data_7ED9 # _model_server_result.job_id MzLM9VEjeQMRaDYEypcyDQ _model_server_result.datetime_utc '2024-10-20 03:41:28' _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 7ed9 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 7ED9 # _exptl.entry_id 7ED9 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 2 _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 7ED9 _cell.length_a 90.74 _cell.length_b 90.74 _cell.length_c 112.6 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ED9 _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall 'P 4nw 2abw' _symmetry.space_group_name_H-M 'P 43 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,D,E,I 1 1 B,F,G,H,J 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 ? 2 C N N ? 2 F 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 OD1 ASN 53 A ASN 32 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc2 A OD1 ASP 59 A ASP 38 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc3 A OD2 ASP 59 A ASP 38 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc4 A OD1 ASP 61 A ASP 40 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc5 A OD2 ASP 61 A ASP 40 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.378 ? metalc ? metalc6 C O2B ADP . A ADP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc7 C O2A ADP . A ADP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? metalc ? metalc8 C O2B ADP . A ADP 201 1_555 E MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.491 ? metalc ? metalc9 D MG MG . A MG 202 1_555 I O HOH . A HOH 313 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? metalc ? metalc10 E MG MG . A MG 203 1_555 I O HOH . A HOH 349 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.47 ? metalc ? metalc11 E MG MG . A MG 203 1_555 I O HOH . A HOH 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.782 ? metalc ? metalc12 E MG MG . A MG 203 1_555 I O HOH . A HOH 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc13 B OD1 ASN 53 B ASN 32 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? metalc ? metalc14 B OD1 ASP 59 B ASP 38 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc15 B OD2 ASP 59 B ASP 38 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc16 B OD1 ASP 61 B ASP 40 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? metalc ? metalc17 B OD2 ASP 61 B ASP 40 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? metalc ? metalc18 F O1B ADP . B ADP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? metalc ? metalc19 F O1A ADP . B ADP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? metalc ? metalc20 F O1B ADP . B ADP 201 1_555 H MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.457 ? metalc ? metalc21 G MG MG . B MG 202 1_555 J O HOH . B HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc22 H MG MG . B MG 203 1_555 J O HOH . B HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc23 H MG MG . B MG 203 1_555 J O HOH . B HOH 335 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc24 H MG MG . B MG 203 1_555 J O HOH . B HOH 336 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.532 ? # _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 7ED9 _atom_sites.fract_transf_matrix[1][1] 0.01102 _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] 0.01102 _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] 0.008881 _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 C 2 ADP A 1 201 1 ADP ADP . D 3 MG A 1 202 1 MG MG . E 3 MG A 1 203 4 MG MG . F 2 ADP B 1 201 2 ADP ADP . G 3 MG B 1 202 2 MG MG . H 3 MG B 1 203 3 MG MG . I 4 HOH A 1 301 105 HOH HOH . I 4 HOH A 2 302 88 HOH HOH . I 4 HOH A 3 303 67 HOH HOH . I 4 HOH A 4 304 27 HOH HOH . I 4 HOH A 5 305 41 HOH HOH . I 4 HOH A 6 306 69 HOH HOH . I 4 HOH A 7 307 49 HOH HOH . I 4 HOH A 8 308 52 HOH HOH . I 4 HOH A 9 309 36 HOH HOH . I 4 HOH A 10 310 40 HOH HOH . I 4 HOH A 11 311 75 HOH HOH . I 4 HOH A 12 312 101 HOH HOH . I 4 HOH A 13 313 1 HOH HOH . I 4 HOH A 14 314 57 HOH HOH . I 4 HOH A 15 315 78 HOH HOH . I 4 HOH A 16 316 18 HOH HOH . I 4 HOH A 17 317 56 HOH HOH . I 4 HOH A 18 318 10 HOH HOH . I 4 HOH A 19 319 39 HOH HOH . I 4 HOH A 20 320 102 HOH HOH . I 4 HOH A 21 321 12 HOH HOH . I 4 HOH A 22 322 66 HOH HOH . I 4 HOH A 23 323 20 HOH HOH . I 4 HOH A 24 324 64 HOH HOH . I 4 HOH A 25 325 59 HOH HOH . I 4 HOH A 26 326 100 HOH HOH . I 4 HOH A 27 327 13 HOH HOH . I 4 HOH A 28 328 104 HOH HOH . I 4 HOH A 29 329 81 HOH HOH . I 4 HOH A 30 330 77 HOH HOH . I 4 HOH A 31 331 8 HOH HOH . I 4 HOH A 32 332 15 HOH HOH . I 4 HOH A 33 333 11 HOH HOH . I 4 HOH A 34 334 53 HOH HOH . I 4 HOH A 35 335 89 HOH HOH . I 4 HOH A 36 336 35 HOH HOH . I 4 HOH A 37 337 72 HOH HOH . I 4 HOH A 38 338 23 HOH HOH . I 4 HOH A 39 339 96 HOH HOH . I 4 HOH A 40 340 48 HOH HOH . I 4 HOH A 41 341 103 HOH HOH . I 4 HOH A 42 342 43 HOH HOH . I 4 HOH A 43 343 24 HOH HOH . I 4 HOH A 44 344 33 HOH HOH . I 4 HOH A 45 345 62 HOH HOH . I 4 HOH A 46 346 79 HOH HOH . I 4 HOH A 47 347 9 HOH HOH . I 4 HOH A 48 348 51 HOH HOH . I 4 HOH A 49 349 55 HOH HOH . I 4 HOH A 50 350 85 HOH HOH . I 4 HOH A 51 351 5 HOH HOH . I 4 HOH A 52 352 17 HOH HOH . I 4 HOH A 53 353 3 HOH HOH . I 4 HOH A 54 354 46 HOH HOH . I 4 HOH A 55 355 4 HOH HOH . I 4 HOH A 56 356 108 HOH HOH . I 4 HOH A 57 357 44 HOH HOH . I 4 HOH A 58 358 28 HOH HOH . I 4 HOH A 59 359 84 HOH HOH . I 4 HOH A 60 360 45 HOH HOH . I 4 HOH A 61 361 90 HOH HOH . I 4 HOH A 62 362 97 HOH HOH . I 4 HOH A 63 363 107 HOH HOH . I 4 HOH A 64 364 14 HOH HOH . I 4 HOH A 65 365 80 HOH HOH . I 4 HOH A 66 366 91 HOH HOH . I 4 HOH A 67 367 7 HOH HOH . J 4 HOH B 1 301 31 HOH HOH . J 4 HOH B 2 302 95 HOH HOH . J 4 HOH B 3 303 29 HOH HOH . J 4 HOH B 4 304 73 HOH HOH . J 4 HOH B 5 305 63 HOH HOH . J 4 HOH B 6 306 30 HOH HOH . J 4 HOH B 7 307 54 HOH HOH . J 4 HOH B 8 308 50 HOH HOH . J 4 HOH B 9 309 2 HOH HOH . J 4 HOH B 10 310 37 HOH HOH . J 4 HOH B 11 311 42 HOH HOH . J 4 HOH B 12 312 93 HOH HOH . J 4 HOH B 13 313 74 HOH HOH . J 4 HOH B 14 314 65 HOH HOH . J 4 HOH B 15 315 47 HOH HOH . J 4 HOH B 16 316 83 HOH HOH . J 4 HOH B 17 317 38 HOH HOH . J 4 HOH B 18 318 22 HOH HOH . J 4 HOH B 19 319 6 HOH HOH . J 4 HOH B 20 320 106 HOH HOH . J 4 HOH B 21 321 58 HOH HOH . J 4 HOH B 22 322 32 HOH HOH . J 4 HOH B 23 323 26 HOH HOH . J 4 HOH B 24 324 70 HOH HOH . J 4 HOH B 25 325 19 HOH HOH . J 4 HOH B 26 326 82 HOH HOH . J 4 HOH B 27 327 76 HOH HOH . J 4 HOH B 28 328 98 HOH HOH . J 4 HOH B 29 329 60 HOH HOH . J 4 HOH B 30 330 94 HOH HOH . J 4 HOH B 31 331 61 HOH HOH . J 4 HOH B 32 332 16 HOH HOH . J 4 HOH B 33 333 99 HOH HOH . J 4 HOH B 34 334 71 HOH HOH . J 4 HOH B 35 335 87 HOH HOH . J 4 HOH B 36 336 86 HOH HOH . J 4 HOH B 37 337 34 HOH HOH . J 4 HOH B 38 338 25 HOH HOH . J 4 HOH B 39 339 92 HOH HOH . J 4 HOH B 40 340 68 HOH HOH . J 4 HOH B 41 341 21 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 . . . C 2 26.864 -10.024 -20.759 1 28.96 ? PB ADP 201 A 1 HETATM 2 O O1B ADP . . . C 2 26.399 -10.586 -22.082 1 28.61 ? O1B ADP 201 A 1 HETATM 3 O O2B ADP . . . C 2 25.82 -9.197 -20.048 1 29.18 ? O2B ADP 201 A 1 HETATM 4 O O3B ADP . . . C 2 28.233 -9.387 -20.791 1 29.32 ? O3B ADP 201 A 1 HETATM 5 P PA ADP . . . C 2 26.294 -11.574 -18.442 1 28.18 ? PA ADP 201 A 1 HETATM 6 O O1A ADP . . . C 2 25.009 -12.299 -18.766 1 28.14 ? O1A ADP 201 A 1 HETATM 7 O O2A ADP . . . C 2 26.233 -10.296 -17.639 1 28.29 ? O2A ADP 201 A 1 HETATM 8 O O3A ADP . . . C 2 27.05 -11.341 -19.847 1 28.63 ? O3A ADP 201 A 1 HETATM 9 O O5' ADP . . . C 2 27.247 -12.617 -17.671 1 27.93 ? O5' ADP 201 A 1 HETATM 10 C C5' ADP . . . C 2 28.569 -12.276 -17.264 1 27.56 ? C5' ADP 201 A 1 HETATM 11 C C4' ADP . . . C 2 29.234 -13.563 -16.796 1 27.43 ? C4' ADP 201 A 1 HETATM 12 O O4' ADP . . . C 2 29.463 -14.433 -17.909 1 27.44 ? O4' ADP 201 A 1 HETATM 13 C C3' ADP . . . C 2 30.593 -13.341 -16.155 1 27.37 ? C3' ADP 201 A 1 HETATM 14 O O3' ADP . . . C 2 30.479 -13.161 -14.742 1 27.37 ? O3' ADP 201 A 1 HETATM 15 C C2' ADP . . . C 2 31.343 -14.616 -16.473 1 27.69 ? C2' ADP 201 A 1 HETATM 16 O O2' ADP . . . C 2 31.198 -15.532 -15.385 1 27.59 ? O2' ADP 201 A 1 HETATM 17 C C1' ADP . . . C 2 30.659 -15.19 -17.702 1 28.11 ? C1' ADP 201 A 1 HETATM 18 N N9 ADP . . . C 2 31.583 -15.028 -18.85 1 29.33 ? N9 ADP 201 A 1 HETATM 19 C C8 ADP . . . C 2 31.524 -14.063 -19.789 1 29.84 ? C8 ADP 201 A 1 HETATM 20 N N7 ADP . . . C 2 32.525 -14.199 -20.696 1 29.91 ? N7 ADP 201 A 1 HETATM 21 C C5 ADP . . . C 2 33.252 -15.274 -20.337 1 30.12 ? C5 ADP 201 A 1 HETATM 22 C C6 ADP . . . C 2 34.449 -15.98 -20.854 1 30.51 ? C6 ADP 201 A 1 HETATM 23 N N6 ADP . . . C 2 35.092 -15.556 -21.97 1 30.37 ? N6 ADP 201 A 1 HETATM 24 N N1 ADP . . . C 2 34.88 -17.066 -20.175 1 30.59 ? N1 ADP 201 A 1 HETATM 25 C C2 ADP . . . C 2 34.256 -17.502 -19.066 1 30.41 ? C2 ADP 201 A 1 HETATM 26 N N3 ADP . . . C 2 33.168 -16.913 -18.541 1 30.15 ? N3 ADP 201 A 1 HETATM 27 C C4 ADP . . . C 2 32.627 -15.815 -19.12 1 29.81 ? C4 ADP 201 A 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 266 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #