data_5SUP # _model_server_result.job_id mAIyAnbokfiTbc8JY_zfjg _model_server_result.datetime_utc '2025-06-28 07:37:04' _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 5sup # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":3000}' # _entry.id 5SUP # _exptl.entry_id 5SUP _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 120 _cell.entry_id 5SUP _cell.length_a 99.346 _cell.length_b 99.346 _cell.length_c 247.469 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5SUP _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 trimeric 3 author_and_software_defined_assembly 1 PISA trimeric 3 author_and_software_defined_assembly 2 PISA trimeric 3 author_and_software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,G,J,K,L,S 1 1 B,D,I,M,N,O,T 2 1 C,F,H,P,Q,R,U 3 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 ? 4 J N N ? 4 M N N ? 4 P 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 covale ? covale1 A NZ LYS 357 A LYS 413 1_555 A OE2 GLU 358 A GLU 414 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.414 ? metalc ? metalc1 J O2B ADP . A ADP 1000 1_555 K BE BEF . A BEF 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.625 ? metalc ? metalc2 J O1B ADP . A ADP 1000 1_555 L MG MG . A MG 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc3 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc4 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc5 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1107 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.111 ? metalc ? metalc6 L MG MG . A MG 1002 1_555 S O HOH . A HOH 1111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? metalc ? metalc7 M O3B ADP . B ADP 2000 1_555 N BE BEF . B BEF 2001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.569 ? metalc ? metalc8 M O2B ADP . B ADP 2000 1_555 O MG MG . B MG 2002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.141 ? metalc ? metalc9 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc10 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc11 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc12 O MG MG . B MG 2002 1_555 T O HOH . B HOH 2108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc13 P O2B ADP . C ADP 3000 1_555 Q BE BEF . C BEF 3001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.602 ? metalc ? metalc14 P O1B ADP . C ADP 3000 1_555 R MG MG . C MG 3002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc15 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc16 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc17 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3104 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? metalc ? metalc18 R MG MG . C MG 3002 1_555 U O HOH . C HOH 3105 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.09 ? # _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 5SUP _atom_sites.fract_transf_matrix[1][1] 0.010066 _atom_sites.fract_transf_matrix[1][2] 0.005812 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011623 _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] 0.004041 _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 J 4 ADP A 1 1000 1000 ADP ADP . K 5 BEF A 1 1001 1001 BEF BEF . L 6 MG A 1 1002 1002 MG MG . M 4 ADP B 1 2000 2000 ADP ADP . N 5 BEF B 1 2001 2001 BEF BEF . O 6 MG B 1 2002 2002 MG MG . P 4 ADP C 1 3000 3000 ADP ADP . Q 5 BEF C 1 3001 3001 BEF BEF . R 6 MG C 1 3002 3002 MG MG . S 7 HOH A 1 1101 20 HOH HOH . S 7 HOH A 2 1102 5 HOH HOH . S 7 HOH A 3 1103 21 HOH HOH . S 7 HOH A 4 1104 6 HOH HOH . S 7 HOH A 5 1105 19 HOH HOH . S 7 HOH A 6 1106 16 HOH HOH . S 7 HOH A 7 1107 7 HOH HOH . S 7 HOH A 8 1108 22 HOH HOH . S 7 HOH A 9 1109 10 HOH HOH . S 7 HOH A 10 1110 18 HOH HOH . S 7 HOH A 11 1111 8 HOH HOH . S 7 HOH A 12 1112 9 HOH HOH . S 7 HOH A 13 1113 23 HOH HOH . T 7 HOH B 1 2101 3 HOH HOH . T 7 HOH B 2 2102 17 HOH HOH . T 7 HOH B 3 2103 2 HOH HOH . T 7 HOH B 4 2104 26 HOH HOH . T 7 HOH B 5 2105 25 HOH HOH . T 7 HOH B 6 2106 1 HOH HOH . T 7 HOH B 7 2107 24 HOH HOH . T 7 HOH B 8 2108 4 HOH HOH . T 7 HOH B 9 2109 27 HOH HOH . U 7 HOH C 1 3101 12 HOH HOH . U 7 HOH C 2 3102 11 HOH HOH . U 7 HOH C 3 3103 15 HOH HOH . U 7 HOH C 4 3104 13 HOH HOH . U 7 HOH C 5 3105 14 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 . . . P 4 32.012 55.311 103.322 1 46.95 ? PB ADP 3000 C 1 HETATM 2 O O1B ADP . . . P 4 30.52 55.245 103.098 1 47.78 ? O1B ADP 3000 C 1 HETATM 3 O O2B ADP . . . P 4 32.571 56.713 103.303 1 52.88 ? O2B ADP 3000 C 1 HETATM 4 O O3B ADP . . . P 4 32.521 54.441 104.445 1 46.28 ? O3B ADP 3000 C 1 HETATM 5 P PA ADP . . . P 4 31.802 54.444 100.656 1 53.91 ? PA ADP 3000 C 1 HETATM 6 O O1A ADP . . . P 4 31.5 55.808 100.083 1 53.2 ? O1A ADP 3000 C 1 HETATM 7 O O2A ADP . . . P 4 30.697 53.453 100.919 1 50.65 ? O2A ADP 3000 C 1 HETATM 8 O O3A ADP . . . P 4 32.649 54.627 102.012 1 41.08 ? O3A ADP 3000 C 1 HETATM 9 O O5' ADP . . . P 4 32.887 53.728 99.712 1 38.3 ? O5' ADP 3000 C 1 HETATM 10 C C5' ADP . . . P 4 34.012 54.456 99.228 1 48.73 ? C5' ADP 3000 C 1 HETATM 11 C C4' ADP . . . P 4 34.428 53.861 97.893 1 57.69 ? C4' ADP 3000 C 1 HETATM 12 O O4' ADP . . . P 4 35.025 52.579 98.092 1 58.69 ? O4' ADP 3000 C 1 HETATM 13 C C3' ADP . . . P 4 33.22 53.663 96.993 1 49.3 ? C3' ADP 3000 C 1 HETATM 14 O O3' ADP . . . P 4 33.4 54.403 95.784 1 62.28 ? O3' ADP 3000 C 1 HETATM 15 C C2' ADP . . . P 4 33.169 52.185 96.677 1 64.39 ? C2' ADP 3000 C 1 HETATM 16 O O2' ADP . . . P 4 33.022 51.997 95.267 1 72.93 ? O2' ADP 3000 C 1 HETATM 17 C C1' ADP . . . P 4 34.506 51.64 97.148 1 62.72 ? C1' ADP 3000 C 1 HETATM 18 N N9 ADP . . . P 4 34.319 50.319 97.797 1 63.67 ? N9 ADP 3000 C 1 HETATM 19 C C8 ADP . . . P 4 33.526 50.064 98.855 1 66.45 ? C8 ADP 3000 C 1 HETATM 20 N N7 ADP . . . P 4 33.585 48.753 99.204 1 56.06 ? N7 ADP 3000 C 1 HETATM 21 C C5 ADP . . . P 4 34.435 48.148 98.353 1 59.67 ? C5 ADP 3000 C 1 HETATM 22 C C6 ADP . . . P 4 34.955 46.775 98.158 1 70.01 ? C6 ADP 3000 C 1 HETATM 23 N N6 ADP . . . P 4 34.564 45.759 98.964 1 73.82 ? N6 ADP 3000 C 1 HETATM 24 N N1 ADP . . . P 4 35.83 46.571 97.148 1 67.33 ? N1 ADP 3000 C 1 HETATM 25 C C2 ADP . . . P 4 36.226 47.572 96.339 1 64.15 ? C2 ADP 3000 C 1 HETATM 26 N N3 ADP . . . P 4 35.796 48.84 96.459 1 60.75 ? N3 ADP 3000 C 1 HETATM 27 C C4 ADP . . . P 4 34.917 49.185 97.429 1 60.77 ? C4 ADP 3000 C 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 27 #