data_4DRZ # _model_server_result.job_id s_fWZhfMLI12DpFPYgo1bA _model_server_result.datetime_utc '2024-11-16 14:49:37' _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 4drz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":201}' # _entry.id 4DRZ # _exptl.entry_id 4DRZ _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 108.95 _cell.angle_gamma 90 _cell.entry_id 4DRZ _cell.length_a 42.686 _cell.length_b 40.487 _cell.length_c 46.486 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4DRZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 44 A SER 25 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.41 ? metalc ? metalc2 A OD2 ASP 85 A ASP 66 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc3 B O1B GDP . A GDP 201 1_555 C CA CA . A CA 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.317 ? metalc ? metalc4 C CA CA . A CA 202 1_555 D O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.608 ? metalc ? metalc5 C CA CA . A CA 202 1_555 D O HOH . A HOH 334 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.345 ? metalc ? metalc6 C CA CA . A CA 202 1_555 D O HOH . A HOH 340 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.591 ? # _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 4DRZ _atom_sites.fract_transf_matrix[1][1] 0.023427 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008044 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024699 _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] 0.022745 _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 1 201 502 GDP GDP . C 3 CA A 1 202 1 CA CA . D 4 HOH A 1 301 301 HOH HOH . D 4 HOH A 2 302 302 HOH HOH . D 4 HOH A 3 303 303 HOH HOH . D 4 HOH A 4 304 304 HOH HOH . D 4 HOH A 5 305 305 HOH HOH . D 4 HOH A 6 306 306 HOH HOH . D 4 HOH A 7 307 308 HOH HOH . D 4 HOH A 8 308 309 HOH HOH . D 4 HOH A 9 309 311 HOH HOH . D 4 HOH A 10 310 313 HOH HOH . D 4 HOH A 11 311 314 HOH HOH . D 4 HOH A 12 312 315 HOH HOH . D 4 HOH A 13 313 316 HOH HOH . D 4 HOH A 14 314 317 HOH HOH . D 4 HOH A 15 315 318 HOH HOH . D 4 HOH A 16 316 319 HOH HOH . D 4 HOH A 17 317 320 HOH HOH . D 4 HOH A 18 318 321 HOH HOH . D 4 HOH A 19 319 322 HOH HOH . D 4 HOH A 20 320 323 HOH HOH . D 4 HOH A 21 321 324 HOH HOH . D 4 HOH A 22 322 325 HOH HOH . D 4 HOH A 23 323 326 HOH HOH . D 4 HOH A 24 324 327 HOH HOH . D 4 HOH A 25 325 328 HOH HOH . D 4 HOH A 26 326 329 HOH HOH . D 4 HOH A 27 327 330 HOH HOH . D 4 HOH A 28 328 331 HOH HOH . D 4 HOH A 29 329 332 HOH HOH . D 4 HOH A 30 330 333 HOH HOH . D 4 HOH A 31 331 334 HOH HOH . D 4 HOH A 32 332 335 HOH HOH . D 4 HOH A 33 333 336 HOH HOH . D 4 HOH A 34 334 338 HOH HOH . D 4 HOH A 35 335 340 HOH HOH . D 4 HOH A 36 336 341 HOH HOH . D 4 HOH A 37 337 342 HOH HOH . D 4 HOH A 38 338 343 HOH HOH . D 4 HOH A 39 339 344 HOH HOH . D 4 HOH A 40 340 345 HOH HOH . D 4 HOH A 41 341 346 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 7.151 9.412 2.029 1 17.87 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . B 2 8.612 9.601 2.318 1 18.77 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . B 2 6.735 8.035 2.406 1 16.75 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . B 2 6.716 9.91 0.669 1 18.78 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . B 2 6.268 10.284 3.061 1 18.64 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . B 2 6.772 11.584 3.896 1 20.4 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . B 2 7.627 11.145 5.058 1 20 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . B 2 7.325 12.599 2.915 1 22 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . B 2 5.382 12.137 4.491 1 21.18 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . B 2 4.371 12.701 3.642 1 21.95 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . B 2 3.402 13.504 4.478 1 22.92 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . B 2 2.931 12.66 5.539 1 21.81 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . B 2 4.069 14.707 5.114 1 24.84 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . B 2 3.18 15.84 5.107 1 26.79 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . B 2 4.361 14.23 6.519 1 24.37 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . B 2 4.415 15.271 7.478 1 26.36 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . B 2 3.2 13.297 6.789 1 22.97 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . B 2 3.508 12.27 7.8 1 21.83 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . B 2 4.538 11.424 7.783 1 20.73 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . B 2 4.486 10.619 8.87 1 20.49 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . B 2 3.404 10.962 9.6 1 20.98 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . B 2 2.763 10.521 10.858 1 21.22 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . B 2 3.215 9.586 11.543 1 20.66 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . B 2 1.65 11.146 11.257 1 22.44 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . B 2 1.101 12.15 10.542 1 23.14 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . B 2 -0.008 12.749 10.978 1 24.46 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . B 2 1.646 12.599 9.386 1 23.16 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . B 2 2.776 12.043 8.88 1 21.99 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 22 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 398 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 28 #