data_3CMW # _model_server_result.job_id G7R-c_rvl0NU8N5m2GxEtg _model_server_result.datetime_utc '2024-11-15 10:34:24' _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 3cmw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"Q","auth_seq_id":2502}' # _entry.id 3CMW # _exptl.entry_id 3CMW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 5 _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 3CMW _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 3CMW _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S 1 1 B,D,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA 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 ? 5 O N N ? 5 P N N ? 5 Q N N ? 5 R N N ? 5 S N N ? 5 DA N N ? 5 EA N N ? 5 FA N N ? 5 GA N N ? 5 HA 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 C OG1 THR 48 A THR 73 1_555 E MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc2 E MG MG . A MG 500 1_555 O O1B ADP . A ADP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc3 C OG1 THR 397 A THR 1073 1_555 G MG MG . A MG 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.144 ? metalc ? metalc4 G MG MG . A MG 1500 1_555 P O1B ADP . A ADP 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc5 C OG1 THR 746 A THR 2073 1_555 I MG MG . A MG 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? metalc ? metalc6 I MG MG . A MG 2500 1_555 Q O1B ADP . A ADP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc7 C OG1 THR 1096 A THR 3073 1_555 K MG MG . A MG 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.179 ? metalc ? metalc8 K MG MG . A MG 3500 1_555 R O1B ADP . A ADP 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc9 C OG1 THR 1445 A THR 4073 1_555 M MG MG . A MG 4500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? metalc ? metalc10 M MG MG . A MG 4500 1_555 S O1B ADP . A ADP 4502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc11 D OG1 THR 48 C THR 73 1_555 T MG MG . C MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.175 ? metalc ? metalc12 T MG MG . C MG 500 1_555 DA O1B ADP . C ADP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc13 D OG1 THR 397 C THR 1073 1_555 V MG MG . C MG 1500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc14 V MG MG . C MG 1500 1_555 EA O1B ADP . C ADP 1502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc15 D OG1 THR 746 C THR 2073 1_555 X MG MG . C MG 2500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.157 ? metalc ? metalc16 X MG MG . C MG 2500 1_555 FA O1B ADP . C ADP 2502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.176 ? metalc ? metalc17 D OG1 THR 1096 C THR 3073 1_555 Z MG MG . C MG 3500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.195 ? metalc ? metalc18 Z MG MG . C MG 3500 1_555 GA O1B ADP . C ADP 3502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.17 ? metalc ? metalc19 D OG1 THR 1445 C THR 4073 1_555 BA MG MG . C MG 4500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc20 BA MG MG . C MG 4500 1_555 HA O1B ADP . C ADP 4502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.205 ? # _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 3CMW _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 E 3 MG A 1 500 500 MG MG . F 4 ALF A 1 501 501 ALF ALF . G 3 MG A 1 1500 1500 MG MG . H 4 ALF A 1 1501 1501 ALF ALF . I 3 MG A 1 2500 2500 MG MG . J 4 ALF A 1 2501 2501 ALF ALF . K 3 MG A 1 3500 3500 MG MG . L 4 ALF A 1 3501 3501 ALF ALF . M 3 MG A 1 4500 4500 MG MG . N 4 ALF A 1 4501 4501 ALF ALF . O 5 ADP A 1 502 502 ADP ADP . P 5 ADP A 1 1502 1502 ADP ADP . Q 5 ADP A 1 2502 2502 ADP ADP . R 5 ADP A 1 3502 3502 ADP ADP . S 5 ADP A 1 4502 4502 ADP ADP . T 3 MG C 1 500 500 MG MG . U 4 ALF C 1 501 501 ALF ALF . V 3 MG C 1 1500 1500 MG MG . W 4 ALF C 1 1501 1501 ALF ALF . X 3 MG C 1 2500 2500 MG MG . Y 4 ALF C 1 2501 2501 ALF ALF . Z 3 MG C 1 3500 3500 MG MG . AA 4 ALF C 1 3501 3501 ALF ALF . BA 3 MG C 1 4500 4500 MG MG . CA 4 ALF C 1 4501 4501 ALF ALF . DA 5 ADP C 1 502 502 ADP ADP . EA 5 ADP C 1 1502 1502 ADP ADP . FA 5 ADP C 1 2502 2502 ADP ADP . GA 5 ADP C 1 3502 3502 ADP ADP . HA 5 ADP C 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 . . . Q 5 46.456 21.671 3.701 1 41.57 ? PB ADP 2502 A 1 HETATM 2 O O1B ADP . . . Q 5 47.351 20.686 2.99 1 41.01 ? O1B ADP 2502 A 1 HETATM 3 O O2B ADP . . . Q 5 47.135 22.948 4.134 1 43.25 ? O2B ADP 2502 A 1 HETATM 4 O O3B ADP . . . Q 5 45.687 20.989 4.824 1 42.36 ? O3B ADP 2502 A 1 HETATM 5 P PA ADP . . . Q 5 45.33 21.758 1.101 1 38.83 ? PA ADP 2502 A 1 HETATM 6 O O1A ADP . . . Q 5 46.485 22.217 0.238 1 37.03 ? O1A ADP 2502 A 1 HETATM 7 O O2A ADP . . . Q 5 45.126 20.262 1.226 1 40 ? O2A ADP 2502 A 1 HETATM 8 O O3A ADP . . . Q 5 45.422 22.292 2.628 1 38.12 ? O3A ADP 2502 A 1 HETATM 9 O O5' ADP . . . Q 5 44.032 22.525 0.558 1 37.63 ? O5' ADP 2502 A 1 HETATM 10 C C5' ADP . . . Q 5 44.049 23.959 0.538 1 41.2 ? C5' ADP 2502 A 1 HETATM 11 C C4' ADP . . . Q 5 42.766 24.494 -0.093 1 44.42 ? C4' ADP 2502 A 1 HETATM 12 O O4' ADP . . . Q 5 42.522 23.823 -1.343 1 45.36 ? O4' ADP 2502 A 1 HETATM 13 C C3' ADP . . . Q 5 41.555 24.236 0.797 1 44.61 ? C3' ADP 2502 A 1 HETATM 14 O O3' ADP . . . Q 5 40.588 25.29 0.702 1 42.26 ? O3' ADP 2502 A 1 HETATM 15 C C2' ADP . . . Q 5 40.987 22.962 0.209 1 45.3 ? C2' ADP 2502 A 1 HETATM 16 O O2' ADP . . . Q 5 39.595 22.79 0.499 1 47.55 ? O2' ADP 2502 A 1 HETATM 17 C C1' ADP . . . Q 5 41.302 23.088 -1.276 1 44.07 ? C1' ADP 2502 A 1 HETATM 18 N N9 ADP . . . Q 5 41.434 21.712 -1.778 1 42.14 ? N9 ADP 2502 A 1 HETATM 19 C C8 ADP . . . Q 5 42.273 20.771 -1.326 1 42.08 ? C8 ADP 2502 A 1 HETATM 20 N N7 ADP . . . Q 5 42.114 19.607 -2.013 1 42.97 ? N7 ADP 2502 A 1 HETATM 21 C C5 ADP . . . Q 5 41.141 19.817 -2.912 1 41.84 ? C5 ADP 2502 A 1 HETATM 22 C C6 ADP . . . Q 5 40.45 19 -3.929 1 43.63 ? C6 ADP 2502 A 1 HETATM 23 N N6 ADP . . . Q 5 40.819 17.699 -4.112 1 43.63 ? N6 ADP 2502 A 1 HETATM 24 N N1 ADP . . . Q 5 39.461 19.6 -4.652 1 42.61 ? N1 ADP 2502 A 1 HETATM 25 C C2 ADP . . . Q 5 39.119 20.889 -4.452 1 42.24 ? C2 ADP 2502 A 1 HETATM 26 N N3 ADP . . . Q 5 39.701 21.686 -3.537 1 41.67 ? N3 ADP 2502 A 1 HETATM 27 C C4 ADP . . . Q 5 40.691 21.205 -2.747 1 41.39 ? C4 ADP 2502 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 40 _model_server_stats.query_time_ms 323 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #