data_9E9H # _model_server_result.job_id 3jEEP05l8lHa2nxPjMrUGg _model_server_result.datetime_utc '2025-02-28 17:51:41' _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 9e9h # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 9E9H # _exptl.entry_id 9E9H _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 9E9H _cell.length_a 40.715 _cell.length_b 40.715 _cell.length_c 341.304 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9E9H _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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 _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 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 covale ? covale1 A SG CYS 26 A CYS 12 1_555 D C16 A1BH6 . A A1BH6 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.809 sing metalc ? metalc1 A OG SER 31 A SER 17 1_555 B CA CA . A CA 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc2 B CA CA . A CA 301 1_555 C O2B GDP . A GDP 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.323 ? metalc ? metalc3 B CA CA . A CA 301 1_555 E O HOH . A HOH 408 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? metalc ? metalc4 B CA CA . A CA 301 1_555 E O HOH . A HOH 418 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc5 B CA CA . A CA 301 1_555 E O HOH . A HOH 419 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? metalc ? metalc6 B CA CA . A CA 301 1_555 E O HOH . A HOH 427 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.324 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 GDP doub 172 n n PB O2B GDP sing 173 n n PB O3B GDP sing 174 n n PB O3A GDP sing 175 n n O2B HOB2 GDP sing 176 n n O3B HOB3 GDP sing 177 n n O3A PA GDP sing 178 n n PA O1A GDP doub 179 n n PA O2A GDP sing 180 n n PA O5' GDP sing 181 n n O2A HOA2 GDP sing 182 n n O5' C5' GDP sing 183 n n C5' C4' GDP sing 184 n n C5' H5' GDP sing 185 n n C5' "H5''" GDP sing 186 n n C4' O4' GDP sing 187 n n C4' C3' GDP sing 188 n n C4' H4' GDP sing 189 n n O4' C1' GDP sing 190 n n C3' O3' GDP sing 191 n n C3' C2' GDP sing 192 n n C3' H3' GDP sing 193 n n O3' HO3' GDP sing 194 n n C2' O2' GDP sing 195 n n C2' C1' GDP sing 196 n n C2' H2' GDP sing 197 n n O2' HO2' GDP sing 198 n n C1' N9 GDP sing 199 n n C1' H1' GDP sing 200 n n N9 C8 GDP sing 201 n y N9 C4 GDP sing 202 n y C8 N7 GDP doub 203 n y C8 H8 GDP sing 204 n n N7 C5 GDP sing 205 n y C5 C6 GDP sing 206 n n C5 C4 GDP doub 207 n y C6 O6 GDP doub 208 n n C6 N1 GDP sing 209 n n N1 C2 GDP sing 210 n n N1 HN1 GDP sing 211 n n C2 N2 GDP sing 212 n n C2 N3 GDP doub 213 n n N2 HN21 GDP sing 214 n n N2 HN22 GDP sing 215 n n N3 C4 GDP sing 216 n n # _atom_sites.entry_id 9E9H _atom_sites.fract_transf_matrix[1][1] 0.024561 _atom_sites.fract_transf_matrix[1][2] 0.01418 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.028361 _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] 0.00293 _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 B 2 CA A 1 301 301 CA CA . C 3 GDP A 1 302 501 GDP GDP . D 4 A1BH6 A 1 303 701 A1BH6 UNL . E 5 HOH A 1 401 23 HOH HOH . E 5 HOH A 2 402 16 HOH HOH . E 5 HOH A 3 403 62 HOH HOH . E 5 HOH A 4 404 45 HOH HOH . E 5 HOH A 5 405 44 HOH HOH . E 5 HOH A 6 406 82 HOH HOH . E 5 HOH A 7 407 17 HOH HOH . E 5 HOH A 8 408 403 HOH HOH . E 5 HOH A 9 409 12 HOH HOH . E 5 HOH A 10 410 70 HOH HOH . E 5 HOH A 11 411 88 HOH HOH . E 5 HOH A 12 412 30 HOH HOH . E 5 HOH A 13 413 1 HOH HOH . E 5 HOH A 14 414 25 HOH HOH . E 5 HOH A 15 415 74 HOH HOH . E 5 HOH A 16 416 28 HOH HOH . E 5 HOH A 17 417 40 HOH HOH . E 5 HOH A 18 418 404 HOH HOH . E 5 HOH A 19 419 401 HOH HOH . E 5 HOH A 20 420 63 HOH HOH . E 5 HOH A 21 421 10 HOH HOH . E 5 HOH A 22 422 24 HOH HOH . E 5 HOH A 23 423 35 HOH HOH . E 5 HOH A 24 424 27 HOH HOH . E 5 HOH A 25 425 9 HOH HOH . E 5 HOH A 26 426 8 HOH HOH . E 5 HOH A 27 427 402 HOH HOH . E 5 HOH A 28 428 26 HOH HOH . E 5 HOH A 29 429 13 HOH HOH . E 5 HOH A 30 430 75 HOH HOH . E 5 HOH A 31 431 55 HOH HOH . E 5 HOH A 32 432 18 HOH HOH . E 5 HOH A 33 433 76 HOH HOH . E 5 HOH A 34 434 51 HOH HOH . E 5 HOH A 35 435 14 HOH HOH . E 5 HOH A 36 436 31 HOH HOH . E 5 HOH A 37 437 15 HOH HOH . E 5 HOH A 38 438 6 HOH HOH . E 5 HOH A 39 439 21 HOH HOH . E 5 HOH A 40 440 38 HOH HOH . E 5 HOH A 41 441 65 HOH HOH . E 5 HOH A 42 442 61 HOH HOH . E 5 HOH A 43 443 48 HOH HOH . E 5 HOH A 44 444 37 HOH HOH . E 5 HOH A 45 445 66 HOH HOH . E 5 HOH A 46 446 83 HOH HOH . E 5 HOH A 47 447 2 HOH HOH . E 5 HOH A 48 448 77 HOH HOH . E 5 HOH A 49 449 57 HOH HOH . E 5 HOH A 50 450 20 HOH HOH . E 5 HOH A 51 451 78 HOH HOH . E 5 HOH A 52 452 32 HOH HOH . E 5 HOH A 53 453 5 HOH HOH . E 5 HOH A 54 454 39 HOH HOH . E 5 HOH A 55 455 3 HOH HOH . E 5 HOH A 56 456 42 HOH HOH . E 5 HOH A 57 457 43 HOH HOH . E 5 HOH A 58 458 50 HOH HOH . E 5 HOH A 59 459 19 HOH HOH . E 5 HOH A 60 460 41 HOH HOH . E 5 HOH A 61 461 33 HOH HOH . E 5 HOH A 62 462 52 HOH HOH . E 5 HOH A 63 463 7 HOH HOH . E 5 HOH A 64 464 64 HOH HOH . E 5 HOH A 65 465 53 HOH HOH . E 5 HOH A 66 466 68 HOH HOH . E 5 HOH A 67 467 29 HOH HOH . E 5 HOH A 68 468 4 HOH HOH . E 5 HOH A 69 469 56 HOH HOH . E 5 HOH A 70 470 47 HOH HOH . E 5 HOH A 71 471 46 HOH HOH . E 5 HOH A 72 472 22 HOH HOH . E 5 HOH A 73 473 73 HOH HOH . E 5 HOH A 74 474 87 HOH HOH . E 5 HOH A 75 475 86 HOH HOH . E 5 HOH A 76 476 72 HOH HOH . E 5 HOH A 77 477 81 HOH HOH . E 5 HOH A 78 478 11 HOH HOH . E 5 HOH A 79 479 71 HOH HOH . E 5 HOH A 80 480 36 HOH HOH . E 5 HOH A 81 481 84 HOH HOH . E 5 HOH A 82 482 80 HOH HOH . E 5 HOH A 83 483 49 HOH HOH . E 5 HOH A 84 484 79 HOH HOH . E 5 HOH A 85 485 89 HOH HOH . E 5 HOH A 86 486 69 HOH HOH . E 5 HOH A 87 487 34 HOH HOH . E 5 HOH A 88 488 58 HOH HOH . E 5 HOH A 89 489 85 HOH HOH . E 5 HOH A 90 490 54 HOH HOH . E 5 HOH A 91 491 67 HOH HOH . E 5 HOH A 92 492 60 HOH HOH . E 5 HOH A 93 493 59 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 GDP . . . C 3 -13.023 -14.153 13.207 1 26.98 ? PB GDP 302 A 1 HETATM 2 O O1B GDP . . . C 3 -12.205 -13.172 14.029 1 27.57 ? O1B GDP 302 A 1 HETATM 3 O O2B GDP . . . C 3 -12.24 -14.922 12.166 1 26.46 ? O2B GDP 302 A 1 HETATM 4 O O3B GDP . . . C 3 -13.949 -14.993 14.029 1 27.34 ? O3B GDP 302 A 1 HETATM 5 O O3A GDP . . . C 3 -13.96 -13.126 12.4 1 27.79 ? O3A GDP 302 A 1 HETATM 6 P PA GDP . . . C 3 -14.538 -13.311 10.911 1 28.44 ? PA GDP 302 A 1 HETATM 7 O O1A GDP . . . C 3 -13.543 -13.016 9.835 1 28.07 ? O1A GDP 302 A 1 HETATM 8 O O2A GDP . . . C 3 -15.279 -14.635 10.924 1 28.1 ? O2A GDP 302 A 1 HETATM 9 O O5' GDP . . . C 3 -15.619 -12.131 10.924 1 29.54 ? O5' GDP 302 A 1 HETATM 10 C C5' GDP . . . C 3 -16.709 -12.157 11.847 1 31.61 ? C5' GDP 302 A 1 HETATM 11 C C4' GDP . . . C 3 -17.88 -11.358 11.299 1 33.56 ? C4' GDP 302 A 1 HETATM 12 O O4' GDP . . . C 3 -17.501 -9.986 11.179 1 33.05 ? O4' GDP 302 A 1 HETATM 13 C C3' GDP . . . C 3 -18.287 -11.816 9.907 1 34.64 ? C3' GDP 302 A 1 HETATM 14 O O3' GDP . . . C 3 -19.713 -11.79 9.793 1 37.25 ? O3' GDP 302 A 1 HETATM 15 C C2' GDP . . . C 3 -17.643 -10.809 8.978 1 34.11 ? C2' GDP 302 A 1 HETATM 16 O O2' GDP . . . C 3 -18.357 -10.633 7.757 1 35.64 ? O2' GDP 302 A 1 HETATM 17 C C1' GDP . . . C 3 -17.637 -9.547 9.823 1 31.94 ? C1' GDP 302 A 1 HETATM 18 N N9 GDP . . . C 3 -16.515 -8.627 9.539 1 31.87 ? N9 GDP 302 A 1 HETATM 19 C C8 GDP . . . C 3 -15.206 -8.935 9.532 1 31.09 ? C8 GDP 302 A 1 HETATM 20 N N7 GDP . . . C 3 -14.457 -7.834 9.273 1 31.99 ? N7 GDP 302 A 1 HETATM 21 C C5 GDP . . . C 3 -15.31 -6.795 9.13 1 31.88 ? C5 GDP 302 A 1 HETATM 22 C C6 GDP . . . C 3 -15.194 -5.348 8.862 1 32.7 ? C6 GDP 302 A 1 HETATM 23 O O6 GDP . . . C 3 -14.074 -4.815 8.691 1 32.1 ? O6 GDP 302 A 1 HETATM 24 N N1 GDP . . . C 3 -16.321 -4.621 8.8 1 32.82 ? N1 GDP 302 A 1 HETATM 25 C C2 GDP . . . C 3 -17.546 -5.162 8.983 1 32.94 ? C2 GDP 302 A 1 HETATM 26 N N2 GDP . . . C 3 -18.635 -4.361 8.915 1 34.17 ? N2 GDP 302 A 1 HETATM 27 N N3 GDP . . . C 3 -17.729 -6.482 9.249 1 32.28 ? N3 GDP 302 A 1 HETATM 28 C C4 GDP . . . C 3 -16.663 -7.322 9.327 1 31.74 ? C4 GDP 302 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 17 _model_server_stats.element_count 28 #