data_4XCD # _model_server_result.job_id SJKiwS_oywSdMekXI6gGUw _model_server_result.datetime_utc '2025-04-13 04:45:29' _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 4xcd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":600}' # _entry.id 4XCD # _exptl.entry_id 4XCD _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 6 _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 120 _cell.entry_id 4XCD _cell.length_a 163.36 _cell.length_b 163.36 _cell.length_c 327.29 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XCD _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octadecameric _pdbx_struct_assembly.oligomeric_count 18 _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,K,L _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_645 -y+1,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 245.04 -141.47391 0 3 'crystal symmetry operation' 3_765 -x+y+2,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 245.04 141.47391 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 H N N ? 2 I N N ? 2 J N N ? 2 K N N ? 2 L N N # _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 4XCD _atom_sites.fract_transf_matrix[1][1] 0.006121 _atom_sites.fract_transf_matrix[1][2] 0.003534 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007068 _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] 0.003055 _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 G 2 ADP A 1 600 600 ADP ADP . H 2 ADP B 1 600 600 ADP ADP . I 2 ADP C 1 600 600 ADP ADP . J 2 ADP D 1 600 600 ADP ADP . K 2 ADP E 1 600 600 ADP ADP . L 2 ADP F 1 600 600 ADP ADP . # 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 . . . K 2 225.843 2.154 99.433 1 136.22 ? PB ADP 600 E 1 HETATM 2 O O1B ADP . . . K 2 225.091 1.782 98.179 1 138.81 -1 O1B ADP 600 E 1 HETATM 3 O O2B ADP . . . K 2 227.309 1.769 99.358 1 131.45 ? O2B ADP 600 E 1 HETATM 4 O O3B ADP . . . K 2 225.079 1.646 100.668 1 138.54 ? O3B ADP 600 E 1 HETATM 5 P PA ADP . . . K 2 225.777 4.703 98.19 1 133.47 ? PA ADP 600 E 1 HETATM 6 O O1A ADP . . . K 2 224.573 4.399 97.319 1 128.21 ? O1A ADP 600 E 1 HETATM 7 O O2A ADP . . . K 2 225.74 6.115 98.629 1 140.2 -1 O2A ADP 600 E 1 HETATM 8 O O3A ADP . . . K 2 225.695 3.736 99.449 1 132.91 ? O3A ADP 600 E 1 HETATM 9 O O5' ADP . . . K 2 227.123 4.273 97.418 1 138.83 ? O5' ADP 600 E 1 HETATM 10 C C5' ADP . . . K 2 227.146 3.281 96.372 1 142.49 ? C5' ADP 600 E 1 HETATM 11 C C4' ADP . . . K 2 228.405 3.382 95.547 1 147.95 ? C4' ADP 600 E 1 HETATM 12 O O4' ADP . . . K 2 228.818 4.753 95.408 1 142.31 ? O4' ADP 600 E 1 HETATM 13 C C3' ADP . . . K 2 229.618 2.653 96.121 1 159.01 ? C3' ADP 600 E 1 HETATM 14 O O3' ADP . . . K 2 229.75 1.349 95.56 1 166.93 ? O3' ADP 600 E 1 HETATM 15 C C2' ADP . . . K 2 230.812 3.551 95.737 1 159.24 ? C2' ADP 600 E 1 HETATM 16 O O2' ADP . . . K 2 231.74 2.853 94.911 1 167.88 ? O2' ADP 600 E 1 HETATM 17 C C1' ADP . . . K 2 230.16 4.716 94.982 1 148.89 ? C1' ADP 600 E 1 HETATM 18 N N9 ADP . . . K 2 230.779 6.013 95.242 1 147.11 ? N9 ADP 600 E 1 HETATM 19 C C8 ADP . . . K 2 230.716 6.75 96.396 1 148.36 ? C8 ADP 600 E 1 HETATM 20 N N7 ADP . . . K 2 231.404 7.866 96.357 1 144.02 ? N7 ADP 600 E 1 HETATM 21 C C5 ADP . . . K 2 231.958 7.866 95.086 1 142.65 ? C5 ADP 600 E 1 HETATM 22 C C6 ADP . . . K 2 232.804 8.774 94.418 1 134.08 ? C6 ADP 600 E 1 HETATM 23 N N6 ADP . . . K 2 233.232 9.917 94.95 1 131.15 ? N6 ADP 600 E 1 HETATM 24 N N1 ADP . . . K 2 233.19 8.466 93.159 1 135.22 ? N1 ADP 600 E 1 HETATM 25 C C2 ADP . . . K 2 232.751 7.325 92.614 1 141.63 ? C2 ADP 600 E 1 HETATM 26 N N3 ADP . . . K 2 231.945 6.398 93.142 1 142.68 ? N3 ADP 600 E 1 HETATM 27 C C4 ADP . . . K 2 231.581 6.729 94.387 1 146.78 ? C4 ADP 600 E 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 29 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 27 #