data_4X20 # _model_server_result.job_id IEUPhd1xQr0cBXZOusUTiQ _model_server_result.datetime_utc '2024-11-22 23:08:15' _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 4x20 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":501}' # _entry.id 4X20 # _exptl.entry_id 4X20 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 6 _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 4X20 _cell.length_a 66.24 _cell.length_b 128.27 _cell.length_c 254.14 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X20 _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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,E,F,G,H,I,J,K,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 H N N ? 6 M 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 145 A THR 145 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc2 F O2G GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.851 ? metalc ? metalc3 F O2B GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.938 ? metalc ? metalc4 K O3G GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc5 K O2B GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? # _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 200 n n PB O2B GDP sing 201 n n PB O3B GDP sing 202 n n PB O3A GDP sing 203 n n O2B HOB2 GDP sing 204 n n O3B HOB3 GDP sing 205 n n O3A PA GDP sing 206 n n PA O1A GDP doub 207 n n PA O2A GDP sing 208 n n PA O5' GDP sing 209 n n O2A HOA2 GDP sing 210 n n O5' C5' GDP sing 211 n n C5' C4' GDP sing 212 n n C5' H5' GDP sing 213 n n C5' "H5''" GDP sing 214 n n C4' O4' GDP sing 215 n n C4' C3' GDP sing 216 n n C4' H4' GDP sing 217 n n O4' C1' GDP sing 218 n n C3' O3' GDP sing 219 n n C3' C2' GDP sing 220 n n C3' H3' GDP sing 221 n n O3' HO3' GDP sing 222 n n C2' O2' GDP sing 223 n n C2' C1' GDP sing 224 n n C2' H2' GDP sing 225 n n O2' HO2' GDP sing 226 n n C1' N9 GDP sing 227 n n C1' H1' GDP sing 228 n n N9 C8 GDP sing 229 n y N9 C4 GDP sing 230 n y C8 N7 GDP doub 231 n y C8 H8 GDP sing 232 n n N7 C5 GDP sing 233 n y C5 C6 GDP sing 234 n n C5 C4 GDP doub 235 n y C6 O6 GDP doub 236 n n C6 N1 GDP sing 237 n n N1 C2 GDP sing 238 n n N1 HN1 GDP sing 239 n n C2 N2 GDP sing 240 n n C2 N3 GDP doub 241 n n N2 HN21 GDP sing 242 n n N2 HN22 GDP sing 243 n n N3 C4 GDP sing 244 n n # _atom_sites.entry_id 4X20 _atom_sites.fract_transf_matrix[1][1] 0.015097 _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] 0.007803 _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] 0.003938 _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 F 4 GTP A 1 600 600 GTP GTP . G 5 MG A 1 601 601 MG MG . H 6 GDP B 1 501 600 GDP GDP . I 7 LOC B 1 502 601 LOC 618 . J 8 3WY B 1 503 1 3WY PFE . K 4 GTP C 1 600 600 GTP GTP . L 5 MG C 1 601 601 MG MG . M 6 GDP D 1 501 600 GDP GDP . N 7 LOC D 1 502 601 LOC 618 . O 8 3WY D 1 503 1 3WY PFE . # 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 . . . M 6 -41.722 155.559 117.719 1 137.06 ? PB GDP 501 D 1 HETATM 2 O O1B GDP . . . M 6 -41.26 156.912 117.144 1 138.43 ? O1B GDP 501 D 1 HETATM 3 O O2B GDP . . . M 6 -40.905 154.339 117.278 1 136.6 ? O2B GDP 501 D 1 HETATM 4 O O3B GDP . . . M 6 -43.232 155.448 117.434 1 137.65 ? O3B GDP 501 D 1 HETATM 5 O O3A GDP . . . M 6 -41.5 155.69 119.286 1 133.04 ? O3A GDP 501 D 1 HETATM 6 P PA GDP . . . M 6 -40.29 155.811 120.303 1 126.7 ? PA GDP 501 D 1 HETATM 7 O O1A GDP . . . M 6 -38.962 155.547 119.59 1 126.91 ? O1A GDP 501 D 1 HETATM 8 O O2A GDP . . . M 6 -40.418 157.144 120.943 1 124.77 ? O2A GDP 501 D 1 HETATM 9 O O5' GDP . . . M 6 -40.591 154.677 121.355 1 124.59 ? O5' GDP 501 D 1 HETATM 10 C C5' GDP . . . M 6 -40.843 154.885 122.762 1 123.11 ? C5' GDP 501 D 1 HETATM 11 C C4' GDP . . . M 6 -39.802 154.096 123.515 1 120.33 ? C4' GDP 501 D 1 HETATM 12 O O4' GDP . . . M 6 -38.535 154.244 122.841 1 119.66 ? O4' GDP 501 D 1 HETATM 13 C C3' GDP . . . M 6 -39.565 154.505 124.969 1 117.01 ? C3' GDP 501 D 1 HETATM 14 O O3' GDP . . . M 6 -39.474 153.387 125.849 1 117.39 ? O3' GDP 501 D 1 HETATM 15 C C2' GDP . . . M 6 -38.305 155.373 124.888 1 114.34 ? C2' GDP 501 D 1 HETATM 16 O O2' GDP . . . M 6 -37.464 155.231 126.023 1 114.32 ? O2' GDP 501 D 1 HETATM 17 C C1' GDP . . . M 6 -37.561 154.714 123.747 1 116.06 ? C1' GDP 501 D 1 HETATM 18 N N9 GDP . . . M 6 -36.664 155.607 123.032 1 114.62 ? N9 GDP 501 D 1 HETATM 19 C C8 GDP . . . M 6 -36.999 156.602 122.156 1 113.81 ? C8 GDP 501 D 1 HETATM 20 N N7 GDP . . . M 6 -35.967 157.126 121.545 1 114.86 ? N7 GDP 501 D 1 HETATM 21 C C5 GDP . . . M 6 -34.883 156.437 122.064 1 116.27 ? C5 GDP 501 D 1 HETATM 22 C C6 GDP . . . M 6 -33.499 156.517 121.764 1 118.02 ? C6 GDP 501 D 1 HETATM 23 O O6 GDP . . . M 6 -32.978 157.243 120.92 1 121.07 ? O6 GDP 501 D 1 HETATM 24 N N1 GDP . . . M 6 -32.743 155.618 122.498 1 115 ? N1 GDP 501 D 1 HETATM 25 C C2 GDP . . . M 6 -33.243 154.726 123.406 1 113.2 ? C2 GDP 501 D 1 HETATM 26 N N2 GDP . . . M 6 -32.37 153.93 124.009 1 112.77 ? N2 GDP 501 D 1 HETATM 27 N N3 GDP . . . M 6 -34.538 154.625 123.693 1 113.9 ? N3 GDP 501 D 1 HETATM 28 C C4 GDP . . . M 6 -35.298 155.505 122.991 1 115.37 ? C4 GDP 501 D 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 36 _model_server_stats.query_time_ms 356 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #