data_1ZCA # _model_server_result.job_id 6ClPr4-_CAA90tRp0Bn2Hg _model_server_result.datetime_utc '2024-10-18 19:24:07' _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 1zca # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":382}' # _entry.id 1ZCA # _exptl.entry_id 1ZCA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 106.09 _cell.angle_gamma 90 _cell.entry_id 1ZCA _cell.length_a 57.501 _cell.length_b 85.23 _cell.length_c 82.885 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1ZCA _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,E,I 1 1 B,F,G,H,J 2 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 ? 4 E N N ? 4 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 49 A SER 69 1_555 C MG MG . A MG 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.126 ? metalc ? metalc2 A OG1 THR 186 A THR 206 1_555 C MG MG . A MG 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc3 E O2B GDP . A GDP 382 1_555 C MG MG . A MG 383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.288 ? metalc ? metalc4 E O3B GDP . A GDP 382 1_555 D AL ALF . A ALF 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc5 E O2B GDP . A GDP 382 1_555 D AL ALF . A ALF 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.482 ? metalc ? metalc6 C MG MG . A MG 383 1_555 D F4 ALF . A ALF 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.79 ? metalc ? metalc7 C MG MG . A MG 383 1_555 D F1 ALF . A ALF 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.998 ? metalc ? metalc8 C MG MG . A MG 383 1_555 D AL ALF . A ALF 384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.144 ? metalc ? metalc9 C MG MG . A MG 383 1_555 I O HOH . A HOH 386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? metalc ? metalc10 C MG MG . A MG 383 1_555 I O HOH . A HOH 387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.755 ? metalc ? metalc11 D AL ALF . A ALF 384 1_555 I O HOH . A HOH 385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc12 B OG SER 49 B SER 69 1_555 F MG MG . B MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc13 B OG1 THR 186 B THR 206 1_555 F MG MG . B MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.922 ? metalc ? metalc14 H O2B GDP . B GDP 1382 1_555 F MG MG . B MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.074 ? metalc ? metalc15 H O3B GDP . B GDP 1382 1_555 F MG MG . B MG 1383 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.536 ? metalc ? metalc16 H O3B GDP . B GDP 1382 1_555 G AL ALF . B ALF 1384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.954 ? metalc ? metalc17 F MG MG . B MG 1383 1_555 G F4 ALF . B ALF 1384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.771 ? metalc ? metalc18 F MG MG . B MG 1383 1_555 G F1 ALF . B ALF 1384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.589 ? metalc ? metalc19 F MG MG . B MG 1383 1_555 G AL ALF . B ALF 1384 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.714 ? metalc ? metalc20 F MG MG . B MG 1383 1_555 J O HOH . B HOH 1386 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.183 ? metalc ? metalc21 F MG MG . B MG 1383 1_555 J O HOH . B HOH 1387 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc22 G AL ALF . B ALF 1384 1_555 J O HOH . B HOH 1385 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 1ZCA _atom_sites.fract_transf_matrix[1][1] 0.017391 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005015 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011733 _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] 0.012557 _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 C 2 MG A 1 383 383 MG MG . D 3 ALF A 1 384 384 ALF ALF . E 4 GDP A 1 382 382 GDP GDP . F 2 MG B 1 1383 383 MG MG . G 3 ALF B 1 1384 384 ALF ALF . H 4 GDP B 1 1382 382 GDP GDP . I 5 HOH A 1 385 385 HOH HOH . I 5 HOH A 2 386 386 HOH HOH . I 5 HOH A 3 387 387 HOH HOH . J 5 HOH B 1 1385 385 HOH HOH . J 5 HOH B 2 1386 386 HOH HOH . J 5 HOH B 3 1387 387 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 . . . E 4 -5.525 13.098 33.247 1 16.89 ? PB GDP 382 A 1 HETATM 2 O O1B GDP . . . E 4 -5.298 14.357 32.439 1 15.88 ? O1B GDP 382 A 1 HETATM 3 O O2B GDP . . . E 4 -4.221 12.539 33.755 1 19.06 ? O2B GDP 382 A 1 HETATM 4 O O3B GDP . . . E 4 -6.443 13.378 34.405 1 17.23 ? O3B GDP 382 A 1 HETATM 5 O O3A GDP . . . E 4 -6.213 12.03 32.285 1 19.63 ? O3A GDP 382 A 1 HETATM 6 P PA GDP . . . E 4 -5.593 10.568 32.119 1 20.67 ? PA GDP 382 A 1 HETATM 7 O O1A GDP . . . E 4 -4.189 10.614 31.565 1 19.3 ? O1A GDP 382 A 1 HETATM 8 O O2A GDP . . . E 4 -5.656 9.887 33.465 1 19.94 ? O2A GDP 382 A 1 HETATM 9 O O5' GDP . . . E 4 -6.586 9.915 31.03 1 20.59 ? O5' GDP 382 A 1 HETATM 10 C C5' GDP . . . E 4 -7.985 9.973 31.244 1 21.43 ? C5' GDP 382 A 1 HETATM 11 C C4' GDP . . . E 4 -8.687 8.951 30.362 1 23.77 ? C4' GDP 382 A 1 HETATM 12 O O4' GDP . . . E 4 -8.701 9.433 29.018 1 25.73 ? O4' GDP 382 A 1 HETATM 13 C C3' GDP . . . E 4 -8.04 7.573 30.336 1 23.62 ? C3' GDP 382 A 1 HETATM 14 O O3' GDP . . . E 4 -9.031 6.567 30.578 1 21.65 ? O3' GDP 382 A 1 HETATM 15 C C2' GDP . . . E 4 -7.483 7.425 28.942 1 24.43 ? C2' GDP 382 A 1 HETATM 16 O O2' GDP . . . E 4 -7.739 6.117 28.439 1 27 ? O2' GDP 382 A 1 HETATM 17 C C1' GDP . . . E 4 -8.258 8.425 28.119 1 25.69 ? C1' GDP 382 A 1 HETATM 18 N N9 GDP . . . E 4 -7.46 9.074 27.063 1 25.79 ? N9 GDP 382 A 1 HETATM 19 C C8 GDP . . . E 4 -6.387 9.862 27.242 1 26.01 ? C8 GDP 382 A 1 HETATM 20 N N7 GDP . . . E 4 -5.922 10.309 26.049 1 25.83 ? N7 GDP 382 A 1 HETATM 21 C C5 GDP . . . E 4 -6.717 9.812 25.085 1 26.06 ? C5 GDP 382 A 1 HETATM 22 C C6 GDP . . . E 4 -6.799 9.888 23.602 1 26.43 ? C6 GDP 382 A 1 HETATM 23 O O6 GDP . . . E 4 -5.971 10.556 22.952 1 25.95 ? O6 GDP 382 A 1 HETATM 24 N N1 GDP . . . E 4 -7.789 9.225 22.98 1 26.19 ? N1 GDP 382 A 1 HETATM 25 C C2 GDP . . . E 4 -8.69 8.5 23.672 1 25.95 ? C2 GDP 382 A 1 HETATM 26 N N2 GDP . . . E 4 -9.654 7.846 23 1 26.2 ? N2 GDP 382 A 1 HETATM 27 N N3 GDP . . . E 4 -8.687 8.386 25.027 1 25.61 ? N3 GDP 382 A 1 HETATM 28 C C4 GDP . . . E 4 -7.738 9.006 25.767 1 25.94 ? C4 GDP 382 A 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 24 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 337 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #