data_9USB # _model_server_result.job_id qYgpep2mwWTX_EPr1Gwisw _model_server_result.datetime_utc '2025-08-20 23:39:50' _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 9usb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":303}' # _entry.id 9USB # _exptl.entry_id 9USB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 107.19 _cell.angle_gamma 90 _cell.entry_id 9USB _cell.length_a 47.184 _cell.length_b 102.574 _cell.length_c 56.362 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9USB _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_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,D,E,F,M 1 1 B,G,H,I,N 2 1 C,J,K,L,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 ? 4 F N N ? 4 I N N ? 4 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 A OG SER 23 A SER 17 1_555 D MG MG . A MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.069 ? metalc ? metalc2 D MG MG . A MG 301 1_555 F O2B GNP . A GNP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc3 D MG MG . A MG 301 1_555 M O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc4 D MG MG . A MG 301 1_555 M O HOH . A HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc5 D MG MG . A MG 301 1_555 M O HOH . A HOH 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.334 ? metalc ? metalc6 B OG SER 23 B SER 17 1_555 G MG MG . B MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.899 ? metalc ? metalc7 G MG MG . B MG 301 1_555 I O3G GNP . B GNP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.332 ? metalc ? metalc8 G MG MG . B MG 301 1_555 I O1B GNP . B GNP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? metalc ? metalc9 G MG MG . B MG 301 1_555 N O HOH . B HOH 406 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.078 ? metalc ? metalc10 G MG MG . B MG 301 1_555 N O HOH . B HOH 407 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc11 G MG MG . B MG 301 1_555 N O HOH . B HOH 417 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc12 C OG SER 23 C SER 17 1_555 J MG MG . C MG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc13 J MG MG . C MG 301 1_555 L O2G GNP . C GNP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.884 ? metalc ? metalc14 J MG MG . C MG 301 1_555 L O1B GNP . C GNP 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc15 J MG MG . C MG 301 1_555 O O HOH . C HOH 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.194 ? metalc ? metalc16 J MG MG . C MG 301 1_555 O O HOH . C HOH 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc17 J MG MG . C MG 301 1_555 O O HOH . C HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 GNP doub 212 n n PG O2G GNP sing 213 n n PG O3G GNP sing 214 n n PG N3B GNP sing 215 n n O2G HOG2 GNP sing 216 n n O3G HOG3 GNP sing 217 n n N3B PB GNP sing 218 n n N3B HNB3 GNP sing 219 n n PB O1B GNP doub 220 n n PB O2B GNP sing 221 n n PB O3A GNP sing 222 n n O2B HOB2 GNP sing 223 n n O3A PA GNP sing 224 n n PA O1A GNP doub 225 n n PA O2A GNP sing 226 n n PA O5' GNP sing 227 n n O2A HOA2 GNP sing 228 n n O5' C5' GNP sing 229 n n C5' C4' GNP sing 230 n n C5' "H5'2" GNP sing 231 n n C5' "H5'1" GNP sing 232 n n C4' O4' GNP sing 233 n n C4' C3' GNP sing 234 n n C4' H4' GNP sing 235 n n O4' C1' GNP sing 236 n n C3' O3' GNP sing 237 n n C3' C2' GNP sing 238 n n C3' H3' GNP sing 239 n n O3' HO3' GNP sing 240 n n C2' O2' GNP sing 241 n n C2' C1' GNP sing 242 n n C2' H2' GNP sing 243 n n O2' HO2' GNP sing 244 n n C1' N9 GNP sing 245 n n C1' H1' GNP sing 246 n n N9 C8 GNP sing 247 n y N9 C4 GNP sing 248 n y C8 N7 GNP doub 249 n y C8 H8 GNP sing 250 n n N7 C5 GNP sing 251 n y C5 C6 GNP sing 252 n y C5 C4 GNP doub 253 n y C6 O6 GNP doub 254 n n C6 N1 GNP sing 255 n y N1 C2 GNP sing 256 n y N1 HN1 GNP sing 257 n n C2 N2 GNP sing 258 n n C2 N3 GNP doub 259 n y N2 HN21 GNP sing 260 n n N2 HN22 GNP sing 261 n n N3 C4 GNP sing 262 n y # _atom_sites.entry_id 9USB _atom_sites.fract_transf_matrix[1][1] 0.021194 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006557 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009749 _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] 0.018572 _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 1 301 301 MG MG . E 3 A1EN3 A 1 302 302 A1EN3 LIG . F 4 GNP A 1 303 303 GNP GNP . G 2 MG B 1 301 301 MG MG . H 3 A1EN3 B 1 302 302 A1EN3 LIG . I 4 GNP B 1 303 303 GNP GNP . J 2 MG C 1 301 301 MG MG . K 3 A1EN3 C 1 302 302 A1EN3 LIG . L 4 GNP C 1 303 303 GNP GNP . M 5 HOH A 1 401 2 HOH HOH . M 5 HOH A 2 402 1 HOH HOH . M 5 HOH A 3 403 23 HOH HOH . M 5 HOH A 4 404 3 HOH HOH . M 5 HOH A 5 405 15 HOH HOH . M 5 HOH A 6 406 36 HOH HOH . M 5 HOH A 7 407 60 HOH HOH . M 5 HOH A 8 408 17 HOH HOH . M 5 HOH A 9 409 72 HOH HOH . M 5 HOH A 10 410 27 HOH HOH . M 5 HOH A 11 411 40 HOH HOH . M 5 HOH A 12 412 21 HOH HOH . M 5 HOH A 13 413 19 HOH HOH . M 5 HOH A 14 414 62 HOH HOH . M 5 HOH A 15 415 48 HOH HOH . M 5 HOH A 16 416 37 HOH HOH . M 5 HOH A 17 417 10 HOH HOH . M 5 HOH A 18 418 78 HOH HOH . M 5 HOH A 19 419 82 HOH HOH . M 5 HOH A 20 420 68 HOH HOH . M 5 HOH A 21 421 95 HOH HOH . M 5 HOH A 22 422 83 HOH HOH . M 5 HOH A 23 423 79 HOH HOH . M 5 HOH A 24 424 80 HOH HOH . N 5 HOH B 1 401 18 HOH HOH . N 5 HOH B 2 402 49 HOH HOH . N 5 HOH B 3 403 90 HOH HOH . N 5 HOH B 4 404 34 HOH HOH . N 5 HOH B 5 405 91 HOH HOH . N 5 HOH B 6 406 6 HOH HOH . N 5 HOH B 7 407 5 HOH HOH . N 5 HOH B 8 408 85 HOH HOH . N 5 HOH B 9 409 59 HOH HOH . N 5 HOH B 10 410 39 HOH HOH . N 5 HOH B 11 411 43 HOH HOH . N 5 HOH B 12 412 35 HOH HOH . N 5 HOH B 13 413 46 HOH HOH . N 5 HOH B 14 414 31 HOH HOH . N 5 HOH B 15 415 74 HOH HOH . N 5 HOH B 16 416 53 HOH HOH . N 5 HOH B 17 417 4 HOH HOH . N 5 HOH B 18 418 77 HOH HOH . N 5 HOH B 19 419 87 HOH HOH . N 5 HOH B 20 420 66 HOH HOH . N 5 HOH B 21 421 86 HOH HOH . N 5 HOH B 22 422 14 HOH HOH . N 5 HOH B 23 423 94 HOH HOH . O 5 HOH C 1 401 24 HOH HOH . O 5 HOH C 2 402 7 HOH HOH . O 5 HOH C 3 403 9 HOH HOH . O 5 HOH C 4 404 32 HOH HOH . O 5 HOH C 5 405 8 HOH HOH . O 5 HOH C 6 406 55 HOH HOH . O 5 HOH C 7 407 47 HOH HOH . O 5 HOH C 8 408 63 HOH HOH . O 5 HOH C 9 409 50 HOH HOH . O 5 HOH C 10 410 16 HOH HOH . O 5 HOH C 11 411 52 HOH HOH . O 5 HOH C 12 412 13 HOH HOH . O 5 HOH C 13 413 20 HOH HOH . O 5 HOH C 14 414 12 HOH HOH . O 5 HOH C 15 415 28 HOH HOH . O 5 HOH C 16 416 33 HOH HOH . O 5 HOH C 17 417 11 HOH HOH . O 5 HOH C 18 418 45 HOH HOH . O 5 HOH C 19 419 42 HOH HOH . O 5 HOH C 20 420 58 HOH HOH . O 5 HOH C 21 421 92 HOH HOH . O 5 HOH C 22 422 61 HOH HOH . O 5 HOH C 23 423 26 HOH HOH . O 5 HOH C 24 424 84 HOH HOH . O 5 HOH C 25 425 93 HOH HOH . O 5 HOH C 26 426 69 HOH HOH . O 5 HOH C 27 427 71 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 GNP . . . I 4 31.927 -47.513 5.254 1 68.68 ? PG GNP 303 B 1 HETATM 2 O O1G GNP . . . I 4 31.849 -49.022 5.104 1 67.87 ? O1G GNP 303 B 1 HETATM 3 O O2G GNP . . . I 4 33.303 -47.06 4.734 1 67.08 ? O2G GNP 303 B 1 HETATM 4 O O3G GNP . . . I 4 31.746 -47.21 6.753 1 48.84 ? O3G GNP 303 B 1 HETATM 5 N N3B GNP . . . I 4 30.838 -46.747 4.296 1 50.44 ? N3B GNP 303 B 1 HETATM 6 P PB GNP . . . I 4 29.234 -46.859 4.462 1 45.67 ? PB GNP 303 B 1 HETATM 7 O O1B GNP . . . I 4 28.88 -46.568 5.895 1 43.65 ? O1B GNP 303 B 1 HETATM 8 O O2B GNP . . . I 4 28.802 -48.182 3.884 1 43.41 ? O2B GNP 303 B 1 HETATM 9 O O3A GNP . . . I 4 28.567 -45.698 3.558 1 48.4 ? O3A GNP 303 B 1 HETATM 10 P PA GNP . . . I 4 28.553 -44.094 3.808 1 47.3 ? PA GNP 303 B 1 HETATM 11 O O1A GNP . . . I 4 27.273 -43.703 4.451 1 49.39 ? O1A GNP 303 B 1 HETATM 12 O O2A GNP . . . I 4 29.886 -43.886 4.424 1 46.16 ? O2A GNP 303 B 1 HETATM 13 O O5' GNP . . . I 4 28.525 -43.424 2.378 1 44.78 ? O5' GNP 303 B 1 HETATM 14 C C5' GNP . . . I 4 29.653 -43.593 1.498 1 44.79 ? C5' GNP 303 B 1 HETATM 15 C C4' GNP . . . I 4 29.549 -42.541 0.421 1 47.77 ? C4' GNP 303 B 1 HETATM 16 O O4' GNP . . . I 4 28.326 -42.73 -0.347 1 41.17 ? O4' GNP 303 B 1 HETATM 17 C C3' GNP . . . I 4 29.485 -41.091 0.932 1 45.82 ? C3' GNP 303 B 1 HETATM 18 O O3' GNP . . . I 4 30.192 -40.269 0.017 1 54.47 ? O3' GNP 303 B 1 HETATM 19 C C2' GNP . . . I 4 27.976 -40.83 0.968 1 43 ? C2' GNP 303 B 1 HETATM 20 O O2' GNP . . . I 4 27.584 -39.479 0.924 1 49.4 ? O2' GNP 303 B 1 HETATM 21 C C1' GNP . . . I 4 27.545 -41.555 -0.298 1 40.71 ? C1' GNP 303 B 1 HETATM 22 N N9 GNP . . . I 4 26.153 -41.965 -0.288 1 40.31 ? N9 GNP 303 B 1 HETATM 23 C C8 GNP . . . I 4 25.549 -42.769 0.645 1 39.03 ? C8 GNP 303 B 1 HETATM 24 N N7 GNP . . . I 4 24.295 -43.02 0.373 1 38.27 ? N7 GNP 303 B 1 HETATM 25 C C5 GNP . . . I 4 24.074 -42.361 -0.82 1 37.55 ? C5 GNP 303 B 1 HETATM 26 C C6 GNP . . . I 4 22.901 -42.287 -1.59 1 40.79 ? C6 GNP 303 B 1 HETATM 27 O O6 GNP . . . I 4 21.817 -42.842 -1.361 1 38.35 ? O6 GNP 303 B 1 HETATM 28 N N1 GNP . . . I 4 23.117 -41.549 -2.759 1 44.1 ? N1 GNP 303 B 1 HETATM 29 C C2 GNP . . . I 4 24.286 -40.912 -3.109 1 44.76 ? C2 GNP 303 B 1 HETATM 30 N N2 GNP . . . I 4 24.287 -40.232 -4.267 1 40.74 ? N2 GNP 303 B 1 HETATM 31 N N3 GNP . . . I 4 25.393 -40.971 -2.372 1 42.26 ? N3 GNP 303 B 1 HETATM 32 C C4 GNP . . . I 4 25.21 -41.714 -1.252 1 41.5 ? C4 GNP 303 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 287 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #