data_1Z6X # _model_server_result.job_id lu0mqnJdboq8f9BofG8jBQ _model_server_result.datetime_utc '2024-10-11 02:23:47' _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 1z6x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 1Z6X # _exptl.entry_id 1Z6X _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 2 _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 1Z6X _cell.length_a 64.77 _cell.length_b 64.77 _cell.length_c 155.559 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z6X _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 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 ? 3 D N N ? 3 F 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 OG1 THR 31 A THR 31 1_555 C MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.776 ? metalc ? metalc2 A OE2 GLU 54 A GLU 54 1_555 C MG MG . A MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.627 ? metalc ? metalc3 C MG MG . A MG 200 1_555 D O1B GDP . A GDP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.559 ? metalc ? metalc4 B OG1 THR 31 B THR 31 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.318 ? metalc ? metalc5 B OE1 GLU 54 B GLU 54 1_555 E MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc6 E MG MG . B MG 202 1_555 F O1B GDP . B GDP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.234 ? # _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 1Z6X _atom_sites.fract_transf_matrix[1][1] 0.015439 _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] 0.015439 _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] 0.006428 _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 C 2 MG A 1 200 200 MG MG . D 3 GDP A 1 201 201 GDP GDP . E 2 MG B 1 202 202 MG MG . F 3 GDP B 1 203 203 GDP GDP . G 4 HOH A 1 301 301 HOH HOH . G 4 HOH A 2 302 302 HOH HOH . G 4 HOH A 3 303 303 HOH HOH . G 4 HOH A 4 306 306 HOH HOH . G 4 HOH A 5 308 308 HOH HOH . G 4 HOH A 6 309 309 HOH HOH . G 4 HOH A 7 310 310 HOH HOH . G 4 HOH A 8 314 314 HOH HOH . G 4 HOH A 9 315 315 HOH HOH . G 4 HOH A 10 317 317 HOH HOH . G 4 HOH A 11 318 318 HOH HOH . G 4 HOH A 12 320 320 HOH HOH . G 4 HOH A 13 322 322 HOH HOH . G 4 HOH A 14 323 323 HOH HOH . G 4 HOH A 15 325 325 HOH HOH . G 4 HOH A 16 326 326 HOH HOH . G 4 HOH A 17 330 330 HOH HOH . G 4 HOH A 18 333 333 HOH HOH . G 4 HOH A 19 334 334 HOH HOH . G 4 HOH A 20 335 335 HOH HOH . G 4 HOH A 21 336 336 HOH HOH . G 4 HOH A 22 337 337 HOH HOH . G 4 HOH A 23 338 338 HOH HOH . G 4 HOH A 24 339 339 HOH HOH . G 4 HOH A 25 341 341 HOH HOH . G 4 HOH A 26 342 342 HOH HOH . G 4 HOH A 27 343 343 HOH HOH . G 4 HOH A 28 344 344 HOH HOH . G 4 HOH A 29 346 346 HOH HOH . G 4 HOH A 30 347 347 HOH HOH . G 4 HOH A 31 348 348 HOH HOH . G 4 HOH A 32 349 349 HOH HOH . G 4 HOH A 33 350 350 HOH HOH . G 4 HOH A 34 351 351 HOH HOH . G 4 HOH A 35 353 353 HOH HOH . G 4 HOH A 36 355 355 HOH HOH . H 4 HOH B 1 304 304 HOH HOH . H 4 HOH B 2 305 305 HOH HOH . H 4 HOH B 3 307 307 HOH HOH . H 4 HOH B 4 311 311 HOH HOH . H 4 HOH B 5 312 312 HOH HOH . H 4 HOH B 6 313 313 HOH HOH . H 4 HOH B 7 316 316 HOH HOH . H 4 HOH B 8 319 319 HOH HOH . H 4 HOH B 9 321 321 HOH HOH . H 4 HOH B 10 324 324 HOH HOH . H 4 HOH B 11 327 327 HOH HOH . H 4 HOH B 12 328 328 HOH HOH . H 4 HOH B 13 329 329 HOH HOH . H 4 HOH B 14 331 331 HOH HOH . H 4 HOH B 15 332 332 HOH HOH . H 4 HOH B 16 340 340 HOH HOH . H 4 HOH B 17 345 345 HOH HOH . H 4 HOH B 18 352 352 HOH HOH . H 4 HOH B 19 354 354 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 . . . D 3 5.494 -16.527 -13.757 1 31.13 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 3 5.906 -15.753 -12.529 1 31.75 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 3 4.556 -15.686 -14.583 1 30.79 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 3 4.826 -17.831 -13.372 1 31.2 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 3 6.78 -16.851 -14.665 1 32.82 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 3 8.231 -17.122 -14.038 1 33.14 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 3 9.156 -15.979 -14.35 1 33.89 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 3 8.12 -17.411 -12.558 1 33.73 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 3 8.747 -18.436 -14.779 1 34.25 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 3 8.679 -18.566 -16.188 1 35.02 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 3 9.765 -19.542 -16.58 1 35.88 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 3 10.342 -19.07 -17.787 1 36.82 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 3 10.875 -19.554 -15.547 1 36.88 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 3 11.431 -20.868 -15.468 1 37.76 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 3 11.89 -18.553 -16.064 1 37.35 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 3 13.235 -18.912 -15.735 1 37.23 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 3 11.662 -18.58 -17.563 1 38.43 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 3 11.76 -17.232 -18.164 1 39.03 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 3 11.341 -16.071 -17.631 1 39.08 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 3 11.596 -15.047 -18.48 1 39.38 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 3 12.178 -15.554 -19.579 1 39.21 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 3 12.706 -15.026 -20.855 1 39.24 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 3 12.652 -13.805 -21.103 1 39.18 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 3 13.237 -15.896 -21.73 1 39.31 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 3 13.3 -17.221 -21.477 1 39.33 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 3 13.846 -18.05 -22.394 1 39.33 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 3 12.841 -17.767 -20.326 1 39.37 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 3 12.281 -16.997 -19.364 1 39.2 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 28 #