data_4X1Y # _model_server_result.job_id tyyKHYu7HRA8DDdr0IDDrw _model_server_result.datetime_utc '2024-11-23 05:58:04' _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 4x1y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 4X1Y # _exptl.entry_id 4X1Y _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 4X1Y _cell.length_a 66.61 _cell.length_b 127.86 _cell.length_c 255.04 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X1Y _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.638 ? metalc ? metalc2 F O2G GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.486 ? metalc ? metalc3 F O2B GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.943 ? metalc ? metalc4 K O2G GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? metalc ? metalc5 K O2B GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? # _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 198 n n PB O2B GDP sing 199 n n PB O3B GDP sing 200 n n PB O3A GDP sing 201 n n O2B HOB2 GDP sing 202 n n O3B HOB3 GDP sing 203 n n O3A PA GDP sing 204 n n PA O1A GDP doub 205 n n PA O2A GDP sing 206 n n PA O5' GDP sing 207 n n O2A HOA2 GDP sing 208 n n O5' C5' GDP sing 209 n n C5' C4' GDP sing 210 n n C5' H5' GDP sing 211 n n C5' "H5''" GDP sing 212 n n C4' O4' GDP sing 213 n n C4' C3' GDP sing 214 n n C4' H4' GDP sing 215 n n O4' C1' GDP sing 216 n n C3' O3' GDP sing 217 n n C3' C2' GDP sing 218 n n C3' H3' GDP sing 219 n n O3' HO3' GDP sing 220 n n C2' O2' GDP sing 221 n n C2' C1' GDP sing 222 n n C2' H2' GDP sing 223 n n O2' HO2' GDP sing 224 n n C1' N9 GDP sing 225 n n C1' H1' GDP sing 226 n n N9 C8 GDP sing 227 n y N9 C4 GDP sing 228 n y C8 N7 GDP doub 229 n y C8 H8 GDP sing 230 n n N7 C5 GDP sing 231 n y C5 C6 GDP sing 232 n n C5 C4 GDP doub 233 n y C6 O6 GDP doub 234 n n C6 N1 GDP sing 235 n n N1 C2 GDP sing 236 n n N1 HN1 GDP sing 237 n n C2 N2 GDP sing 238 n n C2 N3 GDP doub 239 n n N2 HN21 GDP sing 240 n n N2 HN22 GDP sing 241 n n N3 C4 GDP sing 242 n n # _atom_sites.entry_id 4X1Y _atom_sites.fract_transf_matrix[1][1] 0.015013 _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] 0.007822 _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] 0.003922 _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 3WV B 1 503 1 3WV 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 3WV D 1 503 1 3WV 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 -1.637 85.158 92.643 1 110.38 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . H 6 -0.797 86.124 91.793 1 110.87 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . H 6 -1.565 83.706 92.179 1 111.13 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . H 6 -3.045 85.732 92.741 1 106.88 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . H 6 -1.021 85.176 94.108 1 115.73 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . H 6 0.284 84.763 94.913 1 117.34 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . H 6 1.409 84.276 93.99 1 114.54 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . H 6 0.696 85.983 95.644 1 120.08 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . H 6 -0.23 83.657 95.947 1 114.19 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . H 6 -0.187 83.777 97.386 1 113.26 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . H 6 0.707 82.696 97.945 1 117.12 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . H 6 1.858 82.557 97.085 1 117.58 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . H 6 1.258 82.926 99.36 1 121.78 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . H 6 1.244 81.764 100.195 1 123.09 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . H 6 2.679 83.441 99.098 1 120.7 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . H 6 3.561 83.15 100.182 1 120.26 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . H 6 3.036 82.63 97.861 1 118.63 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . H 6 4.114 83.164 97.025 1 117.47 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . H 6 4.132 84.307 96.269 1 115.24 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . H 6 5.173 84.392 95.473 1 116.1 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . H 6 5.896 83.236 95.732 1 118.6 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . H 6 7.156 82.725 95.189 1 119.53 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . H 6 7.806 83.171 94.245 1 118.92 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . H 6 7.558 81.559 95.82 1 120.64 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . H 6 6.87 80.914 96.819 1 118.47 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . H 6 7.462 79.855 97.373 1 117.74 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . H 6 5.69 81.323 97.284 1 116.97 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . H 6 5.264 82.481 96.708 1 118.3 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 55 _model_server_stats.query_time_ms 318 _model_server_stats.encode_time_ms 11 _model_server_stats.element_count 28 #