data_3B89 # _model_server_result.job_id eDEGIGSuRdDiPsvQvC3jrg _model_server_result.datetime_utc '2025-08-30 10:46:34' _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 3b89 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 3B89 # _exptl.entry_id 3B89 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-MONOPHOSPHATE" _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 3B89 _cell.length_a 56.262 _cell.length_b 94.131 _cell.length_c 96.23 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3B89 _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 C ALA 188 A ALA 187 1_555 A N MSE 189 A MSE 188 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale2 A C MSE 189 A MSE 188 1_555 A N ALA 190 A ALA 189 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale3 A C ARG 199 A ARG 198 1_555 A N MSE 200 A MSE 199 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale4 A C MSE 200 A MSE 199 1_555 A N ALA 201 A ALA 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 5GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-5'-MONOPHOSPHATE" _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 P O1P 5GP doub 1 n n P O2P 5GP sing 2 n n P O3P 5GP sing 3 n n P O5' 5GP sing 4 n n O2P HOP2 5GP sing 5 n n O3P HOP3 5GP sing 6 n n O5' C5' 5GP sing 7 n n C5' C4' 5GP sing 8 n n C5' "H5'1" 5GP sing 9 n n C5' "H5'2" 5GP sing 10 n n C4' O4' 5GP sing 11 n n C4' C3' 5GP sing 12 n n C4' H4' 5GP sing 13 n n O4' C1' 5GP sing 14 n n C3' O3' 5GP sing 15 n n C3' C2' 5GP sing 16 n n C3' H3' 5GP sing 17 n n O3' HO3' 5GP sing 18 n n C2' O2' 5GP sing 19 n n C2' C1' 5GP sing 20 n n C2' H2' 5GP sing 21 n n O2' HO2' 5GP sing 22 n n C1' N9 5GP sing 23 n n C1' H1' 5GP sing 24 n n N9 C8 5GP sing 25 n y N9 C4 5GP sing 26 n y C8 N7 5GP doub 27 n y C8 H8 5GP sing 28 n n N7 C5 5GP sing 29 n y C5 C6 5GP sing 30 n n C5 C4 5GP doub 31 n y C6 O6 5GP doub 32 n n C6 N1 5GP sing 33 n n N1 C2 5GP sing 34 n n N1 HN1 5GP sing 35 n n C2 N2 5GP sing 36 n n C2 N3 5GP doub 37 n n N2 HN21 5GP sing 38 n n N2 HN22 5GP sing 39 n n N3 C4 5GP sing 40 n n # _atom_sites.entry_id 3B89 _atom_sites.fract_transf_matrix[1][1] 0.017774 _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] 0.010623 _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] 0.010392 _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 5GP A 1 500 500 5GP 5GP . C 3 HOH A 1 501 1 HOH TIP . C 3 HOH A 2 502 2 HOH TIP . C 3 HOH A 3 503 4 HOH TIP . C 3 HOH A 4 504 5 HOH TIP . C 3 HOH A 5 505 6 HOH TIP . C 3 HOH A 6 506 7 HOH TIP . C 3 HOH A 7 507 8 HOH TIP . C 3 HOH A 8 508 9 HOH TIP . C 3 HOH A 9 509 10 HOH TIP . C 3 HOH A 10 510 11 HOH TIP . C 3 HOH A 11 511 12 HOH TIP . C 3 HOH A 12 512 13 HOH TIP . C 3 HOH A 13 513 14 HOH TIP . C 3 HOH A 14 514 15 HOH TIP . C 3 HOH A 15 515 16 HOH TIP . C 3 HOH A 16 516 17 HOH TIP . C 3 HOH A 17 517 18 HOH TIP . C 3 HOH A 18 518 19 HOH TIP . C 3 HOH A 19 519 20 HOH TIP . C 3 HOH A 20 520 21 HOH TIP . C 3 HOH A 21 521 22 HOH TIP . C 3 HOH A 22 522 23 HOH TIP . C 3 HOH A 23 523 24 HOH TIP . C 3 HOH A 24 524 25 HOH TIP . C 3 HOH A 25 525 26 HOH TIP . C 3 HOH A 26 526 27 HOH TIP . C 3 HOH A 27 527 28 HOH TIP . C 3 HOH A 28 528 29 HOH TIP . C 3 HOH A 29 529 30 HOH TIP . C 3 HOH A 30 530 31 HOH TIP . C 3 HOH A 31 531 32 HOH TIP . C 3 HOH A 32 532 33 HOH TIP . C 3 HOH A 33 533 34 HOH TIP . C 3 HOH A 34 534 35 HOH TIP . C 3 HOH A 35 535 36 HOH TIP . C 3 HOH A 36 536 37 HOH TIP . C 3 HOH A 37 537 38 HOH TIP . C 3 HOH A 38 538 39 HOH TIP . C 3 HOH A 39 539 40 HOH TIP . C 3 HOH A 40 540 41 HOH TIP . # 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 P 5GP . . . B 2 9.34 20.837 28.456 1 82.58 ? P 5GP 500 A 1 HETATM 2 O O1P 5GP . . . B 2 9.649 19.569 29.341 1 83.47 ? O1P 5GP 500 A 1 HETATM 3 O O2P 5GP . . . B 2 7.969 20.522 27.637 1 82.52 ? O2P 5GP 500 A 1 HETATM 4 O O3P 5GP . . . B 2 9.232 22.196 29.127 1 82.45 ? O3P 5GP 500 A 1 HETATM 5 O O5' 5GP . . . B 2 10.507 20.832 27.296 1 80.2 ? O5' 5GP 500 A 1 HETATM 6 C C5' 5GP . . . B 2 10.633 21.811 26.269 1 75.84 ? C5' 5GP 500 A 1 HETATM 7 C C4' 5GP . . . B 2 11.593 22.779 26.929 1 73.55 ? C4' 5GP 500 A 1 HETATM 8 O O4' 5GP . . . B 2 12.918 22.881 26.313 1 72.72 ? O4' 5GP 500 A 1 HETATM 9 C C3' 5GP . . . B 2 11.101 24.267 27.046 1 72.52 ? C3' 5GP 500 A 1 HETATM 10 O O3' 5GP . . . B 2 11.24 24.642 28.467 1 69.96 ? O3' 5GP 500 A 1 HETATM 11 C C2' 5GP . . . B 2 11.972 25.003 26.039 1 71.22 ? C2' 5GP 500 A 1 HETATM 12 O O2' 5GP . . . B 2 12.159 26.379 26.111 1 70.02 ? O2' 5GP 500 A 1 HETATM 13 C C1' 5GP . . . B 2 13.306 24.27 26.055 1 70.44 ? C1' 5GP 500 A 1 HETATM 14 N N9 5GP . . . B 2 14.151 24.167 24.782 1 67.84 ? N9 5GP 500 A 1 HETATM 15 C C8 5GP . . . B 2 13.772 24.11 23.489 1 67.67 ? C8 5GP 500 A 1 HETATM 16 N N7 5GP . . . B 2 14.877 24.013 22.693 1 66.47 ? N7 5GP 500 A 1 HETATM 17 C C5 5GP . . . B 2 15.965 24.01 23.502 1 65.5 ? C5 5GP 500 A 1 HETATM 18 C C6 5GP . . . B 2 17.362 23.929 23.268 1 64.61 ? C6 5GP 500 A 1 HETATM 19 O O6 5GP . . . B 2 17.79 23.841 22.089 1 64.04 ? O6 5GP 500 A 1 HETATM 20 N N1 5GP . . . B 2 18.224 23.949 24.335 1 63.28 ? N1 5GP 500 A 1 HETATM 21 C C2 5GP . . . B 2 17.757 24.046 25.628 1 63.13 ? C2 5GP 500 A 1 HETATM 22 N N2 5GP . . . B 2 18.606 24.067 26.689 1 61.51 ? N2 5GP 500 A 1 HETATM 23 N N3 5GP . . . B 2 16.404 24.124 25.87 1 64.27 ? N3 5GP 500 A 1 HETATM 24 C C4 5GP . . . B 2 15.496 24.103 24.823 1 65.78 ? C4 5GP 500 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 51 _model_server_stats.element_count 24 #