data_5KHW # _model_server_result.job_id Tx0SkyzhCErBUukbLYYpUw _model_server_result.datetime_utc '2024-10-16 16:23:04' _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 5khw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1201}' # _entry.id 5KHW # _exptl.entry_id 5KHW _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 116.74 _cell.angle_gamma 90 _cell.entry_id 5KHW _cell.length_a 45.631 _cell.length_b 146.62 _cell.length_c 49.936 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KHW _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 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,G 1 1 B,E,F,H 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 E 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 C GLU 195 A GLU 1033 1_555 A N PTR 196 A PTR 1034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale2 A C PTR 196 A PTR 1034 1_555 A N PTR 197 A PTR 1035 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.349 ? covale ? covale3 A C PTR 197 A PTR 1035 1_555 A N THR 198 A THR 1036 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.352 ? covale ? covale4 B C GLU 195 B GLU 1033 1_555 B N PTR 196 B PTR 1034 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.355 ? covale ? covale5 B C PTR 196 B PTR 1034 1_555 B N PTR 197 B PTR 1035 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.351 ? covale ? covale6 B C PTR 197 B PTR 1035 1_555 B N THR 198 B THR 1036 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.347 ? metalc ? metalc1 A OD1 ASN 170 A ASN 1008 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.204 ? metalc ? metalc2 C O2B ADP . A ADP 1201 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.577 ? metalc ? metalc3 C O1A ADP . A ADP 1201 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc4 C O3A ADP . A ADP 1201 1_555 D MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? metalc ? metalc5 B OD1 ASN 170 B ASN 1008 1_555 F MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.305 ? metalc ? metalc6 E O2B ADP . B ADP 1201 1_555 F MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.439 ? metalc ? metalc7 E O1A ADP . B ADP 1201 1_555 F MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.382 ? metalc ? metalc8 E O3A ADP . B ADP 1201 1_555 F MG MG . B MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.758 ? # _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 5KHW _atom_sites.fract_transf_matrix[1][1] 0.021915 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.011041 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00682 _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] 0.022424 _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 1201 4000 ADP PFE . D 3 MG A 1 1202 1 MG MG . E 2 ADP B 1 1201 4000 ADP PFE . F 3 MG B 1 1202 2 MG MG . G 4 HOH A 1 1301 57 HOH HOH . G 4 HOH A 2 1302 98 HOH HOH . G 4 HOH A 3 1303 83 HOH HOH . G 4 HOH A 4 1304 101 HOH HOH . G 4 HOH A 5 1305 28 HOH HOH . G 4 HOH A 6 1306 10 HOH HOH . G 4 HOH A 7 1307 50 HOH HOH . G 4 HOH A 8 1308 45 HOH HOH . G 4 HOH A 9 1309 66 HOH HOH . G 4 HOH A 10 1310 94 HOH HOH . G 4 HOH A 11 1311 43 HOH HOH . G 4 HOH A 12 1312 21 HOH HOH . G 4 HOH A 13 1313 95 HOH HOH . G 4 HOH A 14 1314 17 HOH HOH . G 4 HOH A 15 1315 42 HOH HOH . G 4 HOH A 16 1316 61 HOH HOH . G 4 HOH A 17 1317 27 HOH HOH . G 4 HOH A 18 1318 3 HOH HOH . G 4 HOH A 19 1319 56 HOH HOH . G 4 HOH A 20 1320 85 HOH HOH . G 4 HOH A 21 1321 9 HOH HOH . G 4 HOH A 22 1322 78 HOH HOH . G 4 HOH A 23 1323 75 HOH HOH . G 4 HOH A 24 1324 6 HOH HOH . G 4 HOH A 25 1325 82 HOH HOH . G 4 HOH A 26 1326 47 HOH HOH . G 4 HOH A 27 1327 20 HOH HOH . G 4 HOH A 28 1328 71 HOH HOH . G 4 HOH A 29 1329 62 HOH HOH . G 4 HOH A 30 1330 77 HOH HOH . G 4 HOH A 31 1331 12 HOH HOH . G 4 HOH A 32 1332 53 HOH HOH . G 4 HOH A 33 1333 23 HOH HOH . G 4 HOH A 34 1334 69 HOH HOH . G 4 HOH A 35 1335 5 HOH HOH . G 4 HOH A 36 1336 33 HOH HOH . G 4 HOH A 37 1337 96 HOH HOH . G 4 HOH A 38 1338 59 HOH HOH . G 4 HOH A 39 1339 4 HOH HOH . G 4 HOH A 40 1340 44 HOH HOH . G 4 HOH A 41 1341 14 HOH HOH . G 4 HOH A 42 1342 11 HOH HOH . G 4 HOH A 43 1343 13 HOH HOH . G 4 HOH A 44 1344 15 HOH HOH . G 4 HOH A 45 1345 35 HOH HOH . G 4 HOH A 46 1346 48 HOH HOH . G 4 HOH A 47 1347 31 HOH HOH . G 4 HOH A 48 1348 92 HOH HOH . G 4 HOH A 49 1349 74 HOH HOH . G 4 HOH A 50 1350 63 HOH HOH . H 4 HOH B 1 1301 99 HOH HOH . H 4 HOH B 2 1302 103 HOH HOH . H 4 HOH B 3 1303 86 HOH HOH . H 4 HOH B 4 1304 70 HOH HOH . H 4 HOH B 5 1305 68 HOH HOH . H 4 HOH B 6 1306 8 HOH HOH . H 4 HOH B 7 1307 19 HOH HOH . H 4 HOH B 8 1308 29 HOH HOH . H 4 HOH B 9 1309 81 HOH HOH . H 4 HOH B 10 1310 60 HOH HOH . H 4 HOH B 11 1311 100 HOH HOH . H 4 HOH B 12 1312 64 HOH HOH . H 4 HOH B 13 1313 55 HOH HOH . H 4 HOH B 14 1314 97 HOH HOH . H 4 HOH B 15 1315 2 HOH HOH . H 4 HOH B 16 1316 93 HOH HOH . H 4 HOH B 17 1317 72 HOH HOH . H 4 HOH B 18 1318 36 HOH HOH . H 4 HOH B 19 1319 41 HOH HOH . H 4 HOH B 20 1320 54 HOH HOH . H 4 HOH B 21 1321 91 HOH HOH . H 4 HOH B 22 1322 102 HOH HOH . H 4 HOH B 23 1323 49 HOH HOH . H 4 HOH B 24 1324 30 HOH HOH . H 4 HOH B 25 1325 51 HOH HOH . H 4 HOH B 26 1326 34 HOH HOH . H 4 HOH B 27 1327 87 HOH HOH . H 4 HOH B 28 1328 84 HOH HOH . H 4 HOH B 29 1329 7 HOH HOH . H 4 HOH B 30 1330 38 HOH HOH . H 4 HOH B 31 1331 25 HOH HOH . H 4 HOH B 32 1332 37 HOH HOH . H 4 HOH B 33 1333 40 HOH HOH . H 4 HOH B 34 1334 46 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 . . . E 2 40.606 18.402 33.483 1 45.72 ? PB ADP 1201 B 1 HETATM 2 O O1B ADP . . . E 2 39.421 18.172 32.637 1 45.9 ? O1B ADP 1201 B 1 HETATM 3 O O2B ADP . . . E 2 41.552 19.636 33.274 1 47.62 ? O2B ADP 1201 B 1 HETATM 4 O O3B ADP . . . E 2 40.262 18.608 35.01 1 47.41 ? O3B ADP 1201 B 1 HETATM 5 P PA ADP . . . E 2 42.689 16.087 33.142 1 42.66 ? PA ADP 1201 B 1 HETATM 6 O O1A ADP . . . E 2 43.527 16.337 31.959 1 45.1 ? O1A ADP 1201 B 1 HETATM 7 O O2A ADP . . . E 2 41.867 14.759 33.221 1 43.67 ? O2A ADP 1201 B 1 HETATM 8 O O3A ADP . . . E 2 41.652 17.219 33.499 1 43.76 ? O3A ADP 1201 B 1 HETATM 9 O O5' ADP . . . E 2 43.542 15.957 34.5 1 40.68 ? O5' ADP 1201 B 1 HETATM 10 C C5' ADP . . . E 2 44.152 16.947 35.263 1 39.19 ? C5' ADP 1201 B 1 HETATM 11 C C4' ADP . . . E 2 45.631 16.643 35.548 1 44.03 ? C4' ADP 1201 B 1 HETATM 12 O O4' ADP . . . E 2 45.728 15.445 36.293 1 49.34 ? O4' ADP 1201 B 1 HETATM 13 C C3' ADP . . . E 2 46.537 16.465 34.307 1 43.05 ? C3' ADP 1201 B 1 HETATM 14 O O3' ADP . . . E 2 46.963 17.728 33.931 1 41.68 ? O3' ADP 1201 B 1 HETATM 15 C C2' ADP . . . E 2 47.664 15.567 34.884 1 47.11 ? C2' ADP 1201 B 1 HETATM 16 O O2' ADP . . . E 2 48.537 16.422 35.547 1 47.4 ? O2' ADP 1201 B 1 HETATM 17 C C1' ADP . . . E 2 46.868 14.712 35.924 1 48.06 ? C1' ADP 1201 B 1 HETATM 18 N N9 ADP . . . E 2 46.427 13.455 35.3 1 44.84 ? N9 ADP 1201 B 1 HETATM 19 C C8 ADP . . . E 2 45.256 13.203 34.54 1 39.3 ? C8 ADP 1201 B 1 HETATM 20 N N7 ADP . . . E 2 45.163 11.927 34.14 1 40.29 ? N7 ADP 1201 B 1 HETATM 21 C C5 ADP . . . E 2 46.312 11.309 34.658 1 46.23 ? C5 ADP 1201 B 1 HETATM 22 C C6 ADP . . . E 2 46.779 9.972 34.582 1 48.37 ? C6 ADP 1201 B 1 HETATM 23 N N6 ADP . . . E 2 46.076 9.029 33.902 1 44.11 ? N6 ADP 1201 B 1 HETATM 24 N N1 ADP . . . E 2 47.96 9.628 35.205 1 51.66 ? N1 ADP 1201 B 1 HETATM 25 C C2 ADP . . . E 2 48.611 10.632 35.868 1 51.25 ? C2 ADP 1201 B 1 HETATM 26 N N3 ADP . . . E 2 48.293 11.944 36.011 1 49.54 ? N3 ADP 1201 B 1 HETATM 27 C C4 ADP . . . E 2 47.107 12.239 35.383 1 48.01 ? C4 ADP 1201 B 1 HETATM 28 H HOB2 ADP . . . E 2 42.009 20.094 33.967 0 48.37 ? HOB2 ADP 1201 B 1 HETATM 29 H HOB3 ADP . . . E 2 39.415 18.413 35.386 0 47.96 ? HOB3 ADP 1201 B 1 HETATM 30 H HOA2 ADP . . . E 2 41.781 14.205 33.986 0 44.55 ? HOA2 ADP 1201 B 1 HETATM 31 H "H5'1" ADP . . . E 2 43.593 17.016 36.224 0 40.14 ? "H5'1" ADP 1201 B 1 HETATM 32 H "H5'2" ADP . . . E 2 44.083 17.937 34.756 0 38.57 ? "H5'2" ADP 1201 B 1 HETATM 33 H H4' ADP . . . E 2 46.025 17.475 36.198 0 44.79 ? H4' ADP 1201 B 1 HETATM 34 H H3' ADP . . . E 2 46.014 15.945 33.462 0 42.04 ? H3' ADP 1201 B 1 HETATM 35 H HO3' ADP . . . E 2 47.759 17.622 33.4 0 41.52 ? HO3' ADP 1201 B 1 HETATM 36 H H2' ADP . . . E 2 48.179 14.948 34.109 0 46.85 ? H2' ADP 1201 B 1 HETATM 37 H HO2' ADP . . . E 2 49.305 15.902 35.812 0 48.3 ? HO2' ADP 1201 B 1 HETATM 38 H H1' ADP . . . E 2 47.446 14.479 36.859 0 49.47 ? H1' ADP 1201 B 1 HETATM 39 H H8 ADP . . . E 2 44.517 13.976 34.332 0 38.47 ? H8 ADP 1201 B 1 HETATM 40 H HN61 ADP . . . E 2 46.402 8.082 33.84 0 44.82 ? HN61 ADP 1201 B 1 HETATM 41 H HN62 ADP . . . E 2 45.218 9.278 33.445 0 43.03 ? HN62 ADP 1201 B 1 HETATM 42 H H2 ADP . . . E 2 49.539 10.315 36.375 0 52.6 ? H2 ADP 1201 B 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 42 #