data_4X20 # _model_server_result.job_id 7M3s77Rs079nXpfUW2TGIA _model_server_result.datetime_utc '2024-11-05 21:28:13' _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":"H","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 . . . H 6 -1.819 85.672 92.355 1 127.14 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . H 6 -1.268 86.683 91.337 1 127.36 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . H 6 -1.689 84.213 91.93 1 125.09 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . H 6 -3.253 86.12 92.657 1 125.73 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . H 6 -0.916 85.824 93.656 1 130.23 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . H 6 0.213 84.931 94.328 1 128.43 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . H 6 0.723 83.963 93.242 1 128.68 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . H 6 1.304 85.78 94.86 1 127.86 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . H 6 -0.529 84.228 95.541 1 124.6 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . H 6 -0.252 84.458 96.935 1 125.14 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . H 6 0.465 83.238 97.456 1 129.6 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . H 6 1.659 83.022 96.674 1 130.8 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . H 6 0.91 83.263 98.922 1 134.04 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . H 6 0.687 82.005 99.562 1 135.9 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . H 6 2.4 83.617 98.827 1 134.18 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . H 6 3.143 83.139 99.947 1 133.69 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . H 6 2.778 82.902 97.531 1 132.45 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . H 6 3.953 83.424 96.822 1 131.11 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . H 6 4.013 84.555 96.049 1 130.92 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . H 6 5.064 84.6 95.265 1 132.31 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . H 6 5.756 83.433 95.558 1 132.77 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . H 6 6.995 82.872 95.018 1 132.68 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . H 6 7.618 83.243 94.018 1 133.44 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . H 6 7.382 81.731 95.701 1 130.4 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . H 6 6.693 81.15 96.735 1 128.05 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . H 6 7.284 80.125 97.348 1 127.38 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . H 6 5.517 81.594 97.18 1 127.43 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . H 6 5.107 82.725 96.556 1 130.31 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 66 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #