data_6USX # _model_server_result.job_id ffjgC16MpitirtMLFN520g _model_server_result.datetime_utc '2024-11-17 22:37:47' _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 6usx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 6USX # _exptl.entry_id 6USX _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 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 6USX _cell.length_a 88.57 _cell.length_b 156.49 _cell.length_c 62.98 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6USX _symmetry.cell_setting ? _symmetry.Int_Tables_number 21 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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 ? 2 C N N ? 2 F 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 covale ? covale1 A SG CYS 13 A CYS 12 1_555 E C32 M1R . A M1R 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.651 ? covale ? covale2 B SG CYS 13 B CYS 12 1_555 H C32 M1R . B M1R 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.662 ? metalc ? metalc1 A OG SER 18 A SER 17 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc2 C O2B GDP . A GDP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.133 ? metalc ? metalc3 D MG MG . A MG 202 1_555 I O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.207 ? metalc ? metalc4 D MG MG . A MG 202 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc5 D MG MG . A MG 202 1_555 I O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.883 ? metalc ? metalc6 D MG MG . A MG 202 1_555 I O HOH . A HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? metalc ? metalc7 B OG SER 18 B SER 17 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc8 F O2B GDP . B GDP 201 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc9 G MG MG . B MG 202 1_555 J O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc10 G MG MG . B MG 202 1_555 J O HOH . B HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.971 ? # _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 6USX _atom_sites.fract_transf_matrix[1][1] 0.011291 _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] 0.00639 _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] 0.015878 _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 GDP A 1 201 201 GDP GDP . D 3 MG A 1 202 202 MG MG . E 4 M1R A 1 203 1 M1R SM1 . F 2 GDP B 1 201 201 GDP GDP . G 3 MG B 1 202 202 MG MG . H 4 M1R B 1 203 1 M1R SM1 . I 5 HOH A 1 301 51 HOH HOH . I 5 HOH A 2 302 61 HOH HOH . I 5 HOH A 3 303 70 HOH HOH . I 5 HOH A 4 304 32 HOH HOH . I 5 HOH A 5 305 63 HOH HOH . I 5 HOH A 6 306 60 HOH HOH . I 5 HOH A 7 307 13 HOH HOH . I 5 HOH A 8 308 41 HOH HOH . I 5 HOH A 9 309 7 HOH HOH . I 5 HOH A 10 310 30 HOH HOH . I 5 HOH A 11 311 39 HOH HOH . I 5 HOH A 12 312 6 HOH HOH . I 5 HOH A 13 313 69 HOH HOH . I 5 HOH A 14 314 26 HOH HOH . I 5 HOH A 15 315 71 HOH HOH . I 5 HOH A 16 316 2 HOH HOH . I 5 HOH A 17 317 53 HOH HOH . I 5 HOH A 18 318 9 HOH HOH . I 5 HOH A 19 319 18 HOH HOH . I 5 HOH A 20 320 21 HOH HOH . I 5 HOH A 21 321 20 HOH HOH . I 5 HOH A 22 322 15 HOH HOH . I 5 HOH A 23 323 28 HOH HOH . I 5 HOH A 24 324 52 HOH HOH . I 5 HOH A 25 325 5 HOH HOH . I 5 HOH A 26 326 45 HOH HOH . I 5 HOH A 27 327 50 HOH HOH . I 5 HOH A 28 328 3 HOH HOH . I 5 HOH A 29 329 14 HOH HOH . I 5 HOH A 30 330 19 HOH HOH . I 5 HOH A 31 331 25 HOH HOH . I 5 HOH A 32 332 47 HOH HOH . I 5 HOH A 33 333 68 HOH HOH . I 5 HOH A 34 334 10 HOH HOH . I 5 HOH A 35 335 54 HOH HOH . I 5 HOH A 36 336 74 HOH HOH . I 5 HOH A 37 337 22 HOH HOH . I 5 HOH A 38 338 24 HOH HOH . I 5 HOH A 39 339 29 HOH HOH . I 5 HOH A 40 340 38 HOH HOH . I 5 HOH A 41 341 66 HOH HOH . I 5 HOH A 42 342 48 HOH HOH . J 5 HOH B 1 301 35 HOH HOH . J 5 HOH B 2 302 62 HOH HOH . J 5 HOH B 3 303 23 HOH HOH . J 5 HOH B 4 304 8 HOH HOH . J 5 HOH B 5 305 46 HOH HOH . J 5 HOH B 6 306 43 HOH HOH . J 5 HOH B 7 307 36 HOH HOH . J 5 HOH B 8 308 56 HOH HOH . J 5 HOH B 9 309 11 HOH HOH . J 5 HOH B 10 310 49 HOH HOH . J 5 HOH B 11 311 37 HOH HOH . J 5 HOH B 12 312 31 HOH HOH . J 5 HOH B 13 313 12 HOH HOH . J 5 HOH B 14 314 27 HOH HOH . J 5 HOH B 15 315 17 HOH HOH . J 5 HOH B 16 316 67 HOH HOH . J 5 HOH B 17 317 44 HOH HOH . J 5 HOH B 18 318 40 HOH HOH . J 5 HOH B 19 319 75 HOH HOH . J 5 HOH B 20 320 42 HOH HOH . J 5 HOH B 21 321 72 HOH HOH . J 5 HOH B 22 322 65 HOH HOH . J 5 HOH B 23 323 34 HOH HOH . J 5 HOH B 24 324 33 HOH HOH . J 5 HOH B 25 325 64 HOH HOH . J 5 HOH B 26 326 57 HOH HOH . J 5 HOH B 27 327 55 HOH HOH . J 5 HOH B 28 328 16 HOH HOH . J 5 HOH B 29 329 59 HOH HOH . J 5 HOH B 30 330 73 HOH HOH . J 5 HOH B 31 331 4 HOH HOH . J 5 HOH B 32 332 1 HOH HOH . J 5 HOH B 33 333 58 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 . . . C 2 -23.66 -18.573 33.884 1 36.35 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . C 2 -23.225 -18.428 32.433 1 33.24 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . C 2 -25.129 -18.423 34.021 1 39.15 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . C 2 -23.091 -19.864 34.469 1 34.07 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . C 2 -23.014 -17.331 34.657 1 37.32 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . C 2 -23.38 -16.625 36.046 1 39.08 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . C 2 -24.366 -15.55 35.791 1 38.46 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . C 2 -23.631 -17.719 37.084 1 43.34 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . C 2 -22.021 -15.841 36.325 1 37.38 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . C 2 -20.955 -16.507 36.988 1 37.11 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . C 2 -20.361 -15.665 38.101 1 35.94 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . C 2 -19.832 -14.484 37.483 1 30.84 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . C 2 -21.37 -15.244 39.168 1 33.01 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . C 2 -20.654 -15.151 40.388 1 32.56 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . C 2 -21.75 -13.888 38.682 1 35.97 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . C 2 -22.101 -12.972 39.651 1 41.14 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . C 2 -20.453 -13.374 38.06 1 36.21 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . C 2 -20.662 -12.459 36.931 1 38.13 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . C 2 -21.44 -12.652 35.865 1 40.4 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . C 2 -21.42 -11.594 35.055 1 35.81 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . C 2 -20.576 -10.743 35.591 1 34.31 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . C 2 -20.025 -9.439 35.181 1 37.4 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . C 2 -20.382 -8.904 34.118 1 35.11 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . C 2 -19.127 -8.876 35.996 1 39.82 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . C 2 -18.719 -9.447 37.15 1 37.33 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . C 2 -17.83 -8.791 37.927 1 37.71 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . C 2 -19.146 -10.682 37.548 1 40.93 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . C 2 -20.07 -11.323 36.811 1 35.03 ? C4 GDP 201 A 1 HETATM 29 H H5' GDP . . . C 2 -21.281 -17.466 37.395 1 36.9 ? H5' GDP 201 A 1 HETATM 30 H "H5''" GDP . . . C 2 -20.168 -16.707 36.263 1 36.85 ? "H5''" GDP 201 A 1 HETATM 31 H H4' GDP . . . C 2 -19.549 -16.231 38.577 1 34.56 ? H4' GDP 201 A 1 HETATM 32 H H3' GDP . . . C 2 -22.228 -15.93 39.197 1 34.04 ? H3' GDP 201 A 1 HETATM 33 H HO3' GDP . . . C 2 -21.381 -14.756 41.091 0 34.74 ? HO3' GDP 201 A 1 HETATM 34 H H2' GDP . . . C 2 -22.541 -13.969 37.926 1 36.37 ? H2' GDP 201 A 1 HETATM 35 H HO2' GDP . . . C 2 -22.948 -13.299 40.116 0 42.18 ? HO2' GDP 201 A 1 HETATM 36 H H1' GDP . . . C 2 -19.814 -12.927 38.835 1 35.44 ? H1' GDP 201 A 1 HETATM 37 H H8 GDP . . . C 2 -22.084 -13.506 35.721 1 38.55 ? H8 GDP 201 A 1 HETATM 38 H HN1 GDP . . . C 2 -18.757 -7.941 35.742 1 38.48 ? HN1 GDP 201 A 1 HETATM 39 H HN21 GDP . . . C 2 -17.502 -9.217 38.782 1 37.57 ? HN21 GDP 201 A 1 HETATM 40 H HN22 GDP . . . C 2 -17.469 -7.893 37.645 1 37.57 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 333 _model_server_stats.encode_time_ms 35 _model_server_stats.element_count 40 #