data_4JD2 # _model_server_result.job_id kKcSbL9IRz95ytxAzD2i_A _model_server_result.datetime_utc '2024-11-04 23:23:46' _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 4jd2 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":502}' # _entry.id 4JD2 # _exptl.entry_id 4JD2 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 507.181 _entity.id 10 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "ADENOSINE-5'-TRIPHOSPHATE" _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 120 _cell.entry_id 4JD2 _cell.length_a 231.538 _cell.length_b 231.538 _cell.length_c 109.743 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JD2 _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details octameric _pdbx_struct_assembly.oligomeric_count 8 _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 _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 ? 10 J N N ? 10 L 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 I CA CA . A CA 501 1_555 J O1B ATP . A ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.578 ? metalc ? metalc2 I CA CA . A CA 501 1_555 J O2G ATP . A ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.643 ? metalc ? metalc3 K CA CA . B CA 501 1_555 L O1B ATP . B ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.566 ? metalc ? metalc4 K CA CA . B CA 501 1_555 L O2G ATP . B ATP 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.697 ? # _chem_comp.formula 'C10 H16 N5 O13 P3' _chem_comp.formula_weight 507.181 _chem_comp.id ATP _chem_comp.mon_nstd_flag . _chem_comp.name "ADENOSINE-5'-TRIPHOSPHATE" _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 PG O1G ATP doub 70 n n PG O2G ATP sing 71 n n PG O3G ATP sing 72 n n PG O3B ATP sing 73 n n O2G HOG2 ATP sing 74 n n O3G HOG3 ATP sing 75 n n PB O1B ATP doub 76 n n PB O2B ATP sing 77 n n PB O3B ATP sing 78 n n PB O3A ATP sing 79 n n O2B HOB2 ATP sing 80 n n PA O1A ATP doub 81 n n PA O2A ATP sing 82 n n PA O3A ATP sing 83 n n PA O5' ATP sing 84 n n O2A HOA2 ATP sing 85 n n O5' C5' ATP sing 86 n n C5' C4' ATP sing 87 n n C5' "H5'1" ATP sing 88 n n C5' "H5'2" ATP sing 89 n n C4' O4' ATP sing 90 n n C4' C3' ATP sing 91 n n C4' H4' ATP sing 92 n n O4' C1' ATP sing 93 n n C3' O3' ATP sing 94 n n C3' C2' ATP sing 95 n n C3' H3' ATP sing 96 n n O3' HO3' ATP sing 97 n n C2' O2' ATP sing 98 n n C2' C1' ATP sing 99 n n C2' H2' ATP sing 100 n n O2' HO2' ATP sing 101 n n C1' N9 ATP sing 102 n n C1' H1' ATP sing 103 n n N9 C8 ATP sing 104 n y N9 C4 ATP sing 105 n y C8 N7 ATP doub 106 n y C8 H8 ATP sing 107 n n N7 C5 ATP sing 108 n y C5 C6 ATP sing 109 n y C5 C4 ATP doub 110 n y C6 N6 ATP sing 111 n n C6 N1 ATP doub 112 n y N6 HN61 ATP sing 113 n n N6 HN62 ATP sing 114 n n N1 C2 ATP sing 115 n y C2 N3 ATP doub 116 n y C2 H2 ATP sing 117 n n N3 C4 ATP sing 118 n y # _atom_sites.entry_id 4JD2 _atom_sites.fract_transf_matrix[1][1] 0.004319 _atom_sites.fract_transf_matrix[1][2] 0.002494 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.004987 _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] 0.009112 _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 I 9 CA A 1 501 500 CA CA . J 10 ATP A 1 502 1001 ATP ATP . K 9 CA B 1 501 501 CA CA . L 10 ATP B 1 502 1002 ATP ATP . M 11 PG4 B 1 503 1 PG4 PG4 . N 11 PG4 F 1 201 1 PG4 PG4 . # 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 PG ATP . . . J 10 41.816 -93.609 15.128 1 62.41 ? PG ATP 502 A 1 HETATM 2 O O1G ATP . . . J 10 41.488 -92.507 16.099 1 60.34 ? O1G ATP 502 A 1 HETATM 3 O O2G ATP . . . J 10 41.132 -93.487 13.778 1 66.95 ? O2G ATP 502 A 1 HETATM 4 O O3G ATP . . . J 10 43.286 -93.894 14.989 1 65.48 ? O3G ATP 502 A 1 HETATM 5 P PB ATP . . . J 10 40.428 -96.1 15.017 1 66.37 ? PB ATP 502 A 1 HETATM 6 O O1B ATP . . . J 10 40.902 -96.087 13.576 1 70.47 ? O1B ATP 502 A 1 HETATM 7 O O2B ATP . . . J 10 40.522 -97.364 15.829 1 64.54 ? O2B ATP 502 A 1 HETATM 8 O O3B ATP . . . J 10 41.222 -94.942 15.827 1 64.42 ? O3B ATP 502 A 1 HETATM 9 P PA ATP . . . J 10 37.704 -96.276 14.175 1 67.29 ? PA ATP 502 A 1 HETATM 10 O O1A ATP . . . J 10 37.499 -95.488 12.9 1 66.38 ? O1A ATP 502 A 1 HETATM 11 O O2A ATP . . . J 10 37.91 -97.763 14.146 1 66.62 ? O2A ATP 502 A 1 HETATM 12 O O3A ATP . . . J 10 38.891 -95.6 15.038 1 67.17 ? O3A ATP 502 A 1 HETATM 13 O O5' ATP . . . J 10 36.42 -96.042 15.113 1 69.59 ? O5' ATP 502 A 1 HETATM 14 C C5' ATP . . . J 10 36.368 -96.555 16.443 1 69.39 ? C5' ATP 502 A 1 HETATM 15 C C4' ATP . . . J 10 35.348 -95.759 17.251 1 71.05 ? C4' ATP 502 A 1 HETATM 16 O O4' ATP . . . J 10 34.104 -95.688 16.548 1 71.83 ? O4' ATP 502 A 1 HETATM 17 C C3' ATP . . . J 10 35.037 -96.403 18.596 1 71.93 ? C3' ATP 502 A 1 HETATM 18 O O3' ATP . . . J 10 35.196 -95.438 19.641 1 71.97 ? O3' ATP 502 A 1 HETATM 19 C C2' ATP . . . J 10 33.592 -96.855 18.479 1 71.53 ? C2' ATP 502 A 1 HETATM 20 O O2' ATP . . . J 10 32.889 -96.77 19.713 1 72.33 ? O2' ATP 502 A 1 HETATM 21 C C1' ATP . . . J 10 33.033 -95.867 17.477 1 72.36 ? C1' ATP 502 A 1 HETATM 22 N N9 ATP . . . J 10 31.776 -96.315 16.829 1 73.21 ? N9 ATP 502 A 1 HETATM 23 C C8 ATP . . . J 10 31.579 -97.454 16.154 1 75.74 ? C8 ATP 502 A 1 HETATM 24 N N7 ATP . . . J 10 30.304 -97.531 15.692 1 78.04 ? N7 ATP 502 A 1 HETATM 25 C C5 ATP . . . J 10 29.668 -96.419 16.065 1 77.73 ? C5 ATP 502 A 1 HETATM 26 C C6 ATP . . . J 10 28.302 -95.868 15.909 1 82.15 ? C6 ATP 502 A 1 HETATM 27 N N6 ATP . . . J 10 27.335 -96.534 15.243 1 82.75 ? N6 ATP 502 A 1 HETATM 28 N N1 ATP . . . J 10 28.05 -94.663 16.455 1 84.86 ? N1 ATP 502 A 1 HETATM 29 C C2 ATP . . . J 10 29.006 -93.986 17.131 1 83.75 ? C2 ATP 502 A 1 HETATM 30 N N3 ATP . . . J 10 30.263 -94.432 17.317 1 79.3 ? N3 ATP 502 A 1 HETATM 31 C C4 ATP . . . J 10 30.646 -95.622 16.814 1 75.66 ? C4 ATP 502 A 1 # _model_server_stats.io_time_ms 34 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 276 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 31 #