data_6PDW # _model_server_result.job_id DI3yFl3Q8ykruwmuDBde1g _model_server_result.datetime_utc '2024-11-04 22:42:00' _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 6pdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":501}' # _entry.id 6PDW # _exptl.entry_id 6PDW _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 4 _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 6PDW _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PDW _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 _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 G N N ? 3 J N N ? 3 M N N ? 3 P 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 133 B THR 161 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc2 G O2B ADP . B ADP 501 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.703 ? metalc ? metalc3 H F1 BEF . B BEF 502 1_555 I MG MG . B MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc4 B OG1 THR 133 C THR 161 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc5 J O2B ADP . C ADP 501 1_555 K MG MG . C MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.625 ? metalc ? metalc6 K MG MG . C MG 502 1_555 L F1 BEF . C BEF 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc7 C OG1 THR 133 D THR 161 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc8 C OD2 ASP 185 D ASP 213 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.837 ? metalc ? metalc9 M O2B ADP . D ADP 501 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.798 ? metalc ? metalc10 N F3 BEF . D BEF 502 1_555 O MG MG . D MG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? metalc ? metalc11 D OG1 THR 133 E THR 161 1_555 Q MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? metalc ? metalc12 P O3B ADP . E ADP 501 1_555 Q MG MG . E MG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? # _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 6PDW _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 G 3 ADP B 1 501 501 ADP ADP . H 4 BEF B 1 502 502 BEF BEF . I 5 MG B 1 503 601 MG MG . J 3 ADP C 1 501 501 ADP ADP . K 5 MG C 1 502 601 MG MG . L 4 BEF C 1 503 502 BEF BEF . M 3 ADP D 1 501 501 ADP ADP . N 4 BEF D 1 502 502 BEF BEF . O 5 MG D 1 503 601 MG MG . P 3 ADP E 1 501 501 ADP ADP . Q 5 MG E 1 502 601 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 . . . G 3 143.805 133.049 104.923 1 52.9 ? PB ADP 501 B 1 HETATM 2 O O1B ADP . . . G 3 143.979 131.752 104.178 1 52.9 -1 O1B ADP 501 B 1 HETATM 3 O O2B ADP . . . G 3 142.381 133.385 105.275 1 52.9 -1 O2B ADP 501 B 1 HETATM 4 O O3B ADP . . . G 3 144.779 133.262 106.05 1 52.9 ? O3B ADP 501 B 1 HETATM 5 P PA ADP . . . G 3 143.127 134.534 102.691 1 52.9 ? PA ADP 501 B 1 HETATM 6 O O1A ADP . . . G 3 142.974 133.344 101.782 1 52.9 -1 O1A ADP 501 B 1 HETATM 7 O O2A ADP . . . G 3 141.92 135.138 103.36 1 52.9 ? O2A ADP 501 B 1 HETATM 8 O O3A ADP . . . G 3 144.186 134.163 103.836 1 52.9 ? O3A ADP 501 B 1 HETATM 9 O O5' ADP . . . G 3 143.902 135.686 101.887 1 52.9 ? O5' ADP 501 B 1 HETATM 10 C C5' ADP . . . G 3 143.163 136.651 101.149 1 52.9 ? C5' ADP 501 B 1 HETATM 11 C C4' ADP . . . G 3 144.11 137.367 100.204 1 52.9 ? C4' ADP 501 B 1 HETATM 12 O O4' ADP . . . G 3 145.4 136.769 100.293 1 52.9 ? O4' ADP 501 B 1 HETATM 13 C C3' ADP . . . G 3 143.642 137.226 98.769 1 52.9 ? C3' ADP 501 B 1 HETATM 14 O O3' ADP . . . G 3 143.237 138.497 98.261 1 52.9 ? O3' ADP 501 B 1 HETATM 15 C C2' ADP . . . G 3 144.836 136.715 97.996 1 52.9 ? C2' ADP 501 B 1 HETATM 16 O O2' ADP . . . G 3 145.187 137.653 96.976 1 52.9 ? O2' ADP 501 B 1 HETATM 17 C C1' ADP . . . G 3 145.968 136.589 98.998 1 52.9 ? C1' ADP 501 B 1 HETATM 18 N N9 ADP . . . G 3 146.538 135.227 98.913 1 52.9 ? N9 ADP 501 B 1 HETATM 19 C C8 ADP . . . G 3 146.682 134.378 99.944 1 52.9 ? C8 ADP 501 B 1 HETATM 20 N N7 ADP . . . G 3 147.24 133.211 99.541 1 52.9 ? N7 ADP 501 B 1 HETATM 21 C C5 ADP . . . G 3 147.461 133.307 98.221 1 52.9 ? C5 ADP 501 B 1 HETATM 22 C C6 ADP . . . G 3 148.03 132.434 97.174 1 52.9 ? C6 ADP 501 B 1 HETATM 23 N N6 ADP . . . G 3 148.479 131.191 97.468 1 52.9 ? N6 ADP 501 B 1 HETATM 24 N N1 ADP . . . G 3 148.084 132.92 95.916 1 52.9 ? N1 ADP 501 B 1 HETATM 25 C C2 ADP . . . G 3 147.64 134.153 95.612 1 52.9 ? C2 ADP 501 B 1 HETATM 26 N N3 ADP . . . G 3 147.116 134.997 96.513 1 52.9 ? N3 ADP 501 B 1 HETATM 27 C C4 ADP . . . G 3 147.005 134.64 97.812 1 52.9 ? C4 ADP 501 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 242 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 27 #