data_6NJP # _model_server_result.job_id H69U0QPH5E93EPhI-c6SOQ _model_server_result.datetime_utc '2024-11-15 05:29:59' _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 6njp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":600}' # _entry.id 6NJP # _exptl.entry_id 6NJP _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 6NJP _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6NJP _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 PISA _pdbx_struct_assembly.oligomeric_details heptameric _pdbx_struct_assembly.oligomeric_count 7 _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 _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 H N N ? 3 K N N ? 3 N N N ? 3 Q 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 B OG SER 187 B SER 184 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.814 ? metalc ? metalc2 H O2B ADP . B ADP 600 1_555 I MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc3 I MG MG . B MG 601 1_555 T O HOH . B HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.518 ? metalc ? metalc4 I MG MG . B MG 601 1_555 T O HOH . B HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc5 C OG SER 187 C SER 184 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.842 ? metalc ? metalc6 K O2B ADP . C ADP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc7 L MG MG . C MG 601 1_555 U O HOH . C HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc8 L MG MG . C MG 601 1_555 U O HOH . C HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc9 D OG SER 187 D SER 184 1_555 O MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc10 N O2B ADP . D ADP 600 1_555 O MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc11 O MG MG . D MG 601 1_555 V O HOH . D HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.413 ? metalc ? metalc12 O MG MG . D MG 601 1_555 V O HOH . D HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc13 E OG SER 187 E SER 184 1_555 R MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc14 Q O1B ADP . E ADP 600 1_555 R MG MG . E MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.525 ? metalc ? metalc15 R MG MG . E MG 601 1_555 W O HOH . E HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc16 R MG MG . E MG 601 1_555 W O HOH . E HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? # _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 6NJP _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 H 3 ADP B 1 600 600 ADP ADP . I 4 MG B 1 601 601 MG MG . J 5 AF3 B 1 602 602 AF3 AF3 . K 3 ADP C 1 600 600 ADP ADP . L 4 MG C 1 601 601 MG MG . M 5 AF3 C 1 602 602 AF3 AF3 . N 3 ADP D 1 600 600 ADP ADP . O 4 MG D 1 601 601 MG MG . P 5 AF3 D 1 602 602 AF3 AF3 . Q 3 ADP E 1 600 600 ADP ADP . R 4 MG E 1 601 601 MG MG . S 5 AF3 E 1 602 602 AF3 AF3 . T 6 HOH B 1 1001 1001 HOH HOH . T 6 HOH B 2 1002 1002 HOH HOH . T 6 HOH B 3 1003 1003 HOH HOH . T 6 HOH B 4 1004 1004 HOH HOH . T 6 HOH B 5 1005 1005 HOH HOH . T 6 HOH B 6 1006 1006 HOH HOH . U 6 HOH C 1 1001 1001 HOH HOH . U 6 HOH C 2 1002 1002 HOH HOH . U 6 HOH C 3 1003 1003 HOH HOH . U 6 HOH C 4 1004 1004 HOH HOH . U 6 HOH C 5 1005 1005 HOH HOH . V 6 HOH D 1 1001 1001 HOH HOH . V 6 HOH D 2 1002 1002 HOH HOH . V 6 HOH D 3 1003 1003 HOH HOH . V 6 HOH D 4 1005 1005 HOH HOH . V 6 HOH D 5 1006 1006 HOH HOH . W 6 HOH E 1 1001 1001 HOH HOH . W 6 HOH E 2 1002 1002 HOH HOH . W 6 HOH E 3 1003 1003 HOH HOH . W 6 HOH E 4 1004 1004 HOH HOH . W 6 HOH E 5 1005 1005 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 . . . H 3 108.766 94.789 129.149 1 32.61 ? PB ADP 600 B 1 HETATM 2 O O1B ADP . . . H 3 108.359 94.419 127.743 1 35.64 ? O1B ADP 600 B 1 HETATM 3 O O2B ADP . . . H 3 107.899 94.186 130.228 1 33.48 ? O2B ADP 600 B 1 HETATM 4 O O3B ADP . . . H 3 109.074 96.254 129.343 1 36.43 ? O3B ADP 600 B 1 HETATM 5 P PA ADP . . . H 3 110.815 93.871 130.815 1 31.87 ? PA ADP 600 B 1 HETATM 6 O O1A ADP . . . H 3 111.262 95.223 131.318 1 31.03 ? O1A ADP 600 B 1 HETATM 7 O O2A ADP . . . H 3 109.853 93.043 131.633 1 30.5 ? O2A ADP 600 B 1 HETATM 8 O O3A ADP . . . H 3 110.19 94.063 129.344 1 33.85 ? O3A ADP 600 B 1 HETATM 9 O O5' ADP . . . H 3 112.126 92.982 130.527 1 29.94 ? O5' ADP 600 B 1 HETATM 10 C C5' ADP . . . H 3 112.477 91.908 131.397 1 32.27 ? C5' ADP 600 B 1 HETATM 11 C C4' ADP . . . H 3 113.79 91.288 130.934 1 34.42 ? C4' ADP 600 B 1 HETATM 12 O O4' ADP . . . H 3 114.68 92.315 130.491 1 35.89 ? O4' ADP 600 B 1 HETATM 13 C C3' ADP . . . H 3 114.472 90.534 132.066 1 34.83 ? C3' ADP 600 B 1 HETATM 14 O O3' ADP . . . H 3 114.586 89.146 131.724 1 34.84 ? O3' ADP 600 B 1 HETATM 15 C C2' ADP . . . H 3 115.824 91.205 132.267 1 34.92 ? C2' ADP 600 B 1 HETATM 16 O O2' ADP . . . H 3 116.925 90.308 132.068 1 37.49 ? O2' ADP 600 B 1 HETATM 17 C C1' ADP . . . H 3 115.892 92.334 131.25 1 35.6 ? C1' ADP 600 B 1 HETATM 18 N N9 ADP . . . H 3 116.021 93.635 131.953 1 35.28 ? N9 ADP 600 B 1 HETATM 19 C C8 ADP . . . H 3 115.189 94.685 131.822 1 36.88 ? C8 ADP 600 B 1 HETATM 20 N N7 ADP . . . H 3 115.585 95.724 132.602 1 36.09 ? N7 ADP 600 B 1 HETATM 21 C C5 ADP . . . H 3 116.699 95.339 133.252 1 35.56 ? C5 ADP 600 B 1 HETATM 22 C C6 ADP . . . H 3 117.629 95.949 134.231 1 33.64 ? C6 ADP 600 B 1 HETATM 23 N N6 ADP . . . H 3 117.442 97.214 134.681 1 34.51 ? N6 ADP 600 B 1 HETATM 24 N N1 ADP . . . H 3 118.671 95.202 134.659 1 33.89 ? N1 ADP 600 B 1 HETATM 25 C C2 ADP . . . H 3 118.868 93.945 134.22 1 35.55 ? C2 ADP 600 B 1 HETATM 26 N N3 ADP . . . H 3 118.065 93.329 133.334 1 36.46 ? N3 ADP 600 B 1 HETATM 27 C C4 ADP . . . H 3 116.982 93.961 132.821 1 34.47 ? C4 ADP 600 B 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #