data_3K30 # _model_server_result.job_id EA_nuAKtgwxqSLXEYhRekg _model_server_result.datetime_utc '2024-11-22 14:45:31' _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 3k30 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":803}' # _entry.id 3K30 # _exptl.entry_id 3K30 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 427.201 _entity.id 4 _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 3K30 _cell.length_a 101.141 _cell.length_b 107.035 _cell.length_c 153.352 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3K30 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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,H,I,J _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 ? 4 E N N ? 4 H 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 SG CYS 348 A CYS 348 1_555 C FE4 SF4 . A SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc2 A SG CYS 351 A CYS 351 1_555 C FE3 SF4 . A SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.211 ? metalc ? metalc3 A SG CYS 354 A CYS 354 1_555 C FE1 SF4 . A SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.264 ? metalc ? metalc4 A SG CYS 366 A CYS 366 1_555 C FE2 SF4 . A SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? metalc ? metalc5 B SG CYS 348 B CYS 348 1_555 F FE4 SF4 . B SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? metalc ? metalc6 B SG CYS 351 B CYS 351 1_555 F FE2 SF4 . B SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc7 B SG CYS 354 B CYS 354 1_555 F FE3 SF4 . B SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.28 ? metalc ? metalc8 B SG CYS 366 B CYS 366 1_555 F FE1 SF4 . B SF4 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? # _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 3K30 _atom_sites.fract_transf_matrix[1][1] 0.009887 _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] 0.009343 _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] 0.006521 _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 SF4 A 1 801 801 SF4 SF4 . D 3 FMN A 1 802 802 FMN FMN . E 4 ADP A 1 803 803 ADP ADP . F 2 SF4 B 1 801 801 SF4 SF4 . G 3 FMN B 1 802 802 FMN FMN . H 4 ADP B 1 803 803 ADP ADP . I 5 HOH A 1 902 902 HOH HOH . I 5 HOH A 2 905 905 HOH HOH . J 5 HOH B 1 901 901 HOH HOH . J 5 HOH B 2 902 902 HOH HOH . J 5 HOH B 3 903 903 HOH HOH . J 5 HOH B 4 904 904 HOH HOH . J 5 HOH B 5 905 905 HOH HOH . J 5 HOH B 6 906 906 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 . . . H 4 20.203 -3.864 46.328 1 10.23 ? PB ADP 803 B 1 HETATM 2 O O1B ADP . . . H 4 19.865 -4.762 45.19 1 9.84 ? O1B ADP 803 B 1 HETATM 3 O O2B ADP . . . H 4 21.228 -2.829 46.06 1 12.17 ? O2B ADP 803 B 1 HETATM 4 O O3B ADP . . . H 4 19.04 -3.272 47.061 1 15.23 ? O3B ADP 803 B 1 HETATM 5 P PA ADP . . . H 4 21.418 -4.389 48.871 1 9.14 ? PA ADP 803 B 1 HETATM 6 O O1A ADP . . . H 4 22.683 -5.13 49.109 1 11.46 ? O1A ADP 803 B 1 HETATM 7 O O2A ADP . . . H 4 21.47 -2.933 49.09 1 10.63 ? O2A ADP 803 B 1 HETATM 8 O O3A ADP . . . H 4 20.831 -4.854 47.432 1 10.28 ? O3A ADP 803 B 1 HETATM 9 O O5' ADP . . . H 4 20.398 -5.006 49.94 1 12.6 ? O5' ADP 803 B 1 HETATM 10 C C5' ADP . . . H 4 20.101 -6.394 49.927 1 11.96 ? C5' ADP 803 B 1 HETATM 11 C C4' ADP . . . H 4 19.419 -6.688 51.234 1 13.37 ? C4' ADP 803 B 1 HETATM 12 O O4' ADP . . . H 4 18.882 -8.011 51.205 1 14.4 ? O4' ADP 803 B 1 HETATM 13 C C3' ADP . . . H 4 20.368 -6.61 52.431 1 15.84 ? C3' ADP 803 B 1 HETATM 14 O O3' ADP . . . H 4 19.788 -5.644 53.322 1 17.87 ? O3' ADP 803 B 1 HETATM 15 C C2' ADP . . . H 4 20.38 -8.024 53.024 1 15.36 ? C2' ADP 803 B 1 HETATM 16 O O2' ADP . . . H 4 20.294 -8.084 54.452 1 15.05 ? O2' ADP 803 B 1 HETATM 17 C C1' ADP . . . H 4 19.073 -8.584 52.497 1 15.22 ? C1' ADP 803 B 1 HETATM 18 N N9 ADP . . . H 4 19.105 -10.034 52.393 1 15.74 ? N9 ADP 803 B 1 HETATM 19 C C8 ADP . . . H 4 20.052 -10.776 51.833 1 16.92 ? C8 ADP 803 B 1 HETATM 20 N N7 ADP . . . H 4 19.739 -12.081 51.913 1 18.02 ? N7 ADP 803 B 1 HETATM 21 C C5 ADP . . . H 4 18.568 -12.169 52.546 1 18.25 ? C5 ADP 803 B 1 HETATM 22 C C6 ADP . . . H 4 17.66 -13.254 52.975 1 17.78 ? C6 ADP 803 B 1 HETATM 23 N N6 ADP . . . H 4 17.976 -14.529 52.701 1 18.14 ? N6 ADP 803 B 1 HETATM 24 N N1 ADP . . . H 4 16.521 -12.939 53.606 1 15.19 ? N1 ADP 803 B 1 HETATM 25 C C2 ADP . . . H 4 16.22 -11.668 53.869 1 17.14 ? C2 ADP 803 B 1 HETATM 26 N N3 ADP . . . H 4 16.994 -10.624 53.517 1 19.46 ? N3 ADP 803 B 1 HETATM 27 C C4 ADP . . . H 4 18.159 -10.812 52.86 1 18.11 ? C4 ADP 803 B 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 27 #