . . . W 3 119.534 132.675 165.729 1 22.43 ? C4 ADP 1001 F 1 HETATM 28 H "H5'1" ADP . . . W 3 123.479 131.837 168.856 1 22.43 ? "H5'1" ADP 1001 F 1 HETATM 29 H "H5'2" ADP . . . W 3 125.089 131.37 168.349 1 22.43 ? "H5'2" ADP 1001 F 1 HETATM 30 H H4' ADP . . . W 3 124.896 132.299 166.278 1 22.43 ? H4' ADP 1001 F 1 HETATM 31 H H3' ADP . . . W 3 123.455 134.489 167.634 1 22.43 ? H3' ADP 1001 F 1 HETATM 32 H HO3' ADP . . . W 3 124.697 135.623 166.02 1 22.43 ? HO3' ADP 1001 F 1 HETATM 33 H H2' ADP . . . W 3 121.768 134.695 166.172 1 22.43 ? H2' ADP 1001 F 1 HETATM 34 H HO2' ADP . . . W 3 123.026 135.453 164.474 1 22.43 ? HO2' ADP 1001 F 1 HETATM 35 H H1' ADP . . . W 3 122.003 132.312 164.673 1 22.43 ? H1' ADP 1001 F 1 HETATM 36 H H8 ADP . . . W 3 121.349 132.561 168.357 1 22.43 ? H8 ADP 1001 F 1 HETATM 37 H HN61 ADP . . . W 3 116.456 132.599 168.348 1 22.43 ? HN61 ADP 1001 F 1 HETATM 38 H HN62 ADP . . . W 3 115.212 132.657 167.117 1 22.43 ? HN62 ADP 1001 F 1 HETATM 39 H H2 ADP . . . W 3 117.482 132.783 163.131 1 22.43 ? H2 ADP 1001 F 1 # _model_server_stats.io_time_ms 147 _model_server_stats.parse_time_ms 140 _model_server_stats.create_model_time_ms 83 _model_server_stats.query_time_ms 230 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 39 #