data_6HD0 # _model_server_result.job_id 4YrG1C_ERWuOJFZljDFGyQ _model_server_result.datetime_utc '2024-11-12 20:25:12' _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 6hd0 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"P","auth_seq_id":501}' # _entry.id 6HD0 # _exptl.entry_id 6HD0 _exptl.method 'X-RAY DIFFRACTION' # _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 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 6HD0 _cell.length_a 185.12 _cell.length_b 185.12 _cell.length_c 122.426 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6HD0 _symmetry.cell_setting ? _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dodecameric _pdbx_struct_assembly.oligomeric_count 12 _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,M,N,O,P,Q,R _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 M N N ? 3 N N N ? 3 O N N ? 3 P N N ? 3 Q N N ? 3 R 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 6HD0 _atom_sites.fract_transf_matrix[1][1] 0.005402 _atom_sites.fract_transf_matrix[1][2] 0.003119 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006238 _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] 0.008168 _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 M 3 ADP B 1 501 1 ADP ADP . N 3 ADP T 1 501 1 ADP ADP . O 3 ADP U 1 501 1 ADP ADP . P 3 ADP V 1 501 1 ADP ADP . Q 3 ADP A 1 501 1 ADP ADP . R 3 ADP C 1 501 1 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 . . . P 3 82.971 -58.192 -11.149 1 68.09 ? PB ADP 501 V 1 HETATM 2 O O1B ADP . . . P 3 83.093 -58.941 -12.457 1 71.31 ? O1B ADP 501 V 1 HETATM 3 O O2B ADP . . . P 3 84.024 -57.108 -10.995 1 64.57 ? O2B ADP 501 V 1 HETATM 4 O O3B ADP . . . P 3 82.906 -59.129 -9.96 1 69.48 ? O3B ADP 501 V 1 HETATM 5 P PA ADP . . . P 3 80.715 -56.561 -10.165 1 66.69 ? PA ADP 501 V 1 HETATM 6 O O1A ADP . . . P 3 80.081 -55.413 -10.883 1 67.87 ? O1A ADP 501 V 1 HETATM 7 O O2A ADP . . . P 3 81.594 -56.248 -8.997 1 63.44 ? O2A ADP 501 V 1 HETATM 8 O O3A ADP . . . P 3 81.555 -57.418 -11.227 1 66.26 ? O3A ADP 501 V 1 HETATM 9 O O5' ADP . . . P 3 79.575 -57.618 -9.734 1 67.59 ? O5' ADP 501 V 1 HETATM 10 C C5' ADP . . . P 3 79.95 -58.999 -9.46 1 69.79 ? C5' ADP 501 V 1 HETATM 11 C C4' ADP . . . P 3 78.739 -59.814 -9.068 1 72.24 ? C4' ADP 501 V 1 HETATM 12 O O4' ADP . . . P 3 78.026 -59.133 -8.005 1 72.82 ? O4' ADP 501 V 1 HETATM 13 C C3' ADP . . . P 3 77.713 -60.09 -10.178 1 72.79 ? C3' ADP 501 V 1 HETATM 14 O O3' ADP . . . P 3 77.402 -61.478 -10.231 1 69.72 ? O3' ADP 501 V 1 HETATM 15 C C2' ADP . . . P 3 76.49 -59.249 -9.795 1 72.67 ? C2' ADP 501 V 1 HETATM 16 O O2' ADP . . . P 3 75.273 -59.899 -10.094 1 71.48 ? O2' ADP 501 V 1 HETATM 17 C C1' ADP . . . P 3 76.648 -59.069 -8.288 1 72.96 ? C1' ADP 501 V 1 HETATM 18 N N9 ADP . . . P 3 76.158 -57.78 -7.817 1 72.88 ? N9 ADP 501 V 1 HETATM 19 C C8 ADP . . . P 3 76.924 -56.69 -7.491 1 71.15 ? C8 ADP 501 V 1 HETATM 20 N N7 ADP . . . P 3 76.22 -55.654 -7.111 1 72.61 ? N7 ADP 501 V 1 HETATM 21 C C5 ADP . . . P 3 74.903 -56.082 -7.199 1 76.02 ? C5 ADP 501 V 1 HETATM 22 C C6 ADP . . . P 3 73.677 -55.438 -6.935 1 76.49 ? C6 ADP 501 V 1 HETATM 23 N N6 ADP . . . P 3 73.579 -54.179 -6.52 1 75.35 ? N6 ADP 501 V 1 HETATM 24 N N1 ADP . . . P 3 72.54 -56.149 -7.131 1 76.97 ? N1 ADP 501 V 1 HETATM 25 C C2 ADP . . . P 3 72.646 -57.416 -7.554 1 77.47 ? C2 ADP 501 V 1 HETATM 26 N N3 ADP . . . P 3 73.739 -58.123 -7.835 1 74.37 ? N3 ADP 501 V 1 HETATM 27 C C4 ADP . . . P 3 74.851 -57.394 -7.635 1 74.95 ? C4 ADP 501 V 1 # _model_server_stats.io_time_ms 56 _model_server_stats.parse_time_ms 32 _model_server_stats.create_model_time_ms 53 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 27 #