data_6DJN # _model_server_result.job_id mdgYX7BTj--KxHqpGqYcig _model_server_result.datetime_utc '2025-07-14 17:28:45' _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 6djn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":802}' # _entry.id 6DJN # _exptl.entry_id 6DJN _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 6DJN _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6DJN _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 tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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 F N N ? 3 I N N ? 3 L N N ? 3 O 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 covale ? covale1 A C GLU 72 A GLU 72 1_555 A N HIC 73 A HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C HIC 73 A HIC 73 1_555 A N GLY 74 A GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale3 B C GLU 72 B GLU 72 1_555 B N HIC 73 B HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale4 B C HIC 73 B HIC 73 1_555 B N GLY 74 B GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale5 C C GLU 72 C GLU 72 1_555 C N HIC 73 C HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 C C HIC 73 C HIC 73 1_555 C N GLY 74 C GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale7 D C GLU 72 D GLU 72 1_555 D N HIC 73 D HIC 73 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale8 D C HIC 73 D HIC 73 1_555 D N GLY 74 D GLY 74 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? metalc ? metalc1 E MG MG . A MG 801 1_555 F O1B ADP . A ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc2 E MG MG . A MG 801 1_555 G O4 PO4 . A PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc3 H MG MG . B MG 801 1_555 I O1B ADP . B ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc4 H MG MG . B MG 801 1_555 J O2 PO4 . B PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc5 K MG MG . C MG 801 1_555 L O1B ADP . C ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 K MG MG . C MG 801 1_555 M O2 PO4 . C PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc7 N MG MG . D MG 801 1_555 O O1B ADP . D ADP 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc8 N MG MG . D MG 801 1_555 P O2 PO4 . D PO4 803 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? # _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 6DJN _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 E 2 MG A 1 801 801 MG MG . F 3 ADP A 1 802 901 ADP ADP . G 4 PO4 A 1 803 951 PO4 PO4 . H 2 MG B 1 801 801 MG MG . I 3 ADP B 1 802 901 ADP ADP . J 4 PO4 B 1 803 951 PO4 PO4 . K 2 MG C 1 801 801 MG MG . L 3 ADP C 1 802 901 ADP ADP . M 4 PO4 C 1 803 951 PO4 PO4 . N 2 MG D 1 801 801 MG MG . O 3 ADP D 1 802 901 ADP ADP . P 4 PO4 D 1 803 951 PO4 PO4 . # 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 . . . L 3 156.286 179.917 157 1 45.78 ? PB ADP 802 C 1 HETATM 2 O O1B ADP . . . L 3 156.022 180.291 155.573 1 45.78 ? O1B ADP 802 C 1 HETATM 3 O O2B ADP . . . L 3 155.138 180.207 157.907 1 45.78 ? O2B ADP 802 C 1 HETATM 4 O O3B ADP . . . L 3 156.935 178.589 157.214 1 45.78 ? O3B ADP 802 C 1 HETATM 5 P PA ADP . . . L 3 157.206 182.513 157.45 1 45.78 ? PA ADP 802 C 1 HETATM 6 O O1A ADP . . . L 3 157.209 183.038 156.048 1 45.78 ? O1A ADP 802 C 1 HETATM 7 O O2A ADP . . . L 3 156.103 182.849 158.395 1 45.78 ? O2A ADP 802 C 1 HETATM 8 O O3A ADP . . . L 3 157.426 180.937 157.422 1 45.78 ? O3A ADP 802 C 1 HETATM 9 O O5' ADP . . . L 3 158.572 182.91 158.158 1 45.78 ? O5' ADP 802 C 1 HETATM 10 C C5' ADP . . . L 3 158.789 182.493 159.497 1 45.78 ? C5' ADP 802 C 1 HETATM 11 C C4' ADP . . . L 3 160.281 182.519 159.756 1 45.78 ? C4' ADP 802 C 1 HETATM 12 O O4' ADP . . . L 3 160.774 183.789 159.368 1 45.78 ? O4' ADP 802 C 1 HETATM 13 C C3' ADP . . . L 3 160.604 182.336 161.216 1 45.78 ? C3' ADP 802 C 1 HETATM 14 O O3' ADP . . . L 3 161.547 181.279 161.346 1 45.78 ? O3' ADP 802 C 1 HETATM 15 C C2' ADP . . . L 3 161.316 183.585 161.65 1 45.78 ? C2' ADP 802 C 1 HETATM 16 O O2' ADP . . . L 3 162.563 183.205 162.225 1 45.78 ? O2' ADP 802 C 1 HETATM 17 C C1' ADP . . . L 3 161.564 184.369 160.389 1 45.78 ? C1' ADP 802 C 1 HETATM 18 N N9 ADP . . . L 3 161.047 185.721 160.603 1 45.78 ? N9 ADP 802 C 1 HETATM 19 C C8 ADP . . . L 3 159.771 185.995 160.881 1 45.78 ? C8 ADP 802 C 1 HETATM 20 N N7 ADP . . . L 3 159.591 187.325 161.026 1 45.78 ? N7 ADP 802 C 1 HETATM 21 C C5 ADP . . . L 3 160.78 187.91 160.84 1 45.78 ? C5 ADP 802 C 1 HETATM 22 C C6 ADP . . . L 3 161.29 189.286 160.857 1 45.78 ? C6 ADP 802 C 1 HETATM 23 N N6 ADP . . . L 3 160.463 190.323 161.108 1 45.78 ? N6 ADP 802 C 1 HETATM 24 N N1 ADP . . . L 3 162.597 189.474 160.616 1 45.78 ? N1 ADP 802 C 1 HETATM 25 C C2 ADP . . . L 3 163.419 188.447 160.37 1 45.78 ? C2 ADP 802 C 1 HETATM 26 N N3 ADP . . . L 3 163.027 187.17 160.339 1 45.78 ? N3 ADP 802 C 1 HETATM 27 C C4 ADP . . . L 3 161.742 186.848 160.564 1 45.78 ? C4 ADP 802 C 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 23 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 772 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #