data_4YZD # _model_server_result.job_id OuUmuupyXPOaIxtvOKOHMA _model_server_result.datetime_utc '2025-01-10 22:08:03' _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 4yzd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1002}' # _entry.id 4YZD # _exptl.entry_id 4YZD _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 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 107.07 _cell.angle_gamma 90 _cell.entry_id 4YZD _cell.length_a 191.751 _cell.length_b 122.492 _cell.length_c 77.876 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YZD _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,I 1 1 B,F,G,J 2 1 C,H,K 3 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 E N N ? 3 G N N ? 3 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 OD1 ASN 132 A ASN 693 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc2 A OD2 ASP 150 A ASP 711 1_555 D MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc3 D MG MG . A MG 1001 1_555 E O2B ADP . A ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc4 D MG MG . A MG 1001 1_555 E O2A ADP . A ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc5 B OD1 ASN 132 B ASN 693 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc6 B OD2 ASP 150 B ASP 711 1_555 F MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.745 ? metalc ? metalc7 F MG MG . B MG 1001 1_555 G O2B ADP . B ADP 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.62 ? # _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 4YZD _atom_sites.fract_transf_matrix[1][1] 0.005215 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.001602 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.008164 _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] 0.013433 _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 D 2 MG A 1 1001 1 MG MG . E 3 ADP A 1 1002 1 ADP ADP . F 2 MG B 1 1001 2 MG MG . G 3 ADP B 1 1002 2 ADP ADP . H 3 ADP C 1 1001 3 ADP ADP . I 4 HOH A 1 1101 25 HOH HOH . I 4 HOH A 2 1102 20 HOH HOH . I 4 HOH A 3 1103 24 HOH HOH . I 4 HOH A 4 1104 23 HOH HOH . I 4 HOH A 5 1105 3 HOH HOH . I 4 HOH A 6 1106 15 HOH HOH . I 4 HOH A 7 1107 2 HOH HOH . I 4 HOH A 8 1108 16 HOH HOH . I 4 HOH A 9 1109 12 HOH HOH . I 4 HOH A 10 1110 17 HOH HOH . I 4 HOH A 11 1111 19 HOH HOH . I 4 HOH A 12 1112 4 HOH HOH . J 4 HOH B 1 1101 1 HOH HOH . J 4 HOH B 2 1102 35 HOH HOH . J 4 HOH B 3 1103 21 HOH HOH . J 4 HOH B 4 1104 31 HOH HOH . J 4 HOH B 5 1105 7 HOH HOH . J 4 HOH B 6 1106 33 HOH HOH . J 4 HOH B 7 1107 5 HOH HOH . J 4 HOH B 8 1108 27 HOH HOH . J 4 HOH B 9 1109 36 HOH HOH . J 4 HOH B 10 1110 32 HOH HOH . J 4 HOH B 11 1111 18 HOH HOH . J 4 HOH B 12 1112 34 HOH HOH . K 4 HOH C 1 1101 13 HOH HOH . K 4 HOH C 2 1102 14 HOH HOH . K 4 HOH C 3 1103 11 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 . . . E 3 253.175 -7.221 -7.675 1 78.24 ? PB ADP 1002 A 1 HETATM 2 O O1B ADP . . . E 3 253.297 -6.046 -8.622 1 77.93 ? O1B ADP 1002 A 1 HETATM 3 O O2B ADP . . . E 3 251.758 -7.559 -7.278 1 100.44 ? O2B ADP 1002 A 1 HETATM 4 O O3B ADP . . . E 3 254.127 -7.202 -6.501 1 93.12 ? O3B ADP 1002 A 1 HETATM 5 P PA ADP . . . E 3 252.785 -9.842 -8.619 1 81.66 ? PA ADP 1002 A 1 HETATM 6 O O1A ADP . . . E 3 253.506 -10.838 -9.492 1 75.82 ? O1A ADP 1002 A 1 HETATM 7 O O2A ADP . . . E 3 252.35 -10.218 -7.226 1 81.77 ? O2A ADP 1002 A 1 HETATM 8 O O3A ADP . . . E 3 253.663 -8.493 -8.542 1 92.7 ? O3A ADP 1002 A 1 HETATM 9 O O5' ADP . . . E 3 251.471 -9.349 -9.405 1 80.55 ? O5' ADP 1002 A 1 HETATM 10 C C5' ADP . . . E 3 251.57 -8.411 -10.471 1 85.36 ? C5' ADP 1002 A 1 HETATM 11 C C4' ADP . . . E 3 250.192 -8.202 -11.077 1 83.08 ? C4' ADP 1002 A 1 HETATM 12 O O4' ADP . . . E 3 249.494 -9.45 -11.106 1 83.01 ? O4' ADP 1002 A 1 HETATM 13 C C3' ADP . . . E 3 249.337 -7.215 -10.289 1 81.79 ? C3' ADP 1002 A 1 HETATM 14 O O3' ADP . . . E 3 249.311 -5.919 -10.904 1 82.62 ? O3' ADP 1002 A 1 HETATM 15 C C2' ADP . . . E 3 247.954 -7.845 -10.258 1 78.85 ? C2' ADP 1002 A 1 HETATM 16 O O2' ADP . . . E 3 247.026 -7.102 -11.06 1 78.4 ? O2' ADP 1002 A 1 HETATM 17 C C1' ADP . . . E 3 248.109 -9.249 -10.826 1 74.49 ? C1' ADP 1002 A 1 HETATM 18 N N9 ADP . . . E 3 247.648 -10.268 -9.852 1 64.85 ? N9 ADP 1002 A 1 HETATM 19 C C8 ADP . . . E 3 248.388 -10.778 -8.849 1 77.31 ? C8 ADP 1002 A 1 HETATM 20 N N7 ADP . . . E 3 247.673 -11.69 -8.141 1 69.53 ? N7 ADP 1002 A 1 HETATM 21 C C5 ADP . . . E 3 246.456 -11.771 -8.7 1 62.56 ? C5 ADP 1002 A 1 HETATM 22 C C6 ADP . . . E 3 245.218 -12.532 -8.451 1 67.77 ? C6 ADP 1002 A 1 HETATM 23 N N6 ADP . . . E 3 245.158 -13.407 -7.429 1 73.88 ? N6 ADP 1002 A 1 HETATM 24 N N1 ADP . . . E 3 244.159 -12.33 -9.259 1 58.93 ? N1 ADP 1002 A 1 HETATM 25 C C2 ADP . . . E 3 244.211 -11.455 -10.281 1 68.99 ? C2 ADP 1002 A 1 HETATM 26 N N3 ADP . . . E 3 245.31 -10.724 -10.565 1 69.82 ? N3 ADP 1002 A 1 HETATM 27 C C4 ADP . . . E 3 246.441 -10.834 -9.826 1 62.51 ? C4 ADP 1002 A 1 HETATM 28 H "H5'1" ADP . . . E 3 252.258 -8.786 -11.232 1 102.43 ? "H5'1" ADP 1002 A 1 HETATM 29 H "H5'2" ADP . . . E 3 251.959 -7.462 -10.096 1 102.43 ? "H5'2" ADP 1002 A 1 HETATM 30 H H4' ADP . . . E 3 250.313 -7.821 -12.101 1 99.7 ? H4' ADP 1002 A 1 HETATM 31 H H3' ADP . . . E 3 249.723 -7.143 -9.262 1 98.15 ? H3' ADP 1002 A 1 HETATM 32 H H2' ADP . . . E 3 247.604 -7.907 -9.218 1 94.62 ? H2' ADP 1002 A 1 HETATM 33 H HO2' ADP . . . E 3 246.942 -6.205 -10.709 1 94.08 ? HO2' ADP 1002 A 1 HETATM 34 H H1' ADP . . . E 3 247.524 -9.323 -11.753 1 89.39 ? H1' ADP 1002 A 1 HETATM 35 H H8 ADP . . . E 3 249.412 -10.497 -8.635 1 92.77 ? H8 ADP 1002 A 1 HETATM 36 H HN61 ADP . . . E 3 245.963 -13.545 -6.834 1 88.66 ? HN61 ADP 1002 A 1 HETATM 37 H HN62 ADP . . . E 3 244.31 -13.93 -7.261 1 88.66 ? HN62 ADP 1002 A 1 HETATM 38 H H2 ADP . . . E 3 243.332 -11.33 -10.901 1 82.79 ? H2 ADP 1002 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 319 _model_server_stats.encode_time_ms 12 _model_server_stats.element_count 38 #