data_7NJN # _model_server_result.job_id wMUvkW38v8tnUnV7nCTprw _model_server_result.datetime_utc '2024-10-20 07:37:53' _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 7njn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"AA","auth_seq_id":600}' # _entry.id 7NJN # _exptl.entry_id 7NJN _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 7NJN _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7NJN _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 eicosameric _pdbx_struct_assembly.oligomeric_count 20 _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,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 ? 11 AA N N ? 11 CA 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 179 A THR 179 1_555 V MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc2 U O2G ATP . A ATP 600 1_555 V MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc3 U O2B ATP . A ATP 600 1_555 V MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc4 V MG MG . A MG 601 1_555 FA O HOH . A HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc5 V MG MG . A MG 601 1_555 FA O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc6 V MG MG . A MG 601 1_555 FA O HOH . A HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc7 B OG1 THR 179 B THR 179 1_555 X MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc8 W O2G ATP . B ATP 600 1_555 X MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc9 W O2B ATP . B ATP 600 1_555 X MG MG . B MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc10 X MG MG . B MG 601 1_555 GA O HOH . B HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc11 X MG MG . B MG 601 1_555 GA O HOH . B HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc12 X MG MG . B MG 601 1_555 GA O HOH . B HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc13 C OG1 THR 179 C THR 179 1_555 Z MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc14 Y O2G ATP . C ATP 600 1_555 Z MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc15 Y O2B ATP . C ATP 600 1_555 Z MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc16 Z MG MG . C MG 601 1_555 HA O HOH . C HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc17 Z MG MG . C MG 601 1_555 HA O HOH . C HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc18 Z MG MG . C MG 601 1_555 HA O HOH . C HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc19 D OG1 THR 167 D THR 167 1_555 BA MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc20 AA O2B ADP . D ADP 600 1_555 BA MG MG . D MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc21 BA MG MG . D MG 601 1_555 IA O HOH . D HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc22 BA MG MG . D MG 601 1_555 IA O HOH . D HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc23 BA MG MG . D MG 601 1_555 IA O HOH . D HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc24 BA MG MG . D MG 601 1_555 IA O HOH . D HOH 704 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc25 F OG1 THR 167 F THR 167 1_555 EA MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc26 DA O2G ATP . F ATP 600 1_555 EA MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.178 ? metalc ? metalc27 DA O2B ATP . F ATP 600 1_555 EA MG MG . F MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc28 EA MG MG . F MG 601 1_555 JA O HOH . F HOH 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc29 EA MG MG . F MG 601 1_555 JA O HOH . F HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc30 EA MG MG . F MG 601 1_555 JA O HOH . F HOH 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? # _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 7NJN _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 U 9 ATP A 1 600 600 ATP ATP . V 10 MG A 1 601 601 MG MG . W 9 ATP B 1 600 600 ATP ATP . X 10 MG B 1 601 601 MG MG . Y 9 ATP C 1 600 600 ATP ATP . Z 10 MG C 1 601 601 MG MG . AA 11 ADP D 1 600 600 ADP ADP . BA 10 MG D 1 601 601 MG MG . CA 11 ADP E 1 600 600 ADP ADP . DA 9 ATP F 1 600 600 ATP ATP . EA 10 MG F 1 601 601 MG MG . FA 12 HOH A 1 701 701 HOH HOH . FA 12 HOH A 2 702 703 HOH HOH . FA 12 HOH A 3 703 702 HOH HOH . GA 12 HOH B 1 701 702 HOH HOH . GA 12 HOH B 2 702 703 HOH HOH . GA 12 HOH B 3 703 701 HOH HOH . HA 12 HOH C 1 701 701 HOH HOH . HA 12 HOH C 2 702 703 HOH HOH . HA 12 HOH C 3 703 702 HOH HOH . IA 12 HOH D 1 701 702 HOH HOH . IA 12 HOH D 2 702 701 HOH HOH . IA 12 HOH D 3 703 703 HOH HOH . IA 12 HOH D 4 704 704 HOH HOH . JA 12 HOH F 1 701 702 HOH HOH . JA 12 HOH F 2 702 701 HOH HOH . JA 12 HOH F 3 703 703 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 . . . AA 11 205.845 174.464 246.705 1 44.02 ? PB ADP 600 D 1 HETATM 2 O O1B ADP . . . AA 11 206.707 174.52 245.479 1 44.02 ? O1B ADP 600 D 1 HETATM 3 O O2B ADP . . . AA 11 206.227 173.382 247.676 1 44.02 ? O2B ADP 600 D 1 HETATM 4 O O3B ADP . . . AA 11 205.599 175.802 247.341 1 44.02 ? O3B ADP 600 D 1 HETATM 5 P PA ADP . . . AA 11 204.199 172.717 245.263 1 44.02 ? PA ADP 600 D 1 HETATM 6 O O1A ADP . . . AA 11 205.541 172.054 245.139 1 44.02 ? O1A ADP 600 D 1 HETATM 7 O O2A ADP . . . AA 11 203.021 171.948 245.799 1 44.02 ? O2A ADP 600 D 1 HETATM 8 O O3A ADP . . . AA 11 204.393 174.022 246.173 1 44.02 ? O3A ADP 600 D 1 HETATM 9 O O5' ADP . . . AA 11 203.773 173.311 243.841 1 44.02 ? O5' ADP 600 D 1 HETATM 10 C C5' ADP . . . AA 11 203.065 174.539 243.755 1 44.02 ? C5' ADP 600 D 1 HETATM 11 C C4' ADP . . . AA 11 202.023 174.452 242.646 1 44.02 ? C4' ADP 600 D 1 HETATM 12 O O4' ADP . . . AA 11 202.599 174.671 241.358 1 44.02 ? O4' ADP 600 D 1 HETATM 13 C C3' ADP . . . AA 11 201.352 173.093 242.561 1 44.02 ? C3' ADP 600 D 1 HETATM 14 O O3' ADP . . . AA 11 200.224 173.011 243.421 1 44.02 ? O3' ADP 600 D 1 HETATM 15 C C2' ADP . . . AA 11 200.965 172.971 241.108 1 44.02 ? C2' ADP 600 D 1 HETATM 16 O O2' ADP . . . AA 11 199.648 173.47 240.87 1 44.02 ? O2' ADP 600 D 1 HETATM 17 C C1' ADP . . . AA 11 201.984 173.822 240.387 1 44.02 ? C1' ADP 600 D 1 HETATM 18 N N9 ADP . . . AA 11 203.001 172.91 239.833 1 44.02 ? N9 ADP 600 D 1 HETATM 19 C C8 ADP . . . AA 11 204.149 172.595 240.446 1 44.02 ? C8 ADP 600 D 1 HETATM 20 N N7 ADP . . . AA 11 204.868 171.73 239.696 1 44.02 ? N7 ADP 600 D 1 HETATM 21 C C5 ADP . . . AA 11 204.167 171.483 238.581 1 44.02 ? C5 ADP 600 D 1 HETATM 22 C C6 ADP . . . AA 11 204.358 170.664 237.372 1 44.02 ? C6 ADP 600 D 1 HETATM 23 N N6 ADP . . . AA 11 205.473 169.917 237.213 1 44.02 ? N6 ADP 600 D 1 HETATM 24 N N1 ADP . . . AA 11 203.385 170.689 236.44 1 44.02 ? N1 ADP 600 D 1 HETATM 25 C C2 ADP . . . AA 11 202.271 171.428 236.587 1 44.02 ? C2 ADP 600 D 1 HETATM 26 N N3 ADP . . . AA 11 202.04 172.193 237.664 1 44.02 ? N3 ADP 600 D 1 HETATM 27 C C4 ADP . . . AA 11 202.933 172.262 238.674 1 44.02 ? C4 ADP 600 D 1 HETATM 28 H "H5'1" ADP . . . AA 11 203.761 175.352 243.543 1 44.02 ? "H5'1" ADP 600 D 1 HETATM 29 H "H5'2" ADP . . . AA 11 202.572 174.75 244.706 1 44.02 ? "H5'2" ADP 600 D 1 HETATM 30 H H4' ADP . . . AA 11 201.25 175.209 242.837 1 44.02 ? H4' ADP 600 D 1 HETATM 31 H H3' ADP . . . AA 11 202.068 172.296 242.798 1 44.02 ? H3' ADP 600 D 1 HETATM 32 H HO3' ADP . . . AA 11 199.909 172.098 243.437 1 44.02 ? HO3' ADP 600 D 1 HETATM 33 H H2' ADP . . . AA 11 201.057 171.925 240.785 1 44.02 ? H2' ADP 600 D 1 HETATM 34 H HO2' ADP . . . AA 11 199.004 172.924 241.341 1 44.02 ? HO2' ADP 600 D 1 HETATM 35 H H1' ADP . . . AA 11 201.497 174.408 239.595 1 44.02 ? H1' ADP 600 D 1 HETATM 36 H H8 ADP . . . AA 11 204.453 172.98 241.41 1 44.02 ? H8 ADP 600 D 1 HETATM 37 H HN61 ADP . . . AA 11 206.187 169.919 237.927 1 44.02 ? HN61 ADP 600 D 1 HETATM 38 H HN62 ADP . . . AA 11 205.592 169.359 236.38 1 44.02 ? HN62 ADP 600 D 1 HETATM 39 H H2 ADP . . . AA 11 201.526 171.402 235.802 1 44.02 ? H2 ADP 600 D 1 # _model_server_stats.io_time_ms 24 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 151 _model_server_stats.query_time_ms 461 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 39 #