data_4WA7 # _model_server_result.job_id y3284EZq26_CfWioCOVXpQ _model_server_result.datetime_utc '2025-01-11 17:34:34' _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 4wa7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4WA7 # _exptl.entry_id 4WA7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _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 4WA7 _cell.length_a 82.493 _cell.length_b 82.493 _cell.length_c 40.761 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4WA7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _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,D _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 metalc ? metalc1 A OG SER 18 A SER 17 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc2 B O2B GDP . A GDP 201 1_555 C MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc3 C MG MG . A MG 202 1_555 D O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.168 ? metalc ? metalc4 C MG MG . A MG 202 1_555 D O HOH . A HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc5 C MG MG . A MG 202 1_555 D O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.18 ? metalc ? metalc6 C MG MG . A MG 202 1_555 D O HOH . A HOH 331 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 4WA7 _atom_sites.fract_transf_matrix[1][1] 0.012122 _atom_sites.fract_transf_matrix[1][2] 0.006999 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013998 _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] 0.024533 _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 GDP A 1 201 201 GDP GDP . C 3 MG A 1 202 202 MG MG . D 4 HOH A 1 301 308 HOH HOH . D 4 HOH A 2 302 330 HOH HOH . D 4 HOH A 3 303 309 HOH HOH . D 4 HOH A 4 304 318 HOH HOH . D 4 HOH A 5 305 312 HOH HOH . D 4 HOH A 6 307 326 HOH HOH . D 4 HOH A 7 308 317 HOH HOH . D 4 HOH A 8 309 332 HOH HOH . D 4 HOH A 9 310 313 HOH HOH . D 4 HOH A 10 311 331 HOH HOH . D 4 HOH A 11 312 314 HOH HOH . D 4 HOH A 12 313 335 HOH HOH . D 4 HOH A 13 314 319 HOH HOH . D 4 HOH A 14 315 328 HOH HOH . D 4 HOH A 15 316 341 HOH HOH . D 4 HOH A 16 317 301 HOH HOH . D 4 HOH A 17 318 302 HOH HOH . D 4 HOH A 18 319 303 HOH HOH . D 4 HOH A 19 320 304 HOH HOH . D 4 HOH A 20 321 305 HOH HOH . D 4 HOH A 21 322 306 HOH HOH . D 4 HOH A 22 323 307 HOH HOH . D 4 HOH A 23 324 310 HOH HOH . D 4 HOH A 24 325 311 HOH HOH . D 4 HOH A 25 327 320 HOH HOH . D 4 HOH A 26 328 321 HOH HOH . D 4 HOH A 27 329 322 HOH HOH . D 4 HOH A 28 330 323 HOH HOH . D 4 HOH A 29 331 324 HOH HOH . D 4 HOH A 30 332 325 HOH HOH . D 4 HOH A 31 333 327 HOH HOH . D 4 HOH A 32 334 329 HOH HOH . D 4 HOH A 33 335 334 HOH HOH . D 4 HOH A 34 336 336 HOH HOH . D 4 HOH A 35 337 338 HOH HOH . D 4 HOH A 36 338 339 HOH HOH . D 4 HOH A 37 339 340 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 . . . B 2 36.412 8.622 -3.072 1 28.99 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 36.601 9.692 -4.132 1 33.07 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 35.73 7.422 -3.678 1 29.46 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 35.567 9.193 -1.945 1 28.69 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 37.855 8.245 -2.439 1 29.62 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 38.763 6.937 -2.75 1 27.93 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 38.997 6.795 -4.244 1 31.15 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 38.158 5.69 -2.148 1 31.47 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 40.103 7.353 -1.97 1 28.86 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 40.888 8.416 -2.499 1 32.14 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 42.309 8.238 -1.997 1 34.84 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 42.316 8.159 -0.571 1 36.49 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 42.937 6.95 -2.495 1 37.6 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 44.31 7.256 -2.722 1 37.7 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 42.754 5.975 -1.356 1 39.02 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 43.747 4.953 -1.329 1 43.42 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 42.862 6.898 -0.16 1 32.36 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 42.135 6.39 1.012 1 32.15 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 40.845 6.037 1.115 1 29.11 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 40.571 5.646 2.386 1 30.71 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 41.704 5.777 3.109 1 26.99 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 42.141 5.545 4.499 1 26.54 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 41.336 5.135 5.354 1 30.84 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 43.417 5.819 4.805 1 30.75 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 44.303 6.27 3.907 1 34.12 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 45.585 6.523 4.271 1 36.07 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 43.969 6.493 2.624 1 33.33 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 42.72 6.267 2.187 1 28.14 ? C4 GDP 201 A 1 HETATM 29 H H4' GDP . . . B 2 42.919 9.089 -2.333 1 41.81 ? H4' GDP 201 A 1 HETATM 30 H H3' GDP . . . B 2 42.433 6.595 -3.404 1 45.13 ? H3' GDP 201 A 1 HETATM 31 H HO3' GDP . . . B 2 44.772 6.46 -3.022 1 45.24 ? HO3' GDP 201 A 1 HETATM 32 H H2' GDP . . . B 2 41.745 5.542 -1.398 1 46.82 ? H2' GDP 201 A 1 HETATM 33 H HO2' GDP . . . B 2 43.686 4.422 -2.135 1 52.1 ? HO2' GDP 201 A 1 HETATM 34 H H1' GDP . . . B 2 43.925 7.021 0.09 1 38.83 ? H1' GDP 201 A 1 HETATM 35 H H8 GDP . . . B 2 40.132 6.044 0.3 1 34.93 ? H8 GDP 201 A 1 HETATM 36 H HN1 GDP . . . B 2 43.737 5.661 5.782 1 36.9 ? HN1 GDP 201 A 1 HETATM 37 H HN21 GDP . . . B 2 46.246 6.866 3.588 1 43.29 ? HN21 GDP 201 A 1 HETATM 38 H HN22 GDP . . . B 2 45.879 6.368 5.225 1 43.29 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 107 _model_server_stats.parse_time_ms 34 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #