data_4X1I # _model_server_result.job_id j3khnAEN300z5TCl8GyPmA _model_server_result.datetime_utc '2025-04-28 02:21:43' _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 4x1i # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":501}' # _entry.id 4X1I # _exptl.entry_id 4X1I _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 4X1I _cell.length_a 66.14 _cell.length_b 128.21 _cell.length_c 255.14 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4X1I _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc2 F O2G GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc3 F O2B GTP . A GTP 600 1_555 G MG MG . A MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? metalc ? metalc4 K O2G GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.435 ? metalc ? metalc5 K O2B GTP . C GTP 600 1_555 L MG MG . C MG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.947 ? # _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 199 n n PB O2B GDP sing 200 n n PB O3B GDP sing 201 n n PB O3A GDP sing 202 n n O2B HOB2 GDP sing 203 n n O3B HOB3 GDP sing 204 n n O3A PA GDP sing 205 n n PA O1A GDP doub 206 n n PA O2A GDP sing 207 n n PA O5' GDP sing 208 n n O2A HOA2 GDP sing 209 n n O5' C5' GDP sing 210 n n C5' C4' GDP sing 211 n n C5' H5' GDP sing 212 n n C5' "H5''" GDP sing 213 n n C4' O4' GDP sing 214 n n C4' C3' GDP sing 215 n n C4' H4' GDP sing 216 n n O4' C1' GDP sing 217 n n C3' O3' GDP sing 218 n n C3' C2' GDP sing 219 n n C3' H3' GDP sing 220 n n O3' HO3' GDP sing 221 n n C2' O2' GDP sing 222 n n C2' C1' GDP sing 223 n n C2' H2' GDP sing 224 n n O2' HO2' GDP sing 225 n n C1' N9 GDP sing 226 n n C1' H1' GDP sing 227 n n N9 C8 GDP sing 228 n y N9 C4 GDP sing 229 n y C8 N7 GDP doub 230 n y C8 H8 GDP sing 231 n n N7 C5 GDP sing 232 n y C5 C6 GDP sing 233 n n C5 C4 GDP doub 234 n y C6 O6 GDP doub 235 n n C6 N1 GDP sing 236 n n N1 C2 GDP sing 237 n n N1 HN1 GDP sing 238 n n C2 N2 GDP sing 239 n n C2 N3 GDP doub 240 n n N2 HN21 GDP sing 241 n n N2 HN22 GDP sing 242 n n N3 C4 GDP sing 243 n n # _atom_sites.entry_id 4X1I _atom_sites.fract_transf_matrix[1][1] 0.015119 _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] 0.0078 _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] 0.003919 _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 PFE . J 8 3WD B 1 503 1 3WD 101 . 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 PFE . O 8 3WD D 1 503 1 3WD 101 . # 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 -1.654 85.321 92.657 1 91.08 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . H 6 -1.079 86.348 91.667 1 91.6 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . H 6 -1.476 83.841 92.225 1 89.91 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . H 6 -3.085 85.706 92.949 1 89.73 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . H 6 -0.842 85.574 93.998 1 93.05 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . H 6 0.368 84.941 94.802 1 93.57 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . H 6 1.258 84.162 93.853 1 95.31 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . H 6 1.132 86.049 95.414 1 96.85 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . H 6 -0.346 84.047 95.912 1 90.39 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . H 6 -0.232 84.244 97.335 1 91.19 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . H 6 0.666 83.167 97.888 1 95.92 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . H 6 1.822 83.034 97.037 1 96.58 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . H 6 1.19 83.376 99.317 1 100.97 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . H 6 0.96 82.251 100.165 1 102.88 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . H 6 2.687 83.66 99.116 1 101.75 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . H 6 3.498 83.182 100.19 1 103.74 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . H 6 2.967 82.877 97.841 1 98.3 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . H 6 4.127 83.335 97.077 1 96.24 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . H 6 4.238 84.485 96.347 1 94.82 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . H 6 5.326 84.538 95.618 1 96.96 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . H 6 5.987 83.354 95.902 1 98.33 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . H 6 7.253 82.823 95.438 1 99.41 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . H 6 7.99 83.297 94.58 1 100.41 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . H 6 7.573 81.624 96.048 1 99.67 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . H 6 6.797 80.97 96.969 1 97.37 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . H 6 7.295 79.849 97.482 1 95.65 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . H 6 5.608 81.414 97.38 1 97.55 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . H 6 5.267 82.607 96.816 1 98.15 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 135 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 30 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #