data_3CMX # _model_server_result.job_id gWg1qFadeUZev4MBpvAV6g _model_server_result.datetime_utc '2025-02-13 12:44:15' _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 3cmx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"U","auth_seq_id":4502}' # _entry.id 3CMX # _exptl.entry_id 3CMX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 10 _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 3CMX _cell.length_a 159 _cell.length_b 300.5 _cell.length_c 80.1 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3CMX _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 ? trimeric 3 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U 1 1 C,D,F,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA 2 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 x,y,z _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 ? 6 Q N N ? 6 R N N ? 6 S N N ? 6 T N N ? 6 U N N ? 6 FA N N ? 6 GA N N ? 6 HA N N ? 6 IA N N ? 6 JA 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 E OG1 THR 48 A THR 73 1_555 G MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc2 G MG MG . A MG 500 1_555 Q O1B ADP . A ADP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc3 E OG1 THR 397 A THR 1073 1_555 I MG MG . A MG 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc4 I MG MG . A MG 1500 1_555 R O1B ADP . A ADP 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc5 E OG1 THR 746 A THR 2073 1_555 K MG MG . A MG 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc6 K MG MG . A MG 2500 1_555 S O1B ADP . A ADP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc7 E OG1 THR 1096 A THR 3073 1_555 M MG MG . A MG 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc8 M MG MG . A MG 3500 1_555 T O1B ADP . A ADP 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc9 E OG1 THR 1445 A THR 4073 1_555 O MG MG . A MG 4500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.846 ? metalc ? metalc10 F OG1 THR 48 D THR 73 1_555 V MG MG . D MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc11 V MG MG . D MG 500 1_555 FA O1B ADP . D ADP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc12 F OG1 THR 397 D THR 1073 1_555 X MG MG . D MG 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.115 ? metalc ? metalc13 X MG MG . D MG 1500 1_555 GA O1B ADP . D ADP 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc14 F OG1 THR 746 D THR 2073 1_555 Z MG MG . D MG 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc15 Z MG MG . D MG 2500 1_555 HA O1B ADP . D ADP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc16 F OG1 THR 1096 D THR 3073 1_555 BA MG MG . D MG 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.116 ? metalc ? metalc17 BA MG MG . D MG 3500 1_555 IA O1B ADP . D ADP 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.214 ? metalc ? metalc18 F OG1 THR 1445 D THR 4073 1_555 DA MG MG . D MG 4500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc19 DA MG MG . D MG 4500 1_555 JA O1B ADP . D ADP 4502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? hydrog 'DT-DA PAIR' hydrog1 A N3 DT 5 B DT 1003 1_555 B N1 DA 11 C DA 2013 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N3 DT 6 B DT 1004 1_555 B N1 DA 10 C DA 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O4 DT 6 B DT 1004 1_555 B N6 DA 10 C DA 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog4 A N3 DT 7 B DT 1005 1_555 B N1 DA 9 C DA 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N3 DT 9 B DT 1007 1_555 B N1 DA 7 C DA 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O4 DT 9 B DT 1007 1_555 B N6 DA 7 C DA 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog7 A N3 DT 10 B DT 1008 1_555 B N1 DA 6 C DA 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N3 DT 12 B DT 1010 1_555 B N1 DA 4 C DA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O4 DT 12 B DT 1010 1_555 B N6 DA 4 C DA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog10 A N3 DT 13 B DT 1011 1_555 B N1 DA 3 C DA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N3 DT 6 E DT 1004 1_555 D N1 DA 9 F DA 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C O4 DT 6 E DT 1004 1_555 D N6 DA 9 F DA 2012 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog13 C N3 DT 7 E DT 1005 1_555 D N1 DA 8 F DA 2011 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N3 DT 9 E DT 1007 1_555 D N1 DA 6 F DA 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C O4 DT 9 E DT 1007 1_555 D N6 DA 6 F DA 2009 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog16 C N3 DT 10 E DT 1008 1_555 D N1 DA 5 F DA 2008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N3 DT 12 E DT 1010 1_555 D N1 DA 3 F DA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C O4 DT 12 E DT 1010 1_555 D N6 DA 3 F DA 2006 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog 'DT-DA PAIR' hydrog19 C N3 DT 13 E DT 1011 1_555 D N1 DA 2 F DA 2005 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _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 3CMX _atom_sites.fract_transf_matrix[1][1] 0.006289 _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] 0.003328 _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] 0.012484 _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 4 MG A 1 500 500 MG MG . H 5 ALF A 1 501 501 ALF ALF . I 4 MG A 1 1500 1500 MG MG . J 5 ALF A 1 1501 1501 ALF ALF . K 4 MG A 1 2500 2500 MG MG . L 5 ALF A 1 2501 2501 ALF ALF . M 4 MG A 1 3500 3500 MG MG . N 5 ALF A 1 3501 3501 ALF ALF . O 4 MG A 1 4500 4500 MG MG . P 5 ALF A 1 4501 4501 ALF ALF . Q 6 ADP A 1 502 502 ADP ADP . R 6 ADP A 1 1502 1502 ADP ADP . S 6 ADP A 1 2502 2502 ADP ADP . T 6 ADP A 1 3502 3502 ADP ADP . U 6 ADP A 1 4502 4502 ADP ADP . V 4 MG D 1 500 500 MG MG . W 5 ALF D 1 501 501 ALF ALF . X 4 MG D 1 1500 1500 MG MG . Y 5 ALF D 1 1501 1501 ALF ALF . Z 4 MG D 1 2500 2500 MG MG . AA 5 ALF D 1 2501 2501 ALF ALF . BA 4 MG D 1 3500 3500 MG MG . CA 5 ALF D 1 3501 3501 ALF ALF . DA 4 MG D 1 4500 4500 MG MG . EA 5 ALF D 1 4501 4501 ALF ALF . FA 6 ADP D 1 502 502 ADP ADP . GA 6 ADP D 1 1502 1502 ADP ADP . HA 6 ADP D 1 2502 2502 ADP ADP . IA 6 ADP D 1 3502 3502 ADP ADP . JA 6 ADP D 1 4502 4502 ADP ADP . # 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 . . . U 6 11.211 26.463 41.538 1 12.32 ? PB ADP 4502 A 1 HETATM 2 O O1B ADP . . . U 6 11.953 25.225 41.995 1 11.1 ? O1B ADP 4502 A 1 HETATM 3 O O2B ADP . . . U 6 10.867 26.535 40.077 1 13.7 ? O2B ADP 4502 A 1 HETATM 4 O O3B ADP . . . U 6 11.779 27.75 42.036 1 12.86 ? O3B ADP 4502 A 1 HETATM 5 P PA ADP . . . U 6 9.305 25.344 43.3 1 14.95 ? PA ADP 4502 A 1 HETATM 6 O O1A ADP . . . U 6 9.043 24.027 42.62 1 14.19 ? O1A ADP 4502 A 1 HETATM 7 O O2A ADP . . . U 6 10.249 25.383 44.486 1 12.44 ? O2A ADP 4502 A 1 HETATM 8 O O3A ADP . . . U 6 9.758 26.437 42.207 1 13.59 ? O3A ADP 4502 A 1 HETATM 9 O O5' ADP . . . U 6 7.886 26.006 43.67 1 15.04 ? O5' ADP 4502 A 1 HETATM 10 C C5' ADP . . . U 6 6.897 26.288 42.676 1 15.83 ? C5' ADP 4502 A 1 HETATM 11 C C4' ADP . . . U 6 5.62 26.776 43.372 1 19.01 ? C4' ADP 4502 A 1 HETATM 12 O O4' ADP . . . U 6 5.316 26.004 44.56 1 20.05 ? O4' ADP 4502 A 1 HETATM 13 C C3' ADP . . . U 6 5.758 28.235 43.798 1 19.45 ? C3' ADP 4502 A 1 HETATM 14 O O3' ADP . . . U 6 4.543 28.96 43.543 1 17.6 ? O3' ADP 4502 A 1 HETATM 15 C C2' ADP . . . U 6 6.012 28.155 45.287 1 20 ? C2' ADP 4502 A 1 HETATM 16 O O2' ADP . . . U 6 5.46 29.282 45.961 1 20.65 ? O2' ADP 4502 A 1 HETATM 17 C C1' ADP . . . U 6 5.314 26.863 45.707 1 21.76 ? C1' ADP 4502 A 1 HETATM 18 N N9 ADP . . . U 6 6.033 26.282 46.872 1 23.14 ? N9 ADP 4502 A 1 HETATM 19 C C8 ADP . . . U 6 7.331 25.907 46.919 1 23.28 ? C8 ADP 4502 A 1 HETATM 20 N N7 ADP . . . U 6 7.671 25.427 48.144 1 23.26 ? N7 ADP 4502 A 1 HETATM 21 C C5 ADP . . . U 6 6.573 25.502 48.903 1 22.3 ? C5 ADP 4502 A 1 HETATM 22 C C6 ADP . . . U 6 6.256 25.161 50.288 1 21.61 ? C6 ADP 4502 A 1 HETATM 23 N N6 ADP . . . U 6 7.214 24.638 51.089 1 21.55 ? N6 ADP 4502 A 1 HETATM 24 N N1 ADP . . . U 6 4.987 25.395 50.693 1 22.95 ? N1 ADP 4502 A 1 HETATM 25 C C2 ADP . . . U 6 4.036 25.919 49.884 1 23.04 ? C2 ADP 4502 A 1 HETATM 26 N N3 ADP . . . U 6 4.26 26.252 48.605 1 22.9 ? N3 ADP 4502 A 1 HETATM 27 C C4 ADP . . . U 6 5.493 26.068 48.073 1 23.14 ? C4 ADP 4502 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 297 _model_server_stats.encode_time_ms 23 _model_server_stats.element_count 27 #