data_1Z2B # _model_server_result.job_id j4tvl065hHPsIUhbh_gIJQ _model_server_result.datetime_utc '2025-02-26 19:29:16' _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 1z2b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":603}' # _entry.id 1Z2B # _exptl.entry_id 1Z2B _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 120 _cell.entry_id 1Z2B _cell.length_a 324.852 _cell.length_b 324.852 _cell.length_c 54.208 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1Z2B _symmetry.cell_setting ? _symmetry.Int_Tables_number 170 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65' # _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 _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 N GLY 144 A GLY 144 1_555 F MG MG . A MG 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.993 ? metalc ? metalc2 F MG MG . A MG 500 1_555 G O2G GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.67 ? metalc ? metalc3 F MG MG . A MG 500 1_555 G O3G GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.709 ? metalc ? metalc4 F MG MG . A MG 500 1_555 G O2B GTP . A GTP 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc5 C N GLY 144 C GLY 144 1_555 J MG MG . C MG 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.096 ? metalc ? metalc6 J MG MG . C MG 501 1_555 K O2B GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.774 ? metalc ? metalc7 J MG MG . C MG 501 1_555 K O3G GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.661 ? metalc ? metalc8 J MG MG . C MG 501 1_555 K O2G GTP . C GTP 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.928 ? # _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 140 n n PB O2B GDP sing 141 n n PB O3B GDP sing 142 n n PB O3A GDP sing 143 n n O2B HOB2 GDP sing 144 n n O3B HOB3 GDP sing 145 n n O3A PA GDP sing 146 n n PA O1A GDP doub 147 n n PA O2A GDP sing 148 n n PA O5' GDP sing 149 n n O2A HOA2 GDP sing 150 n n O5' C5' GDP sing 151 n n C5' C4' GDP sing 152 n n C5' H5' GDP sing 153 n n C5' "H5''" GDP sing 154 n n C4' O4' GDP sing 155 n n C4' C3' GDP sing 156 n n C4' H4' GDP sing 157 n n O4' C1' GDP sing 158 n n C3' O3' GDP sing 159 n n C3' C2' GDP sing 160 n n C3' H3' GDP sing 161 n n O3' HO3' GDP sing 162 n n C2' O2' GDP sing 163 n n C2' C1' GDP sing 164 n n C2' H2' GDP sing 165 n n O2' HO2' GDP sing 166 n n C1' N9 GDP sing 167 n n C1' H1' GDP sing 168 n n N9 C8 GDP sing 169 n y N9 C4 GDP sing 170 n y C8 N7 GDP doub 171 n y C8 H8 GDP sing 172 n n N7 C5 GDP sing 173 n y C5 C6 GDP sing 174 n n C5 C4 GDP doub 175 n y C6 O6 GDP doub 176 n n C6 N1 GDP sing 177 n n N1 C2 GDP sing 178 n n N1 HN1 GDP sing 179 n n C2 N2 GDP sing 180 n n C2 N3 GDP doub 181 n n N2 HN21 GDP sing 182 n n N2 HN22 GDP sing 183 n n N3 C4 GDP sing 184 n n # _atom_sites.entry_id 1Z2B _atom_sites.fract_transf_matrix[1][1] 0.003078 _atom_sites.fract_transf_matrix[1][2] 0.001777 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003555 _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] 0.018447 _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 MG A 1 500 500 MG MG . G 5 GTP A 1 600 600 GTP GTP . H 6 GDP B 1 602 602 GDP GDP . I 7 CN2 B 1 700 700 CN2 CN2 . J 4 MG C 1 501 501 MG MG . K 5 GTP C 1 601 601 GTP GTP . L 8 VLB C 1 800 800 VLB VLB . M 6 GDP D 1 603 603 GDP GDP . N 7 CN2 D 1 701 701 CN2 CN2 . # 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 10.595 42.637 -2.188 1 117.78 ? PB GDP 603 D 1 HETATM 2 O O1B GDP . . . M 6 11.127 43.763 -1.416 1 117.78 ? O1B GDP 603 D 1 HETATM 3 O O2B GDP . . . M 6 11.668 41.555 -2.295 1 117.78 ? O2B GDP 603 D 1 HETATM 4 O O3B GDP . . . M 6 9.313 42.02 -1.602 1 117.78 ? O3B GDP 603 D 1 HETATM 5 O O3A GDP . . . M 6 10.293 43.309 -3.597 1 117.78 ? O3A GDP 603 D 1 HETATM 6 P PA GDP . . . M 6 10.511 42.407 -4.882 1 117.78 ? PA GDP 603 D 1 HETATM 7 O O1A GDP . . . M 6 11.639 41.55 -4.492 1 117.78 ? O1A GDP 603 D 1 HETATM 8 O O2A GDP . . . M 6 9.231 41.596 -5.231 1 117.78 ? O2A GDP 603 D 1 HETATM 9 O O5' GDP . . . M 6 11.068 43.401 -6.034 1 117.78 ? O5' GDP 603 D 1 HETATM 10 C C5' GDP . . . M 6 10.296 44.442 -6.593 1 117.78 ? C5' GDP 603 D 1 HETATM 11 C C4' GDP . . . M 6 10.984 45.108 -7.796 1 117.78 ? C4' GDP 603 D 1 HETATM 12 O O4' GDP . . . M 6 12.249 44.555 -8.125 1 117.78 ? O4' GDP 603 D 1 HETATM 13 C C3' GDP . . . M 6 10.114 44.995 -9.045 1 117.78 ? C3' GDP 603 D 1 HETATM 14 O O3' GDP . . . M 6 9.901 46.278 -9.592 1 117.78 ? O3' GDP 603 D 1 HETATM 15 C C2' GDP . . . M 6 10.838 44.08 -10.024 1 117.78 ? C2' GDP 603 D 1 HETATM 16 O O2' GDP . . . M 6 10.839 44.54 -11.372 1 117.78 ? O2' GDP 603 D 1 HETATM 17 C C1' GDP . . . M 6 12.245 43.99 -9.441 1 117.78 ? C1' GDP 603 D 1 HETATM 18 N N9 GDP . . . M 6 12.701 42.577 -9.422 1 117.78 ? N9 GDP 603 D 1 HETATM 19 C C8 GDP . . . M 6 12.104 41.524 -8.769 1 117.78 ? C8 GDP 603 D 1 HETATM 20 N N7 GDP . . . M 6 12.844 40.412 -8.999 1 117.78 ? N7 GDP 603 D 1 HETATM 21 C C5 GDP . . . M 6 13.904 40.734 -9.779 1 117.78 ? C5 GDP 603 D 1 HETATM 22 C C6 GDP . . . M 6 14.942 39.986 -10.31 1 117.78 ? C6 GDP 603 D 1 HETATM 23 O O6 GDP . . . M 6 14.802 38.771 -10.382 1 117.78 ? O6 GDP 603 D 1 HETATM 24 N N1 GDP . . . M 6 15.881 40.607 -11.107 1 117.78 ? N1 GDP 603 D 1 HETATM 25 C C2 GDP . . . M 6 15.8 41.952 -11.391 1 117.78 ? C2 GDP 603 D 1 HETATM 26 N N2 GDP . . . M 6 16.243 42.362 -12.566 1 117.78 ? N2 GDP 603 D 1 HETATM 27 N N3 GDP . . . M 6 14.768 42.68 -10.853 1 117.78 ? N3 GDP 603 D 1 HETATM 28 C C4 GDP . . . M 6 13.824 42.09 -10.068 1 117.78 ? C4 GDP 603 D 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 227 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 28 #