data_8EE6 # _model_server_result.job_id faJKk9z21ZMltgGCZsGnNQ _model_server_result.datetime_utc '2025-08-01 23:23:19' _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 8ee6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"DA","auth_seq_id":2226}' # _entry.id 8EE6 # _exptl.entry_id 8EE6 _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 523.247 _entity.id 6 _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 8EE6 _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8EE6 _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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,S,T,U,V,W,X,Y,Z,AA,BA,CA,DA,EA _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 DA N N ? 6 EA N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 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 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 3 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 2 n B NAG 1 C 1 NAG C 2206 NAG 2 n B NAG 2 C 2 NAG C 2207 NAG 2 n B BMA 3 C 3 BMA C 2208 BMA 3 n C NAG 1 B 1 NAG C 2209 NAG 3 n C NAG 2 B 2 NAG C 2210 NAG 3 n C BMA 3 B 3 BMA C 2211 BMA 3 n C BMA 4 B 4 BMA C 2212 BMA 2 n D NAG 1 D 1 NAG C 2214 NAG 2 n D NAG 2 D 2 NAG C 2215 NAG 2 n D BMA 3 D 3 BMA C 2216 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 A SG CYS 54 A CYS 54 1_555 A SG CYS 81 A CYS 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf2 A SG CYS 75 A CYS 75 1_555 A SG CYS 225 A CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 A SG CYS 267 A CYS 267 1_555 A SG CYS 406 A CYS 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf4 A SG CYS 1017 A CYS 1017 1_555 A SG CYS 1150 A CYS 1150 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 A SG CYS 1347 A CYS 1347 1_555 A SG CYS 1359 A CYS 1359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 78 A ASN 78 1_555 E C1 NAG . A NAG 2201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 A ND2 ASN 98 A ASN 98 1_555 F C1 NAG . A NAG 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale3 A ND2 ASN 312 A ASN 312 1_555 G C1 NAG . A NAG 2203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale4 A ND2 ASN 1335 A ASN 1335 1_555 H C1 NAG . A NAG 2204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale5 A ND2 ASN 1381 A ASN 1381 1_555 B C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale6 A ND2 ASN 1386 A ASN 1386 1_555 C C1 NAG . B NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 A ND2 ASN 1457 A ASN 1457 1_555 I C1 NAG . A NAG 2205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale8 A ND2 ASN 1518 A ASN 1518 1_555 D C1 NAG . D NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale9 B O4 NAG . C NAG 1 1_555 B C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale10 B O4 NAG . C NAG 2 1_555 B C1 BMA . C BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale11 C O4 NAG . B NAG 1 1_555 C C1 NAG . B NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale12 C O4 NAG . B NAG 2 1_555 C C1 BMA . B BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale13 C O3 BMA . B BMA 3 1_555 C C1 BMA . B BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale14 D O4 NAG . D NAG 1 1_555 D C1 NAG . D NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale15 D O4 NAG . D NAG 2 1_555 D C1 BMA . D BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? # _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 8EE6 _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 E 4 NAG A 1 2201 2201 NAG NAG . F 4 NAG A 1 2202 2202 NAG NAG . G 4 NAG A 1 2203 2203 NAG NAG . H 4 NAG A 1 2204 2205 NAG NAG . I 4 NAG A 1 2205 2213 NAG NAG . J 5 UNL A 1 2206 1 UNL PLC . K 5 UNL A 1 2207 2 UNL PLC . L 5 UNL A 1 2208 3 UNL PLC . M 5 UNL A 1 2209 4 UNL PLC . N 5 UNL A 1 2210 5 UNL PLC . O 5 UNL A 1 2211 6 UNL PLC . P 5 UNL A 1 2212 7 UNL PLC . Q 5 UNL A 1 2213 8 UNL PLC . R 5 UNL A 1 2214 9 UNL PLC . S 5 UNL A 1 2215 10 UNL PLC . T 5 UNL A 1 2216 11 UNL PLC . U 5 UNL A 1 2217 12 UNL PLC . V 5 UNL A 1 2218 13 UNL PLC . W 5 UNL A 1 2219 14 UNL PLC . X 5 UNL A 1 2220 15 UNL PLC . Y 5 UNL A 1 2221 16 UNL PLC . Z 5 UNL A 1 2222 17 UNL PLC . AA 5 UNL A 1 2223 18 UNL PLC . BA 5 UNL A 1 2224 19 UNL PLC . CA 5 UNL A 1 2225 20 UNL PLC . DA 6 AGS A 1 2226 1 AGS AGS . EA 6 AGS A 1 2227 2 AGS AGS . # 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 . . . DA 6 160.928 148.811 192.174 1 29.61 ? PG AGS 2226 A 1 HETATM 2 S S1G AGS . . . DA 6 161.409 150.501 191.334 1 29.61 ? S1G AGS 2226 A 1 HETATM 3 O O2G AGS . . . DA 6 159.549 148.759 192.78 1 29.61 ? O2G AGS 2226 A 1 HETATM 4 O O3G AGS . . . DA 6 161.94 148.262 193.147 1 29.61 ? O3G AGS 2226 A 1 HETATM 5 P PB AGS . . . DA 6 159.97 147.512 189.735 1 29.61 ? PB AGS 2226 A 1 HETATM 6 O O1B AGS . . . DA 6 158.53 147.454 190.122 1 29.61 ? O1B AGS 2226 A 1 HETATM 7 O O2B AGS . . . DA 6 160.425 148.536 188.751 1 29.61 ? O2B AGS 2226 A 1 HETATM 8 O O3B AGS . . . DA 6 160.859 147.653 191.057 1 29.61 ? O3B AGS 2226 A 1 HETATM 9 P PA AGS . . . DA 6 160.01 145.239 187.902 1 29.61 ? PA AGS 2226 A 1 HETATM 10 O O1A AGS . . . DA 6 158.56 144.89 187.966 1 29.61 ? O1A AGS 2226 A 1 HETATM 11 O O2A AGS . . . DA 6 160.499 145.977 186.699 1 29.61 ? O2A AGS 2226 A 1 HETATM 12 O O3A AGS . . . DA 6 160.425 146.073 189.206 1 29.61 ? O3A AGS 2226 A 1 HETATM 13 O O5' AGS . . . DA 6 160.882 143.909 188.094 1 29.61 ? O5' AGS 2226 A 1 HETATM 14 C C5' AGS . . . DA 6 161.276 143.111 186.946 1 29.61 ? C5' AGS 2226 A 1 HETATM 15 C C4' AGS . . . DA 6 160.069 142.501 186.271 1 29.61 ? C4' AGS 2226 A 1 HETATM 16 O O4' AGS . . . DA 6 159.36 143.534 185.532 1 29.61 ? O4' AGS 2226 A 1 HETATM 17 C C3' AGS . . . DA 6 160.39 141.427 185.22 1 29.61 ? C3' AGS 2226 A 1 HETATM 18 O O3' AGS . . . DA 6 159.273 140.568 185.037 1 29.61 ? O3' AGS 2226 A 1 HETATM 19 C C2' AGS . . . DA 6 160.572 142.299 183.979 1 29.61 ? C2' AGS 2226 A 1 HETATM 20 O O2' AGS . . . DA 6 160.553 141.586 182.763 1 29.61 ? O2' AGS 2226 A 1 HETATM 21 C C1' AGS . . . DA 6 159.378 143.227 184.156 1 29.61 ? C1' AGS 2226 A 1 HETATM 22 N N9 AGS . . . DA 6 159.478 144.473 183.407 1 29.61 ? N9 AGS 2226 A 1 HETATM 23 C C8 AGS . . . DA 6 160.277 144.713 182.318 1 29.61 ? C8 AGS 2226 A 1 HETATM 24 N N7 AGS . . . DA 6 160.16 145.928 181.842 1 29.61 ? N7 AGS 2226 A 1 HETATM 25 C C5 AGS . . . DA 6 159.21 146.526 182.659 1 29.61 ? C5 AGS 2226 A 1 HETATM 26 C C6 AGS . . . DA 6 158.64 147.815 182.665 1 29.61 ? C6 AGS 2226 A 1 HETATM 27 N N6 AGS . . . DA 6 158.952 148.765 181.788 1 29.61 ? N6 AGS 2226 A 1 HETATM 28 N N1 AGS . . . DA 6 157.706 148.082 183.608 1 29.61 ? N1 AGS 2226 A 1 HETATM 29 C C2 AGS . . . DA 6 157.395 147.12 184.486 1 29.61 ? C2 AGS 2226 A 1 HETATM 30 N N3 AGS . . . DA 6 157.868 145.881 184.583 1 29.61 ? N3 AGS 2226 A 1 HETATM 31 C C4 AGS . . . DA 6 158.78 145.637 183.628 1 29.61 ? C4 AGS 2226 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #