data_7OH7 # _model_server_result.job_id zT-IRXF8dx_otKDvWqZ2xA _model_server_result.datetime_utc '2024-12-26 12:25:14' _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 7oh7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":1502}' # _entry.id 7OH7 # _exptl.entry_id 7OH7 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 505.208 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _entity.pdbx_number_of_molecules 1 _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 7OH7 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7OH7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 3 ? 4 3 2 BMA NAG C1 O1 . O4 HO4 . sing 4 ? 4 4 3 BMA BMA C1 O1 . O3 HO3 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 B 1 NAG C 501 NAG 3 n C NAG 2 B 2 NAG C 502 NAG 3 n D NAG 1 D 1 NAG C 503 NAG 3 n D NAG 2 D 2 NAG C 504 NAG 4 n E NAG 1 E 1 NAG C 507 NAG 4 n E NAG 2 E 2 NAG C 508 NAG 4 n E BMA 3 E 3 BMA C 509 BMA 4 n E BMA 4 E 4 BMA C 510 BMA # 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 disulf ? disulf1 B SG CYS 80 C CYS 80 1_555 B SG CYS 123 C CYS 123 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 B SG CYS 176 C CYS 176 1_555 B SG CYS 190 C CYS 190 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 B ND2 ASN 199 C ASN 199 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale2 B ND2 ASN 216 C ASN 216 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale3 B ND2 ASN 288 C ASN 288 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale6 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale7 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale8 E O3 BMA . E BMA 3 1_555 E C1 BMA . E BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? metalc ? metalc1 A OD2 ASP 560 A ASP 560 1_555 H MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc2 A O THR 562 A THR 562 1_555 H MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc3 A OD1 ASP 954 A ASP 954 1_555 H MG MG . A MG 1503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.086 ? metalc ? metalc4 H MG MG . A MG 1503 1_555 I O HOH . A HOH 1601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.089 ? metalc ? metalc5 H MG MG . A MG 1503 1_555 I O HOH . A HOH 1602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc6 H MG MG . A MG 1503 1_555 I O HOH . A HOH 1603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]TRIPHOSPHATE" # 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 ACP doub 150 n n PG O2G ACP sing 151 n n PG O3G ACP sing 152 n n PG C3B ACP sing 153 n n O2G HOG2 ACP sing 154 n n O3G HOG3 ACP sing 155 n n PB O1B ACP doub 156 n n PB O2B ACP sing 157 n n PB C3B ACP sing 158 n n PB O3A ACP sing 159 n n O2B HOB2 ACP sing 160 n n C3B H3B1 ACP sing 161 n n C3B H3B2 ACP sing 162 n n PA O1A ACP doub 163 n n PA O2A ACP sing 164 n n PA O3A ACP sing 165 n n PA O5' ACP sing 166 n n O2A HOA2 ACP sing 167 n n O5' C5' ACP sing 168 n n C5' C4' ACP sing 169 n n C5' "H5'1" ACP sing 170 n n C5' "H5'2" ACP sing 171 n n C4' O4' ACP sing 172 n n C4' C3' ACP sing 173 n n C4' H4' ACP sing 174 n n O4' C1' ACP sing 175 n n C3' O3' ACP sing 176 n n C3' C2' ACP sing 177 n n C3' H3' ACP sing 178 n n O3' HO3' ACP sing 179 n n C2' O2' ACP sing 180 n n C2' C1' ACP sing 181 n n C2' H2' ACP sing 182 n n O2' HO2' ACP sing 183 n n C1' N9 ACP sing 184 n n C1' H1' ACP sing 185 n n N9 C8 ACP sing 186 n y N9 C4 ACP sing 187 n y C8 N7 ACP doub 188 n y C8 H8 ACP sing 189 n n N7 C5 ACP sing 190 n y C5 C6 ACP sing 191 n y C5 C4 ACP doub 192 n y C6 N6 ACP sing 193 n n C6 N1 ACP doub 194 n y N6 HN61 ACP sing 195 n n N6 HN62 ACP sing 196 n n N1 C2 ACP sing 197 n y C2 N3 ACP doub 198 n y C2 H2 ACP sing 199 n n N3 C4 ACP sing 200 n y # _atom_sites.entry_id 7OH7 _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 F 5 2Y5 A 1 1501 1301 2Y5 2Y5 . G 6 ACP A 1 1502 2101 ACP ACP . H 7 MG A 1 1503 2002 MG MG . I 8 HOH A 1 1601 2004 HOH HOH . I 8 HOH A 2 1602 2005 HOH HOH . I 8 HOH A 3 1603 2006 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 ACP . . . G 6 128.861 145.175 187.701 1 184.85 ? PG ACP 1502 A 1 HETATM 2 O O1G ACP . . . G 6 130.113 145.926 187.318 1 184.85 ? O1G ACP 1502 A 1 HETATM 3 O O2G ACP . . . G 6 127.966 145.037 186.492 1 184.85 ? O2G ACP 1502 A 1 HETATM 4 O O3G ACP . . . G 6 128.134 145.931 188.787 1 184.85 ? O3G ACP 1502 A 1 HETATM 5 P PB ACP . . . G 6 127.809 142.618 188.972 1 184.85 ? PB ACP 1502 A 1 HETATM 6 O O1B ACP . . . G 6 127.617 141.317 188.23 1 184.85 ? O1B ACP 1502 A 1 HETATM 7 O O2B ACP . . . G 6 126.599 143.494 188.751 1 184.85 ? O2B ACP 1502 A 1 HETATM 8 C C3B ACP . . . G 6 129.325 143.485 188.328 1 184.85 ? C3B ACP 1502 A 1 HETATM 9 P PA ACP . . . G 6 127.356 141.07 191.415 1 184.85 ? PA ACP 1502 A 1 HETATM 10 O O1A ACP . . . G 6 128.158 140.837 192.672 1 184.85 ? O1A ACP 1502 A 1 HETATM 11 O O2A ACP . . . G 6 127.391 139.826 190.561 1 184.85 ? O2A ACP 1502 A 1 HETATM 12 O O3A ACP . . . G 6 128.002 142.342 190.587 1 184.85 ? O3A ACP 1502 A 1 HETATM 13 O O5' ACP . . . G 6 125.8 141.416 191.836 1 184.85 ? O5' ACP 1502 A 1 HETATM 14 C C5' ACP . . . G 6 125.332 142.725 191.678 1 184.85 ? C5' ACP 1502 A 1 HETATM 15 C C4' ACP . . . G 6 125.639 143.568 192.946 1 184.85 ? C4' ACP 1502 A 1 HETATM 16 O O4' ACP . . . G 6 126.214 142.841 193.861 1 184.85 ? O4' ACP 1502 A 1 HETATM 17 C C3' ACP . . . G 6 126.682 144.655 192.621 1 184.85 ? C3' ACP 1502 A 1 HETATM 18 O O3' ACP . . . G 6 126.068 145.821 192.296 1 184.85 ? O3' ACP 1502 A 1 HETATM 19 C C2' ACP . . . G 6 127.493 144.828 193.921 1 184.85 ? C2' ACP 1502 A 1 HETATM 20 O O2' ACP . . . G 6 127.2 146.162 194.527 1 184.85 ? O2' ACP 1502 A 1 HETATM 21 C C1' ACP . . . G 6 127.105 143.875 194.73 1 184.85 ? C1' ACP 1502 A 1 HETATM 22 N N9 ACP . . . G 6 128.254 143.197 195.273 1 184.85 ? N9 ACP 1502 A 1 HETATM 23 C C8 ACP . . . G 6 129.408 142.997 194.633 1 184.85 ? C8 ACP 1502 A 1 HETATM 24 N N7 ACP . . . G 6 130.227 142.337 195.456 1 184.85 ? N7 ACP 1502 A 1 HETATM 25 C C5 ACP . . . G 6 129.576 142.13 196.61 1 184.85 ? C5 ACP 1502 A 1 HETATM 26 C C6 ACP . . . G 6 129.944 141.508 197.783 1 184.85 ? C6 ACP 1502 A 1 HETATM 27 N N6 ACP . . . G 6 131.135 140.836 198.27 1 184.85 ? N6 ACP 1502 A 1 HETATM 28 N N1 ACP . . . G 6 129.091 141.439 198.791 1 184.85 ? N1 ACP 1502 A 1 HETATM 29 C C2 ACP . . . G 6 127.855 141.979 198.674 1 184.85 ? C2 ACP 1502 A 1 HETATM 30 N N3 ACP . . . G 6 127.492 142.589 197.523 1 184.85 ? N3 ACP 1502 A 1 HETATM 31 C C4 ACP . . . G 6 128.357 142.661 196.496 1 184.85 ? C4 ACP 1502 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 31 #