data_5CE3 # _model_server_result.job_id 43u9xjbkSRLNJygeh6bpPA _model_server_result.datetime_utc '2024-12-19 01:49:17' _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 5ce3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":801}' # _entry.id 5CE3 # _exptl.entry_id 5CE3 _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 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.88 _cell.angle_gamma 90 _cell.entry_id 5CE3 _cell.length_a 108.73 _cell.length_b 121.75 _cell.length_c 118.58 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CE3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 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 G N N ? 5 K 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 O3G ATP . A ATP 401 1_555 F CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.613 ? metalc ? metalc2 E O1B ATP . A ATP 401 1_555 F CA CA . A CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? metalc ? metalc3 F CA CA . A CA 402 1_555 M O HOH . A HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc4 F CA CA . A CA 402 1_555 M O HOH . A HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.555 ? metalc ? metalc5 F CA CA . A CA 402 1_555 M O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc6 B OD1 ASN 186 B ASN 272 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.193 ? metalc ? metalc7 B OD2 ASP 200 B ASP 286 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? metalc ? metalc8 G O2B ADP . B ADP 801 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc9 G O2A ADP . B ADP 801 1_555 H MG MG . B MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? metalc ? metalc10 H MG MG . B MG 802 1_555 N O HOH . B HOH 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc11 H MG MG . B MG 802 1_555 N O HOH . B HOH 903 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc12 I O3G ATP . C ATP 401 1_555 J CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.355 ? metalc ? metalc13 I O1B ATP . C ATP 401 1_555 J CA CA . C CA 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.706 ? metalc ? metalc14 J CA CA . C CA 402 1_555 O O HOH . C HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.417 ? metalc ? metalc15 D OD1 ASN 186 D ASN 272 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? metalc ? metalc16 D OD2 ASP 200 D ASP 286 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc17 K O2B ADP . D ADP 801 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? metalc ? metalc18 K O2A ADP . D ADP 801 1_555 L MG MG . D MG 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? # _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 5CE3 _atom_sites.fract_transf_matrix[1][1] 0.009197 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002444 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008214 _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] 0.008726 _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 ATP A 1 401 1380 ATP ATP . F 4 CA A 1 402 1401 CA CA . G 5 ADP B 1 801 730 ADP ADP . H 6 MG B 1 802 731 MG MG . I 3 ATP C 1 401 1380 ATP ATP . J 4 CA C 1 402 1401 CA CA . K 5 ADP D 1 801 730 ADP ADP . L 6 MG D 1 802 731 MG MG . M 7 HOH A 1 501 8 HOH HOH . M 7 HOH A 2 502 11 HOH HOH . M 7 HOH A 3 503 9 HOH HOH . N 7 HOH B 1 901 3 HOH HOH . N 7 HOH B 2 902 1 HOH HOH . N 7 HOH B 3 903 2 HOH HOH . O 7 HOH C 1 501 13 HOH HOH . P 7 HOH D 1 901 6 HOH HOH . P 7 HOH D 2 902 5 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 . . . G 5 19.965 -1.034 9.201 1 66.3 ? PB ADP 801 B 1 HETATM 2 O O1B ADP . . . G 5 18.453 -1.076 9.208 1 67.19 ? O1B ADP 801 B 1 HETATM 3 O O2B ADP . . . G 5 20.615 -2.394 9.269 1 68.08 ? O2B ADP 801 B 1 HETATM 4 O O3B ADP . . . G 5 20.547 -0.029 10.175 1 61.73 ? O3B ADP 801 B 1 HETATM 5 P PA ADP . . . G 5 21.513 -0.762 6.764 1 61.85 ? PA ADP 801 B 1 HETATM 6 O O1A ADP . . . G 5 22.087 0.585 6.386 1 59.76 ? O1A ADP 801 B 1 HETATM 7 O O2A ADP . . . G 5 22.423 -1.818 7.338 1 59.22 ? O2A ADP 801 B 1 HETATM 8 O O3A ADP . . . G 5 20.24 -0.475 7.711 1 62.33 ? O3A ADP 801 B 1 HETATM 9 O O5' ADP . . . G 5 20.812 -1.4 5.457 1 59.44 ? O5' ADP 801 B 1 HETATM 10 C C5' ADP . . . G 5 20.326 -2.744 5.445 1 59.23 ? C5' ADP 801 B 1 HETATM 11 C C4' ADP . . . G 5 20.84 -3.522 4.231 1 58.02 ? C4' ADP 801 B 1 HETATM 12 O O4' ADP . . . G 5 20.703 -2.738 3.047 1 57.21 ? O4' ADP 801 B 1 HETATM 13 C C3' ADP . . . G 5 22.308 -3.924 4.282 1 55.49 ? C3' ADP 801 B 1 HETATM 14 O O3' ADP . . . G 5 22.515 -5.197 4.887 1 54.95 ? O3' ADP 801 B 1 HETATM 15 C C2' ADP . . . G 5 22.732 -3.945 2.827 1 55.73 ? C2' ADP 801 B 1 HETATM 16 O O2' ADP . . . G 5 22.542 -5.207 2.187 1 51.08 ? O2' ADP 801 B 1 HETATM 17 C C1' ADP . . . G 5 21.8 -2.966 2.164 1 55.77 ? C1' ADP 801 B 1 HETATM 18 N N9 ADP . . . G 5 22.503 -1.702 1.856 1 56.73 ? N9 ADP 801 B 1 HETATM 19 C C8 ADP . . . G 5 22.531 -0.548 2.559 1 58.31 ? C8 ADP 801 B 1 HETATM 20 N N7 ADP . . . G 5 23.28 0.388 1.917 1 57.82 ? N7 ADP 801 B 1 HETATM 21 C C5 ADP . . . G 5 23.727 -0.178 0.781 1 56.8 ? C5 ADP 801 B 1 HETATM 22 C C6 ADP . . . G 5 24.563 0.226 -0.372 1 56.69 ? C6 ADP 801 B 1 HETATM 23 N N6 ADP . . . G 5 25.092 1.471 -0.452 1 55.37 ? N6 ADP 801 B 1 HETATM 24 N N1 ADP . . . G 5 24.785 -0.699 -1.344 1 55.49 ? N1 ADP 801 B 1 HETATM 25 C C2 ADP . . . G 5 24.274 -1.948 -1.29 1 54.7 ? C2 ADP 801 B 1 HETATM 26 N N3 ADP . . . G 5 23.51 -2.378 -0.274 1 56.09 ? N3 ADP 801 B 1 HETATM 27 C C4 ADP . . . G 5 23.214 -1.554 0.756 1 56.19 ? C4 ADP 801 B 1 # _model_server_stats.io_time_ms 36 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 94 _model_server_stats.query_time_ms 350 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #