data_4M21 # _model_server_result.job_id lOT2oDGmO0n5aJmc_INswQ _model_server_result.datetime_utc '2024-10-15 16:25:25' _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 4m21 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 4M21 # _exptl.entry_id 4M21 _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 111.24 _cell.angle_gamma 90 _cell.entry_id 4M21 _cell.length_a 68.561 _cell.length_b 83.931 _cell.length_c 87.056 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4M21 _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 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 PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_defined_assembly 2 PISA monomeric 1 author_and_software_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,H 1 1 B,E,F,I 2 1 C,G,J 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 G N N # _struct_conn.conn_type_id covale _struct_conn.details ? _struct_conn.id covale1 _struct_conn.ptnr1_label_asym_id B _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 13 _struct_conn.ptnr1_auth_asym_id B _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 12 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id E _struct_conn.ptnr2_label_atom_id C21 _struct_conn.ptnr2_label_comp_id 21Y _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id B _struct_conn.ptnr2_auth_comp_id 21Y _struct_conn.ptnr2_auth_seq_id 201 _struct_conn.ptnr2_symmetry 1_555 _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 1.829 _struct_conn.pdbx_value_order ? # _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 129 n n PB O2B GDP sing 130 n n PB O3B GDP sing 131 n n PB O3A GDP sing 132 n n O2B HOB2 GDP sing 133 n n O3B HOB3 GDP sing 134 n n O3A PA GDP sing 135 n n PA O1A GDP doub 136 n n PA O2A GDP sing 137 n n PA O5' GDP sing 138 n n O2A HOA2 GDP sing 139 n n O5' C5' GDP sing 140 n n C5' C4' GDP sing 141 n n C5' H5' GDP sing 142 n n C5' "H5''" GDP sing 143 n n C4' O4' GDP sing 144 n n C4' C3' GDP sing 145 n n C4' H4' GDP sing 146 n n O4' C1' GDP sing 147 n n C3' O3' GDP sing 148 n n C3' C2' GDP sing 149 n n C3' H3' GDP sing 150 n n O3' HO3' GDP sing 151 n n C2' O2' GDP sing 152 n n C2' C1' GDP sing 153 n n C2' H2' GDP sing 154 n n O2' HO2' GDP sing 155 n n C1' N9 GDP sing 156 n n C1' H1' GDP sing 157 n n N9 C8 GDP sing 158 n y N9 C4 GDP sing 159 n y C8 N7 GDP doub 160 n y C8 H8 GDP sing 161 n n N7 C5 GDP sing 162 n y C5 C6 GDP sing 163 n n C5 C4 GDP doub 164 n y C6 O6 GDP doub 165 n n C6 N1 GDP sing 166 n n N1 C2 GDP sing 167 n n N1 HN1 GDP sing 168 n n C2 N2 GDP sing 169 n n C2 N3 GDP doub 170 n n N2 HN21 GDP sing 171 n n N2 HN22 GDP sing 172 n n N3 C4 GDP sing 173 n n # _atom_sites.entry_id 4M21 _atom_sites.fract_transf_matrix[1][1] 0.014586 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005668 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011915 _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] 0.012324 _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 1 201 220 GDP GDP . E 3 21Y B 1 201 210 21Y LIG . F 2 GDP B 1 202 220 GDP GDP . G 2 GDP C 1 201 220 GDP GDP . H 4 HOH A 1 301 2 HOH HOH . H 4 HOH A 2 302 4 HOH HOH . H 4 HOH A 3 303 5 HOH HOH . H 4 HOH A 4 304 9 HOH HOH . H 4 HOH A 5 305 10 HOH HOH . H 4 HOH A 6 306 11 HOH HOH . H 4 HOH A 7 307 12 HOH HOH . H 4 HOH A 8 308 13 HOH HOH . H 4 HOH A 9 309 14 HOH HOH . H 4 HOH A 10 310 17 HOH HOH . H 4 HOH A 11 311 18 HOH HOH . H 4 HOH A 12 312 19 HOH HOH . H 4 HOH A 13 313 24 HOH HOH . H 4 HOH A 14 314 25 HOH HOH . H 4 HOH A 15 315 27 HOH HOH . H 4 HOH A 16 316 29 HOH HOH . H 4 HOH A 17 317 31 HOH HOH . H 4 HOH A 18 318 32 HOH HOH . H 4 HOH A 19 319 36 HOH HOH . H 4 HOH A 20 320 37 HOH HOH . H 4 HOH A 21 321 38 HOH HOH . H 4 HOH A 22 322 39 HOH HOH . H 4 HOH A 23 323 40 HOH HOH . H 4 HOH A 24 324 42 HOH HOH . H 4 HOH A 25 325 43 HOH HOH . H 4 HOH A 26 326 47 HOH HOH . H 4 HOH A 27 327 49 HOH HOH . H 4 HOH A 28 328 51 HOH HOH . H 4 HOH A 29 329 57 HOH HOH . H 4 HOH A 30 330 58 HOH HOH . H 4 HOH A 31 331 59 HOH HOH . H 4 HOH A 32 332 61 HOH HOH . H 4 HOH A 33 333 63 HOH HOH . H 4 HOH A 34 334 65 HOH HOH . H 4 HOH A 35 335 67 HOH HOH . H 4 HOH A 36 336 68 HOH HOH . H 4 HOH A 37 337 72 HOH HOH . H 4 HOH A 38 338 73 HOH HOH . H 4 HOH A 39 339 74 HOH HOH . H 4 HOH A 40 340 76 HOH HOH . H 4 HOH A 41 341 81 HOH HOH . H 4 HOH A 42 342 82 HOH HOH . H 4 HOH A 43 343 85 HOH HOH . H 4 HOH A 44 344 86 HOH HOH . H 4 HOH A 45 345 87 HOH HOH . I 4 HOH B 1 301 1 HOH HOH . I 4 HOH B 2 302 8 HOH HOH . I 4 HOH B 3 303 15 HOH HOH . I 4 HOH B 4 304 16 HOH HOH . I 4 HOH B 5 305 20 HOH HOH . I 4 HOH B 6 306 21 HOH HOH . I 4 HOH B 7 307 23 HOH HOH . I 4 HOH B 8 308 26 HOH HOH . I 4 HOH B 9 309 28 HOH HOH . I 4 HOH B 10 310 34 HOH HOH . I 4 HOH B 11 311 35 HOH HOH . I 4 HOH B 12 312 41 HOH HOH . I 4 HOH B 13 313 45 HOH HOH . I 4 HOH B 14 314 46 HOH HOH . I 4 HOH B 15 315 50 HOH HOH . I 4 HOH B 16 316 52 HOH HOH . I 4 HOH B 17 317 53 HOH HOH . I 4 HOH B 18 318 56 HOH HOH . I 4 HOH B 19 319 62 HOH HOH . I 4 HOH B 20 320 66 HOH HOH . I 4 HOH B 21 321 71 HOH HOH . I 4 HOH B 22 322 75 HOH HOH . I 4 HOH B 23 323 79 HOH HOH . I 4 HOH B 24 324 80 HOH HOH . I 4 HOH B 25 325 83 HOH HOH . I 4 HOH B 26 326 84 HOH HOH . J 4 HOH C 1 301 3 HOH HOH . J 4 HOH C 2 302 6 HOH HOH . J 4 HOH C 3 303 7 HOH HOH . J 4 HOH C 4 304 22 HOH HOH . J 4 HOH C 5 305 30 HOH HOH . J 4 HOH C 6 306 33 HOH HOH . J 4 HOH C 7 307 44 HOH HOH . J 4 HOH C 8 308 48 HOH HOH . J 4 HOH C 9 309 54 HOH HOH . J 4 HOH C 10 310 55 HOH HOH . J 4 HOH C 11 311 60 HOH HOH . J 4 HOH C 12 312 64 HOH HOH . J 4 HOH C 13 313 69 HOH HOH . J 4 HOH C 14 314 70 HOH HOH . J 4 HOH C 15 315 77 HOH HOH . J 4 HOH C 16 316 78 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 65.707 26.543 63.707 1 30.71 ? PB GDP 201 A 1 HETATM 2 O O1B GDP . . . D 2 65.925 27.09 62.325 1 34.47 ? O1B GDP 201 A 1 HETATM 3 O O2B GDP . . . D 2 66.752 25.514 64.055 1 33.56 ? O2B GDP 201 A 1 HETATM 4 O O3B GDP . . . D 2 64.31 25.932 63.754 1 32.86 ? O3B GDP 201 A 1 HETATM 5 O O3A GDP . . . D 2 65.704 27.744 64.763 1 32.85 ? O3A GDP 201 A 1 HETATM 6 P PA GDP . . . D 2 66.95 28.17 65.688 1 34.27 ? PA GDP 201 A 1 HETATM 7 O O1A GDP . . . D 2 68.112 28.51 64.799 1 37.15 ? O1A GDP 201 A 1 HETATM 8 O O2A GDP . . . D 2 67.311 27.128 66.707 1 33.48 ? O2A GDP 201 A 1 HETATM 9 O O5' GDP . . . D 2 66.321 29.467 66.393 1 29.31 ? O5' GDP 201 A 1 HETATM 10 C C5' GDP . . . D 2 66.15 30.674 65.654 1 30.16 ? C5' GDP 201 A 1 HETATM 11 C C4' GDP . . . D 2 66.247 31.851 66.609 1 32.64 ? C4' GDP 201 A 1 HETATM 12 O O4' GDP . . . D 2 65.261 31.75 67.634 1 31.99 ? O4' GDP 201 A 1 HETATM 13 C C3' GDP . . . D 2 67.579 31.917 67.338 1 36.12 ? C3' GDP 201 A 1 HETATM 14 O O3' GDP . . . D 2 67.889 33.298 67.506 1 39.28 ? O3' GDP 201 A 1 HETATM 15 C C2' GDP . . . D 2 67.315 31.292 68.684 1 35.78 ? C2' GDP 201 A 1 HETATM 16 O O2' GDP . . . D 2 68.147 31.779 69.74 1 38.36 ? O2' GDP 201 A 1 HETATM 17 C C1' GDP . . . D 2 65.88 31.712 68.92 1 32.29 ? C1' GDP 201 A 1 HETATM 18 N N9 GDP . . . D 2 65.155 30.755 69.773 1 28.94 ? N9 GDP 201 A 1 HETATM 19 C C8 GDP . . . D 2 65.028 29.419 69.614 1 27.67 ? C8 GDP 201 A 1 HETATM 20 N N7 GDP . . . D 2 64.268 28.903 70.611 1 26.09 ? N7 GDP 201 A 1 HETATM 21 C C5 GDP . . . D 2 63.889 29.93 71.401 1 26.16 ? C5 GDP 201 A 1 HETATM 22 C C6 GDP . . . D 2 63.081 30.111 72.612 1 27.12 ? C6 GDP 201 A 1 HETATM 23 O O6 GDP . . . D 2 62.52 29.138 73.164 1 26.66 ? O6 GDP 201 A 1 HETATM 24 N N1 GDP . . . D 2 62.966 31.36 73.084 1 29.16 ? N1 GDP 201 A 1 HETATM 25 C C2 GDP . . . D 2 63.55 32.428 72.515 1 30.53 ? C2 GDP 201 A 1 HETATM 26 N N2 GDP . . . D 2 63.384 33.651 73.059 1 32.94 ? N2 GDP 201 A 1 HETATM 27 N N3 GDP . . . D 2 64.302 32.338 71.413 1 28.67 ? N3 GDP 201 A 1 HETATM 28 C C4 GDP . . . D 2 64.488 31.14 70.836 1 27.52 ? C4 GDP 201 A 1 HETATM 29 H H4' GDP . . . D 2 66.105 32.781 66.043 1 39.17 ? H4' GDP 201 A 1 HETATM 30 H H3' GDP . . . D 2 68.361 31.373 66.789 1 43.35 ? H3' GDP 201 A 1 HETATM 31 H HO3' GDP . . . D 2 68.721 33.385 67.99 1 47.14 ? HO3' GDP 201 A 1 HETATM 32 H H2' GDP . . . D 2 67.373 30.198 68.606 1 42.94 ? H2' GDP 201 A 1 HETATM 33 H HO2' GDP . . . D 2 69.069 31.559 69.551 1 46.03 ? HO2' GDP 201 A 1 HETATM 34 H H1' GDP . . . D 2 65.869 32.712 69.376 1 38.75 ? H1' GDP 201 A 1 HETATM 35 H H8 GDP . . . D 2 65.48 28.843 68.816 1 33.2 ? H8 GDP 201 A 1 HETATM 36 H HN1 GDP . . . D 2 62.403 31.509 73.946 1 34.99 ? HN1 GDP 201 A 1 HETATM 37 H HN21 GDP . . . D 2 63.816 34.458 72.631 1 39.53 ? HN21 GDP 201 A 1 HETATM 38 H HN22 GDP . . . D 2 62.826 33.761 73.894 1 39.53 ? HN22 GDP 201 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 38 #