data_4DN5 # _model_server_result.job_id 0A8uJWkpJpTovOxJWy0AFA _model_server_result.datetime_utc '2024-10-22 00:17:41' _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 4dn5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":1008}' # _entry.id 4DN5 # _exptl.entry_id 4DN5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.247 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _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 4DN5 _cell.length_a 85.06 _cell.length_b 85.06 _cell.length_c 115.4 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DN5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 76 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41' # 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 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,F,G,H,I,J,N 1 1 B,K,L,M,O 2 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 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 ? 5 J N N ? 5 M 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 196 A ASN 520 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.152 ? metalc ? metalc2 A OD2 ASP 210 A ASP 534 1_555 C MG MG . A MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc3 C MG MG . A MG 1001 1_555 J O1A AGS . A AGS 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc4 C MG MG . A MG 1001 1_555 J O2B AGS . A AGS 1008 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc5 C MG MG . A MG 1001 1_555 N O HOH . A HOH 1118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.177 ? metalc ? metalc6 C MG MG . A MG 1001 1_555 N O HOH . A HOH 1119 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc7 B OD1 ASN 196 B ASN 520 1_555 K MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? metalc ? metalc8 B OD1 ASP 210 B ASP 534 1_555 K MG MG . B MG 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.165 ? metalc ? metalc9 K MG MG . B MG 1001 1_555 M O2A AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.856 ? metalc ? metalc10 K MG MG . B MG 1001 1_555 M O2B AGS . B AGS 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc11 K MG MG . B MG 1001 1_555 O O HOH . B HOH 1108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.08 ? metalc ? metalc12 K MG MG . B MG 1001 1_555 O O HOH . B HOH 1109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.528 ? # _chem_comp.formula 'C10 H16 N5 O12 P3 S' _chem_comp.formula_weight 523.247 _chem_comp.id AGS _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOTHIOPHOSPHORIC ACID-ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ATP-GAMMA-S;ADENOSINE 5'-(3-THIOTRIPHOSPHATE);ADENOSINE 5'-(GAMMA-THIOTRIPHOSPHATE);ADENOSINE-5'-DIPHOSPHATE MONOTHIOPHOSPHATE" # 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 S1G AGS doub 1 n n PG O2G AGS sing 2 n n PG O3G AGS sing 3 n n PG O3B AGS sing 4 n n PB O1B AGS doub 5 n n PB O2B AGS sing 6 n n PB O3B AGS sing 7 n n PB O3A AGS sing 8 n n PA O1A AGS doub 9 n n PA O2A AGS sing 10 n n PA O3A AGS sing 11 n n PA O5' AGS sing 12 n n O5' C5' AGS sing 13 n n C5' C4' AGS sing 14 n n C4' O4' AGS sing 15 n n C4' C3' AGS sing 16 n n O4' C1' AGS sing 17 n n C3' O3' AGS sing 18 n n C3' C2' AGS sing 19 n n C2' O2' AGS sing 20 n n C2' C1' AGS sing 21 n n C1' N9 AGS sing 22 n n N9 C8 AGS sing 23 n y N9 C4 AGS sing 24 n y C8 N7 AGS doub 25 n y N7 C5 AGS sing 26 n y C5 C6 AGS sing 27 n y C5 C4 AGS doub 28 n y C6 N6 AGS sing 29 n n C6 N1 AGS doub 30 n y N1 C2 AGS sing 31 n y C2 N3 AGS doub 32 n y N3 C4 AGS sing 33 n y O2G HOG2 AGS sing 34 n n O3G H21 AGS sing 35 n n O2B HOB2 AGS sing 36 n n O2A HOA2 AGS sing 37 n n C5' "H5'1" AGS sing 38 n n C5' "H5'2" AGS sing 39 n n C4' H4' AGS sing 40 n n C3' H3' AGS sing 41 n n O3' HO3' AGS sing 42 n n C2' H2' AGS sing 43 n n O2' HO2' AGS sing 44 n n C1' H1' AGS sing 45 n n C8 H8 AGS sing 46 n n N6 HN61 AGS sing 47 n n N6 HN62 AGS sing 48 n n C2 H2 AGS sing 49 n n # _atom_sites.entry_id 4DN5 _atom_sites.fract_transf_matrix[1][1] 0.011756 _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] 0.011756 _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] 0.008666 _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 2 MG A 1 1001 1001 MG MG . D 3 GOL A 1 1002 1 GOL GOL . E 4 EDO A 1 1003 2 EDO EDO . F 4 EDO A 1 1004 3 EDO EDO . G 4 EDO A 1 1005 4 EDO EDO . H 4 EDO A 1 1006 5 EDO EDO . I 4 EDO A 1 1007 7 EDO EDO . J 5 AGS A 1 1008 1 AGS AGS . K 2 MG B 1 1001 1001 MG MG . L 4 EDO B 1 1002 6 EDO EDO . M 5 AGS B 1 1003 1 AGS AGS . N 6 HOH A 1 1101 1 HOH HOH . N 6 HOH A 2 1102 2 HOH HOH . N 6 HOH A 3 1103 7 HOH HOH . N 6 HOH A 4 1104 9 HOH HOH . N 6 HOH A 5 1105 10 HOH HOH . N 6 HOH A 6 1106 11 HOH HOH . N 6 HOH A 7 1107 12 HOH HOH . N 6 HOH A 8 1108 14 HOH HOH . N 6 HOH A 9 1109 15 HOH HOH . N 6 HOH A 10 1110 18 HOH HOH . N 6 HOH A 11 1111 19 HOH HOH . N 6 HOH A 12 1112 20 HOH HOH . N 6 HOH A 13 1113 21 HOH HOH . N 6 HOH A 14 1114 22 HOH HOH . N 6 HOH A 15 1115 23 HOH HOH . N 6 HOH A 16 1116 24 HOH HOH . N 6 HOH A 17 1117 25 HOH HOH . N 6 HOH A 18 1118 28 HOH HOH . N 6 HOH A 19 1119 29 HOH HOH . N 6 HOH A 20 1120 30 HOH HOH . N 6 HOH A 21 1121 31 HOH HOH . N 6 HOH A 22 1122 32 HOH HOH . N 6 HOH A 23 1123 33 HOH HOH . N 6 HOH A 24 1124 34 HOH HOH . N 6 HOH A 25 1125 37 HOH HOH . N 6 HOH A 26 1126 38 HOH HOH . N 6 HOH A 27 1127 39 HOH HOH . N 6 HOH A 28 1128 40 HOH HOH . N 6 HOH A 29 1129 41 HOH HOH . N 6 HOH A 30 1130 42 HOH HOH . N 6 HOH A 31 1131 43 HOH HOH . N 6 HOH A 32 1132 44 HOH HOH . N 6 HOH A 33 1133 45 HOH HOH . N 6 HOH A 34 1134 46 HOH HOH . N 6 HOH A 35 1135 47 HOH HOH . N 6 HOH A 36 1136 48 HOH HOH . N 6 HOH A 37 1137 49 HOH HOH . N 6 HOH A 38 1138 50 HOH HOH . N 6 HOH A 39 1139 51 HOH HOH . N 6 HOH A 40 1140 65 HOH HOH . N 6 HOH A 41 1141 66 HOH HOH . N 6 HOH A 42 1142 67 HOH HOH . N 6 HOH A 43 1143 68 HOH HOH . N 6 HOH A 44 1144 70 HOH HOH . N 6 HOH A 45 1145 71 HOH HOH . N 6 HOH A 46 1146 72 HOH HOH . O 6 HOH B 1 1101 3 HOH HOH . O 6 HOH B 2 1102 4 HOH HOH . O 6 HOH B 3 1103 5 HOH HOH . O 6 HOH B 4 1104 6 HOH HOH . O 6 HOH B 5 1105 8 HOH HOH . O 6 HOH B 6 1106 13 HOH HOH . O 6 HOH B 7 1107 16 HOH HOH . O 6 HOH B 8 1108 26 HOH HOH . O 6 HOH B 9 1109 27 HOH HOH . O 6 HOH B 10 1110 35 HOH HOH . O 6 HOH B 11 1111 52 HOH HOH . O 6 HOH B 12 1112 53 HOH HOH . O 6 HOH B 13 1113 54 HOH HOH . O 6 HOH B 14 1114 55 HOH HOH . O 6 HOH B 15 1115 56 HOH HOH . O 6 HOH B 16 1116 57 HOH HOH . O 6 HOH B 17 1117 58 HOH HOH . O 6 HOH B 18 1118 59 HOH HOH . O 6 HOH B 19 1119 60 HOH HOH . O 6 HOH B 20 1120 61 HOH HOH . O 6 HOH B 21 1121 62 HOH HOH . O 6 HOH B 22 1122 63 HOH HOH . O 6 HOH B 23 1123 64 HOH HOH . O 6 HOH B 24 1124 69 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 PG AGS . . . J 5 -15.015 30.72 -6.209 1 49.53 ? PG AGS 1008 A 1 HETATM 2 S S1G AGS . . . J 5 -15.751 29.376 -5.011 1 50.29 ? S1G AGS 1008 A 1 HETATM 3 O O2G AGS . . . J 5 -15.012 30.072 -7.58 1 45.99 ? O2G AGS 1008 A 1 HETATM 4 O O3G AGS . . . J 5 -15.857 31.957 -5.945 1 46.99 ? O3G AGS 1008 A 1 HETATM 5 P PB AGS . . . J 5 -12.257 31.087 -6.889 1 38.15 ? PB AGS 1008 A 1 HETATM 6 O O1B AGS . . . J 5 -12.515 32.086 -7.98 1 38.98 ? O1B AGS 1008 A 1 HETATM 7 O O2B AGS . . . J 5 -12.037 29.649 -7.284 1 39.92 ? O2B AGS 1008 A 1 HETATM 8 O O3B AGS . . . J 5 -13.486 31.132 -5.836 1 43.35 ? O3B AGS 1008 A 1 HETATM 9 P PA AGS . . . J 5 -10.117 30.71 -5.003 1 36.19 ? PA AGS 1008 A 1 HETATM 10 O O1A AGS . . . J 5 -10.439 29.25 -5.176 1 35.31 ? O1A AGS 1008 A 1 HETATM 11 O O2A AGS . . . J 5 -10.237 31.338 -3.635 1 35.04 ? O2A AGS 1008 A 1 HETATM 12 O O3A AGS . . . J 5 -10.98 31.606 -6.044 1 37.65 ? O3A AGS 1008 A 1 HETATM 13 O O5' AGS . . . J 5 -8.599 30.946 -5.501 1 35.66 ? O5' AGS 1008 A 1 HETATM 14 C C5' AGS . . . J 5 -8.164 30.472 -6.775 1 34.87 ? C5' AGS 1008 A 1 HETATM 15 C C4' AGS . . . J 5 -6.95 29.549 -6.655 1 33.97 ? C4' AGS 1008 A 1 HETATM 16 O O4' AGS . . . J 5 -5.814 30.26 -6.161 1 33.77 ? O4' AGS 1008 A 1 HETATM 17 C C3' AGS . . . J 5 -7.154 28.379 -5.699 1 33.83 ? C3' AGS 1008 A 1 HETATM 18 O O3' AGS . . . J 5 -7.67 27.233 -6.374 1 33.5 ? O3' AGS 1008 A 1 HETATM 19 C C2' AGS . . . J 5 -5.768 28.108 -5.154 1 33.94 ? C2' AGS 1008 A 1 HETATM 20 O O2' AGS . . . J 5 -5.1 27.153 -5.983 1 33.85 ? O2' AGS 1008 A 1 HETATM 21 C C1' AGS . . . J 5 -5.058 29.45 -5.249 1 33.52 ? C1' AGS 1008 A 1 HETATM 22 N N9 AGS . . . J 5 -5.035 30.097 -3.913 1 33.49 ? N9 AGS 1008 A 1 HETATM 23 C C8 AGS . . . J 5 -6.081 30.704 -3.324 1 33.28 ? C8 AGS 1008 A 1 HETATM 24 N N7 AGS . . . J 5 -5.703 31.183 -2.12 1 33.32 ? N7 AGS 1008 A 1 HETATM 25 C C5 AGS . . . J 5 -4.403 30.875 -1.954 1 33.59 ? C5 AGS 1008 A 1 HETATM 26 C C6 AGS . . . J 5 -3.495 31.11 -0.926 1 34.01 ? C6 AGS 1008 A 1 HETATM 27 N N6 AGS . . . J 5 -3.89 31.776 0.191 1 34.77 ? N6 AGS 1008 A 1 HETATM 28 N N1 AGS . . . J 5 -2.221 30.66 -1.05 1 33.3 ? N1 AGS 1008 A 1 HETATM 29 C C2 AGS . . . J 5 -1.833 29.997 -2.154 1 33.24 ? C2 AGS 1008 A 1 HETATM 30 N N3 AGS . . . J 5 -2.691 29.76 -3.162 1 33.34 ? N3 AGS 1008 A 1 HETATM 31 C C4 AGS . . . J 5 -3.982 30.188 -3.087 1 33.65 ? C4 AGS 1008 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 25 _model_server_stats.query_time_ms 330 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 31 #