data_9DRZ # _model_server_result.job_id mE66Gvztg8oHftxIeoaRZA _model_server_result.datetime_utc '2024-10-18 05:22:16' _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 9drz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 9DRZ # _exptl.entry_id 9DRZ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 3 _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 9DRZ _cell.length_a 120.469 _cell.length_b 120.469 _cell.length_c 166.733 _cell.Z_PDB 36 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9DRZ _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_defined_assembly 2 ? monomeric 1 author_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,J 1 1 B,F,G,K 2 1 C,H,I,L 3 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 ? 2 D N N ? 2 F N N ? 2 H 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 OG SER 19 A SER 17 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc2 D O2B GDP . A GDP 201 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc3 E MG MG . A MG 202 1_555 J O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc4 E MG MG . A MG 202 1_555 J O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc5 E MG MG . A MG 202 1_555 J O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.996 ? metalc ? metalc6 E MG MG . A MG 202 1_555 J O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc7 B OG SER 19 B SER 17 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc8 F O3B GDP . B GDP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc9 G MG MG . B MG 202 1_555 K O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? metalc ? metalc10 G MG MG . B MG 202 1_555 K O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc11 G MG MG . B MG 202 1_555 K O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? metalc ? metalc12 G MG MG . B MG 202 1_555 K O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? metalc ? metalc13 C OG SER 19 C SER 17 1_555 I MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc14 H O2B GDP . C GDP 201 1_555 I MG MG . C MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? metalc ? metalc15 I MG MG . C MG 202 1_555 L O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc16 I MG MG . C MG 202 1_555 L O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc17 I MG MG . C MG 202 1_555 L O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc18 I MG MG . C MG 202 1_555 L O HOH . C HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? # _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 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 9DRZ _atom_sites.fract_transf_matrix[1][1] 0.008301 _atom_sites.fract_transf_matrix[1][2] 0.004793 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009585 _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] 0.005998 _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 D 2 GDP A 1 201 1 GDP GDP . E 3 MG A 1 202 3 MG MG . F 2 GDP B 1 201 1 GDP GDP . G 3 MG B 1 202 1 MG MG . H 2 GDP C 1 201 1 GDP GDP . I 3 MG C 1 202 2 MG MG . J 4 HOH A 1 301 21 HOH HOH . J 4 HOH A 2 302 18 HOH HOH . J 4 HOH A 3 303 4 HOH HOH . J 4 HOH A 4 304 9 HOH HOH . J 4 HOH A 5 305 5 HOH HOH . J 4 HOH A 6 306 10 HOH HOH . J 4 HOH A 7 307 11 HOH HOH . J 4 HOH A 8 308 24 HOH HOH . J 4 HOH A 9 309 23 HOH HOH . J 4 HOH A 10 310 22 HOH HOH . J 4 HOH A 11 311 2 HOH HOH . J 4 HOH A 12 312 1 HOH HOH . K 4 HOH B 1 301 7 HOH HOH . K 4 HOH B 2 302 16 HOH HOH . K 4 HOH B 3 303 17 HOH HOH . K 4 HOH B 4 304 3 HOH HOH . L 4 HOH C 1 301 13 HOH HOH . L 4 HOH C 2 302 12 HOH HOH . L 4 HOH C 3 303 15 HOH HOH . L 4 HOH C 4 304 14 HOH HOH . L 4 HOH C 5 305 8 HOH HOH . L 4 HOH C 6 306 19 HOH HOH . L 4 HOH C 7 307 20 HOH HOH . # 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 . . . D 2 -16.796 -26.578 3.886 1 50.75 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 2 -15.6 -27.47 3.774 1 44.99 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 2 -18.004 -27.279 4.437 1 45.21 -1 O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 2 -17.128 -25.782 2.646 1 57.67 -1 O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 2 -16.237 -25.454 4.899 1 55.9 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 2 -16.496 -25.223 6.457 1 52.03 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 2 -17.959 -24.979 6.643 1 45.53 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 2 -15.815 -26.354 7.153 1 53.84 -1 O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 2 -15.698 -23.867 6.753 1 47.97 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 2 -14.253 -23.883 6.646 1 51.27 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 2 -13.664 -22.775 7.487 1 53.62 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 2 -14.016 -21.476 6.938 1 55.14 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 2 -14.123 -22.745 8.947 1 56.53 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 2 -13.065 -22.353 9.803 1 58.55 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 2 -15.161 -21.628 8.99 1 61.78 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 2 -15.113 -21.015 10.259 1 71.63 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 2 -14.691 -20.682 7.888 1 57.01 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 2 -15.785 -19.982 7.219 1 58.25 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 2 -16.905 -20.546 6.658 1 63.92 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 2 -17.725 -19.669 6.127 1 68.48 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 2 -17.106 -18.446 6.352 1 59.48 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 2 -17.524 -17.137 6.002 1 53.99 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 2 -18.556 -16.78 5.419 1 60.43 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 2 -16.597 -16.187 6.416 1 53.07 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 2 -15.433 -16.458 7.097 1 57.23 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 2 -14.681 -15.401 7.434 1 57.24 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 2 -15.031 -17.688 7.43 1 52.14 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 2 -15.915 -18.628 7.027 1 55.98 ? C4 GDP 201 A 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 258 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #