data_3J15 # _model_server_result.job_id uV1pHqizEBSRyS90X4vUUQ _model_server_result.datetime_utc '2024-12-22 06:04:31' _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 3j15 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 3J15 # _exptl.entry_id 3J15 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 427.201 _entity.id 3 _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 3J15 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3J15 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 ? 3 C N N ? 3 D 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 disulf ? disulf1 B SG CYS 83 B CYS 83 1_555 B SG CYS 132 B CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc1 B SG CYS 15 B CYS 15 1_555 F FE4 SF4 . B SF4 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.443 ? metalc ? metalc2 B SG CYS 20 B CYS 20 1_555 F FE2 SF4 . B SF4 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.434 ? metalc ? metalc3 B SG CYS 25 B CYS 25 1_555 F FE1 SF4 . B SF4 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.336 ? metalc ? metalc4 B SG CYS 29 B CYS 29 1_555 E FE1 SF4 . B SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.569 ? metalc ? metalc5 B SG CYS 55 B CYS 55 1_555 E FE2 SF4 . B SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc6 B SG CYS 58 B CYS 58 1_555 E FE4 SF4 . B SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.487 ? metalc ? metalc7 B SG CYS 61 B CYS 61 1_555 E FE3 SF4 . B SF4 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.359 ? metalc ? metalc8 B SG CYS 65 B CYS 65 1_555 F FE3 SF4 . B SF4 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.598 ? # _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 3J15 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 3 ADP B 1 601 598 ADP ADP . D 3 ADP B 1 602 599 ADP ADP . E 4 SF4 B 1 603 596 SF4 SF4 . F 4 SF4 B 1 604 597 SF4 SF4 . # 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 . . . D 3 -16.481 65.763 -57.275 1 13.96 ? PB ADP 602 B 1 HETATM 2 O O1B ADP . . . D 3 -16.078 65.288 -58.786 1 13.77 ? O1B ADP 602 B 1 HETATM 3 O O2B ADP . . . D 3 -15.87 64.876 -56.28 1 13.89 ? O2B ADP 602 B 1 HETATM 4 O O3B ADP . . . D 3 -16.204 67.232 -57.19 1 18.01 ? O3B ADP 602 B 1 HETATM 5 P PA ADP . . . D 3 -19.32 66.568 -57.535 1 15.85 ? PA ADP 602 B 1 HETATM 6 O O1A ADP . . . D 3 -19.299 67.201 -58.878 1 17.32 ? O1A ADP 602 B 1 HETATM 7 O O2A ADP . . . D 3 -19.413 67.429 -56.356 1 16.53 ? O2A ADP 602 B 1 HETATM 8 O O3A ADP . . . D 3 -18.05 65.615 -57.335 1 17.29 ? O3A ADP 602 B 1 HETATM 9 O O5' ADP . . . D 3 -20.523 65.564 -57.458 1 19.76 ? O5' ADP 602 B 1 HETATM 10 C C5' ADP . . . D 3 -20.485 64.25 -56.867 1 22.48 ? C5' ADP 602 B 1 HETATM 11 C C4' ADP . . . D 3 -21.589 63.396 -57.454 1 24.66 ? C4' ADP 602 B 1 HETATM 12 O O4' ADP . . . D 3 -22.798 64.188 -57.428 1 26.67 ? O4' ADP 602 B 1 HETATM 13 C C3' ADP . . . D 3 -21.374 62.975 -58.9 1 26.02 ? C3' ADP 602 B 1 HETATM 14 O O3' ADP . . . D 3 -21.704 61.593 -58.979 1 26.74 ? O3' ADP 602 B 1 HETATM 15 C C2' ADP . . . D 3 -22.315 63.844 -59.649 1 27.19 ? C2' ADP 602 B 1 HETATM 16 O O2' ADP . . . D 3 -22.837 63.25 -60.826 1 30.06 ? O2' ADP 602 B 1 HETATM 17 C C1' ADP . . . D 3 -23.458 64.156 -58.686 1 27.81 ? C1' ADP 602 B 1 HETATM 18 N N9 ADP . . . D 3 -24.031 65.476 -58.963 1 29.13 ? N9 ADP 602 B 1 HETATM 19 C C8 ADP . . . D 3 -23.387 66.692 -59.032 1 31.03 ? C8 ADP 602 B 1 HETATM 20 N N7 ADP . . . D 3 -24.147 67.701 -59.305 1 32.31 ? N7 ADP 602 B 1 HETATM 21 C C5 ADP . . . D 3 -25.39 67.112 -59.422 1 33.23 ? C5 ADP 602 B 1 HETATM 22 C C6 ADP . . . D 3 -26.669 67.648 -59.72 1 34.21 ? C6 ADP 602 B 1 HETATM 23 N N6 ADP . . . D 3 -26.813 68.951 -59.929 1 35.77 ? N6 ADP 602 B 1 HETATM 24 N N1 ADP . . . D 3 -27.746 66.804 -59.774 1 32.25 ? N1 ADP 602 B 1 HETATM 25 C C2 ADP . . . D 3 -27.564 65.491 -59.555 1 33.05 ? C2 ADP 602 B 1 HETATM 26 N N3 ADP . . . D 3 -26.404 64.854 -59.264 1 33.93 ? N3 ADP 602 B 1 HETATM 27 C C4 ADP . . . D 3 -25.335 65.749 -59.222 1 31.82 ? C4 ADP 602 B 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 369 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 27 #