data_3KB1 # _model_server_result.job_id vXh9RgPGNCD8kXy0jmZLYQ _model_server_result.datetime_utc '2024-10-30 06:11:51' _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 3kb1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 3KB1 # _exptl.entry_id 3KB1 _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 90.09 _cell.angle_gamma 90 _cell.entry_id 3KB1 _cell.length_a 51.44 _cell.length_b 67.682 _cell.length_c 79.403 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KB1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 VAL 23 A VAL 23 1_555 A N MSE 24 A MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale2 A C MSE 24 A MSE 24 1_555 A N SER 25 A SER 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale3 A C VAL 92 A VAL 92 1_555 A N MSE 93 A MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C MSE 93 A MSE 93 1_555 A N SER 94 A SER 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 A C GLY 115 A GLY 115 1_555 A N MSE 116 A MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale6 A C MSE 116 A MSE 116 1_555 A N ILE 117 A ILE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale7 A C VAL 147 A VAL 147 1_555 A N MSE 148 A MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale8 A C MSE 148 A MSE 148 1_555 A N GLN 149 A GLN 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale9 A C THR 175 A THR 175 1_555 A N MSE 176 A MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 A C MSE 176 A MSE 176 1_555 A N ALA 177 A ALA 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale11 A C ASN 190 A ASN 190 1_555 A N MSE 191 A MSE 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale12 A C MSE 191 A MSE 191 1_555 A N ALA 192 A ALA 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale13 B C VAL 23 B VAL 23 1_555 B N MSE 24 B MSE 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale14 B C MSE 24 B MSE 24 1_555 B N SER 25 B SER 25 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale15 B C VAL 92 B VAL 92 1_555 B N MSE 93 B MSE 93 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale16 B C MSE 93 B MSE 93 1_555 B N SER 94 B SER 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale17 B C GLY 115 B GLY 115 1_555 B N MSE 116 B MSE 116 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale18 B C MSE 116 B MSE 116 1_555 B N ILE 117 B ILE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 B C VAL 147 B VAL 147 1_555 B N MSE 148 B MSE 148 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale20 B C MSE 148 B MSE 148 1_555 B N GLN 149 B GLN 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale21 B C THR 175 B THR 175 1_555 B N MSE 176 B MSE 176 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.334 ? covale ? covale22 B C MSE 176 B MSE 176 1_555 B N ALA 177 B ALA 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale23 B C ASN 190 B ASN 190 1_555 B N MSE 191 B MSE 191 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale24 B C MSE 191 B MSE 191 1_555 B N ALA 192 B ALA 192 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A SG CYS 196 A CYS 196 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.328 ? metalc ? metalc2 A SG CYS 199 A CYS 199 1_555 D ZN ZN . A ZN 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.506 ? metalc ? metalc3 D ZN ZN . A ZN 302 1_555 B SG CYS 196 B CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc4 D ZN ZN . A ZN 302 1_555 B SG CYS 199 B CYS 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.521 ? # _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 3KB1 _atom_sites.fract_transf_matrix[1][1] 0.01944 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000032 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014775 _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] 0.012594 _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 1 301 301 ADP ADP . D 3 ZN A 1 302 302 ZN ZN . E 2 ADP B 1 301 301 ADP ADP . F 4 HOH A 1 263 1 HOH HOH . F 4 HOH A 2 264 2 HOH HOH . F 4 HOH A 3 265 3 HOH HOH . F 4 HOH A 4 266 4 HOH HOH . F 4 HOH A 5 267 5 HOH HOH . F 4 HOH A 6 268 6 HOH HOH . F 4 HOH A 7 269 7 HOH HOH . F 4 HOH A 8 270 8 HOH HOH . F 4 HOH A 9 271 9 HOH HOH . F 4 HOH A 10 272 10 HOH HOH . F 4 HOH A 11 273 11 HOH HOH . F 4 HOH A 12 274 12 HOH HOH . F 4 HOH A 13 275 13 HOH HOH . F 4 HOH A 14 276 14 HOH HOH . F 4 HOH A 15 277 15 HOH HOH . F 4 HOH A 16 278 16 HOH HOH . F 4 HOH A 17 279 17 HOH HOH . F 4 HOH A 18 280 18 HOH HOH . F 4 HOH A 19 281 19 HOH HOH . G 4 HOH B 1 263 20 HOH HOH . G 4 HOH B 2 264 21 HOH HOH . G 4 HOH B 3 265 22 HOH HOH . G 4 HOH B 4 266 23 HOH HOH . G 4 HOH B 5 267 24 HOH HOH . G 4 HOH B 6 268 25 HOH HOH . G 4 HOH B 7 269 26 HOH HOH . G 4 HOH B 8 270 27 HOH HOH . G 4 HOH B 9 271 28 HOH HOH . G 4 HOH B 10 272 29 HOH HOH . G 4 HOH B 11 273 30 HOH HOH . G 4 HOH B 12 274 31 HOH HOH . G 4 HOH B 13 275 32 HOH HOH . G 4 HOH B 14 276 33 HOH HOH . G 4 HOH B 15 277 34 HOH HOH . G 4 HOH B 16 278 35 HOH HOH . G 4 HOH B 17 279 36 HOH HOH . G 4 HOH B 18 280 37 HOH HOH . G 4 HOH B 19 281 38 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 -9.932 -7.321 16.191 1 52.12 ? PB ADP 301 A 1 HETATM 2 O O1B ADP . . . C 2 -10.223 -5.994 15.616 1 53.29 ? O1B ADP 301 A 1 HETATM 3 O O2B ADP . . . C 2 -10.18 -8.426 15.23 1 50.55 ? O2B ADP 301 A 1 HETATM 4 O O3B ADP . . . C 2 -11.039 -7.585 17.443 1 52.18 ? O3B ADP 301 A 1 HETATM 5 P PA ADP . . . C 2 -7.726 -6.422 17.641 1 51.02 ? PA ADP 301 A 1 HETATM 6 O O1A ADP . . . C 2 -8.369 -5.931 18.89 1 50.34 ? O1A ADP 301 A 1 HETATM 7 O O2A ADP . . . C 2 -7.211 -5.367 16.762 1 51.85 ? O2A ADP 301 A 1 HETATM 8 O O3A ADP . . . C 2 -8.589 -7.412 16.872 1 52.63 ? O3A ADP 301 A 1 HETATM 9 O O5' ADP . . . C 2 -6.394 -7.222 18.119 1 48.09 ? O5' ADP 301 A 1 HETATM 10 C C5' ADP . . . C 2 -6.451 -8.103 19.253 1 46.23 ? C5' ADP 301 A 1 HETATM 11 C C4' ADP . . . C 2 -5.354 -7.987 20.365 1 45.72 ? C4' ADP 301 A 1 HETATM 12 O O4' ADP . . . C 2 -4.1 -8.315 19.737 1 43.61 ? O4' ADP 301 A 1 HETATM 13 C C3' ADP . . . C 2 -5.107 -6.568 21.021 1 47.2 ? C3' ADP 301 A 1 HETATM 14 O O3' ADP . . . C 2 -4.593 -6.665 22.374 1 46.98 ? O3' ADP 301 A 1 HETATM 15 C C2' ADP . . . C 2 -4.087 -6.018 20.05 1 46.43 ? C2' ADP 301 A 1 HETATM 16 O O2' ADP . . . C 2 -3.509 -4.83 20.621 1 47.81 ? O2' ADP 301 A 1 HETATM 17 C C1' ADP . . . C 2 -3.162 -7.238 19.938 1 42.61 ? C1' ADP 301 A 1 HETATM 18 N N9 ADP . . . C 2 -2.334 -7.224 18.746 1 38.17 ? N9 ADP 301 A 1 HETATM 19 C C8 ADP . . . C 2 -2.741 -7.092 17.451 1 37.04 ? C8 ADP 301 A 1 HETATM 20 N N7 ADP . . . C 2 -1.78 -7.127 16.586 1 39.1 ? N7 ADP 301 A 1 HETATM 21 C C5 ADP . . . C 2 -0.629 -7.304 17.349 1 37.55 ? C5 ADP 301 A 1 HETATM 22 C C6 ADP . . . C 2 0.749 -7.42 17.02 1 34.04 ? C6 ADP 301 A 1 HETATM 23 N N6 ADP . . . C 2 1.212 -7.385 15.786 1 33.31 ? N6 ADP 301 A 1 HETATM 24 N N1 ADP . . . C 2 1.635 -7.586 18.038 1 32.82 ? N1 ADP 301 A 1 HETATM 25 C C2 ADP . . . C 2 1.198 -7.63 19.308 1 33.21 ? C2 ADP 301 A 1 HETATM 26 N N3 ADP . . . C 2 -0.071 -7.529 19.74 1 36.54 ? N3 ADP 301 A 1 HETATM 27 C C4 ADP . . . C 2 -0.952 -7.366 18.686 1 38.04 ? C4 ADP 301 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 27 #