data_1AGR # _model_server_result.job_id UmVPfYfH5kvhg9F1BYIKng _model_server_result.datetime_utc '2024-11-08 12:52:34' _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 1agr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"K","auth_seq_id":355}' # _entry.id 1AGR # _exptl.entry_id 1AGR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 1AGR _cell.length_a 164 _cell.length_b 97.2 _cell.length_c 110 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1AGR _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 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 ? dimeric 2 author_defined_assembly 1 ? dimeric 2 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,E,F,G,H,M,O 1 1 B,D,I,J,K,L,N,P 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 ? 5 G N N ? 5 K 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 G O3B GDP . A GDP 355 1_555 F F1 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? covale ? covale2 K O3B GDP . D GDP 355 1_555 J F1 ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.346 ? metalc ? metalc1 A OG SER 46 A SER 47 1_555 E MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? metalc ? metalc2 A NH2 ARG 177 A ARG 178 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.689 ? metalc ? metalc3 A OG1 THR 180 A THR 181 1_555 E MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.878 ? metalc ? metalc4 G O2B GDP . A GDP 355 1_555 E MG MG . A MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.101 ? metalc ? metalc5 G O3B GDP . A GDP 355 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc6 G O2B GDP . A GDP 355 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.581 ? metalc ? metalc7 E MG MG . A MG 356 1_555 F F2 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.967 ? metalc ? metalc8 E MG MG . A MG 356 1_555 F F3 ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.972 ? metalc ? metalc9 E MG MG . A MG 356 1_555 F AL ALF . A ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.297 ? metalc ? metalc10 E MG MG . A MG 356 1_555 M O HOH . A HOH 364 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? metalc ? metalc11 E MG MG . A MG 356 1_555 M O HOH . A HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc12 F AL ALF . A ALF 357 1_555 M O HOH . A HOH 359 1_555 ? ? ? A ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc13 B OG SER 46 D SER 47 1_555 I MG MG . D MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? metalc ? metalc14 B NH2 ARG 177 D ARG 178 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.668 ? metalc ? metalc15 B OG1 THR 180 D THR 181 1_555 I MG MG . D MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc16 K O2B GDP . D GDP 355 1_555 I MG MG . D MG 356 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc17 K O3B GDP . D GDP 355 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc18 K O2B GDP . D GDP 355 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.613 ? metalc ? metalc19 I MG MG . D MG 356 1_555 J F3 ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.951 ? metalc ? metalc20 I MG MG . D MG 356 1_555 J F2 ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.956 ? metalc ? metalc21 I MG MG . D MG 356 1_555 J AL ALF . D ALF 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.326 ? metalc ? metalc22 I MG MG . D MG 356 1_555 N O HOH . D HOH 365 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc23 I MG MG . D MG 356 1_555 N O HOH . D HOH 366 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? metalc ? metalc24 J AL ALF . D ALF 357 1_555 N O HOH . D HOH 360 1_555 ? ? ? D ? ? ? ? ? ? ? ? 2.005 ? # _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 107 n n PB O2B GDP sing 108 n n PB O3B GDP sing 109 n n PB O3A GDP sing 110 n n O2B HOB2 GDP sing 111 n n O3B HOB3 GDP sing 112 n n O3A PA GDP sing 113 n n PA O1A GDP doub 114 n n PA O2A GDP sing 115 n n PA O5' GDP sing 116 n n O2A HOA2 GDP sing 117 n n O5' C5' GDP sing 118 n n C5' C4' GDP sing 119 n n C5' H5' GDP sing 120 n n C5' "H5''" GDP sing 121 n n C4' O4' GDP sing 122 n n C4' C3' GDP sing 123 n n C4' H4' GDP sing 124 n n O4' C1' GDP sing 125 n n C3' O3' GDP sing 126 n n C3' C2' GDP sing 127 n n C3' H3' GDP sing 128 n n O3' HO3' GDP sing 129 n n C2' O2' GDP sing 130 n n C2' C1' GDP sing 131 n n C2' H2' GDP sing 132 n n O2' HO2' GDP sing 133 n n C1' N9 GDP sing 134 n n C1' H1' GDP sing 135 n n N9 C8 GDP sing 136 n y N9 C4 GDP sing 137 n y C8 N7 GDP doub 138 n y C8 H8 GDP sing 139 n n N7 C5 GDP sing 140 n y C5 C6 GDP sing 141 n n C5 C4 GDP doub 142 n y C6 O6 GDP doub 143 n n C6 N1 GDP sing 144 n n N1 C2 GDP sing 145 n n N1 HN1 GDP sing 146 n n C2 N2 GDP sing 147 n n C2 N3 GDP doub 148 n n N2 HN21 GDP sing 149 n n N2 HN22 GDP sing 150 n n N3 C4 GDP sing 151 n n # _atom_sites.entry_id 1AGR _atom_sites.fract_transf_matrix[1][1] 0.006098 _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] 0.010288 _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] 0.009091 _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 E 3 MG A 1 356 356 MG MG . F 4 ALF A 1 357 357 ALF ALF . G 5 GDP A 1 355 355 GDP GDP . H 6 CIT A 1 358 358 CIT CIT . I 3 MG D 1 356 356 MG MG . J 4 ALF D 1 357 357 ALF ALF . K 5 GDP D 1 355 355 GDP GDP . L 6 CIT D 1 358 358 CIT CIT . M 7 HOH A 1 359 357 HOH HOH A M 7 HOH A 2 360 402 HOH HOH . M 7 HOH A 3 361 403 HOH HOH . M 7 HOH A 4 362 406 HOH HOH . M 7 HOH A 5 363 409 HOH HOH . M 7 HOH A 6 364 410 HOH HOH . M 7 HOH A 7 365 412 HOH HOH . M 7 HOH A 8 366 414 HOH HOH . M 7 HOH A 9 367 415 HOH HOH . M 7 HOH A 10 368 421 HOH HOH . M 7 HOH A 11 369 424 HOH HOH . M 7 HOH A 12 370 436 HOH HOH . M 7 HOH A 13 371 438 HOH HOH . M 7 HOH A 14 372 442 HOH HOH . M 7 HOH A 15 373 454 HOH HOH . M 7 HOH A 16 374 455 HOH HOH . M 7 HOH A 17 375 457 HOH HOH . M 7 HOH A 18 376 460 HOH HOH . M 7 HOH A 19 377 461 HOH HOH . M 7 HOH A 20 378 470 HOH HOH . M 7 HOH A 21 379 471 HOH HOH . M 7 HOH A 22 380 474 HOH HOH . M 7 HOH A 23 381 476 HOH HOH . M 7 HOH A 24 382 480 HOH HOH . M 7 HOH A 25 383 485 HOH HOH . M 7 HOH A 26 384 434 HOH HOH . N 7 HOH D 1 359 434 HOH HOH . N 7 HOH D 2 360 357 HOH HOH D N 7 HOH D 3 361 402 HOH HOH . N 7 HOH D 4 362 403 HOH HOH . N 7 HOH D 5 363 406 HOH HOH . N 7 HOH D 6 364 409 HOH HOH . N 7 HOH D 7 365 410 HOH HOH . N 7 HOH D 8 366 412 HOH HOH . N 7 HOH D 9 367 414 HOH HOH . N 7 HOH D 10 368 415 HOH HOH . N 7 HOH D 11 369 421 HOH HOH . N 7 HOH D 12 370 424 HOH HOH . N 7 HOH D 13 371 436 HOH HOH . N 7 HOH D 14 372 438 HOH HOH . N 7 HOH D 15 373 442 HOH HOH . N 7 HOH D 16 374 454 HOH HOH . N 7 HOH D 17 375 455 HOH HOH . N 7 HOH D 18 376 457 HOH HOH . N 7 HOH D 19 377 460 HOH HOH . N 7 HOH D 20 378 461 HOH HOH . N 7 HOH D 21 379 470 HOH HOH . N 7 HOH D 22 380 471 HOH HOH . N 7 HOH D 23 381 474 HOH HOH . N 7 HOH D 24 382 476 HOH HOH . N 7 HOH D 25 383 480 HOH HOH . N 7 HOH D 26 384 485 HOH HOH . O 7 HOH E 1 206 413 HOH HOH . O 7 HOH E 2 207 469 HOH HOH . O 7 HOH E 3 208 481 HOH HOH . P 7 HOH H 1 206 413 HOH HOH . P 7 HOH H 2 207 469 HOH HOH . P 7 HOH H 3 208 481 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 . . . K 5 28.294 -29.252 16.045 1 27.46 ? PB GDP 355 D 1 HETATM 2 O O1B GDP . . . K 5 29.567 -28.466 15.987 1 17.66 ? O1B GDP 355 D 1 HETATM 3 O O2B GDP . . . K 5 27.353 -29.112 14.891 1 17.69 ? O2B GDP 355 D 1 HETATM 4 O O3B GDP . . . K 5 28.495 -30.675 16.405 1 31.48 ? O3B GDP 355 D 1 HETATM 5 O O3A GDP . . . K 5 27.466 -28.693 17.367 1 19.42 ? O3A GDP 355 D 1 HETATM 6 P PA GDP . . . K 5 25.849 -28.586 17.312 1 21.39 ? PA GDP 355 D 1 HETATM 7 O O1A GDP . . . K 5 25.573 -27.603 16.282 1 27.2 ? O1A GDP 355 D 1 HETATM 8 O O2A GDP . . . K 5 25.129 -29.854 17.088 1 30.57 ? O2A GDP 355 D 1 HETATM 9 O O5' GDP . . . K 5 25.485 -28.025 18.755 1 25.34 ? O5' GDP 355 D 1 HETATM 10 C C5' GDP . . . K 5 25.766 -28.719 19.938 1 23.25 ? C5' GDP 355 D 1 HETATM 11 C C4' GDP . . . K 5 24.596 -28.536 20.925 1 23.44 ? C4' GDP 355 D 1 HETATM 12 O O4' GDP . . . K 5 24.665 -27.31 21.702 1 33.69 ? O4' GDP 355 D 1 HETATM 13 C C3' GDP . . . K 5 23.229 -28.561 20.349 1 17.37 ? C3' GDP 355 D 1 HETATM 14 O O3' GDP . . . K 5 22.373 -29.001 21.418 1 15.56 ? O3' GDP 355 D 1 HETATM 15 C C2' GDP . . . K 5 22.939 -27.03 20.195 1 28.13 ? C2' GDP 355 D 1 HETATM 16 O O2' GDP . . . K 5 21.584 -26.682 20.564 1 32.56 ? O2' GDP 355 D 1 HETATM 17 C C1' GDP . . . K 5 23.642 -26.376 21.339 1 30.01 ? C1' GDP 355 D 1 HETATM 18 N N9 GDP . . . K 5 24.342 -25.064 21.169 1 40.91 ? N9 GDP 355 D 1 HETATM 19 C C8 GDP . . . K 5 25.156 -24.579 20.193 1 39.58 ? C8 GDP 355 D 1 HETATM 20 N N7 GDP . . . K 5 25.678 -23.419 20.392 1 41.83 ? N7 GDP 355 D 1 HETATM 21 C C5 GDP . . . K 5 25.16 -23.071 21.623 1 43.51 ? C5 GDP 355 D 1 HETATM 22 C C6 GDP . . . K 5 25.354 -21.898 22.374 1 45.21 ? C6 GDP 355 D 1 HETATM 23 O O6 GDP . . . K 5 26.066 -20.945 22.056 1 38 ? O6 GDP 355 D 1 HETATM 24 N N1 GDP . . . K 5 24.612 -21.956 23.587 1 45.81 ? N1 GDP 355 D 1 HETATM 25 C C2 GDP . . . K 5 23.805 -23.007 24.005 1 33.3 ? C2 GDP 355 D 1 HETATM 26 N N2 GDP . . . K 5 23.228 -22.963 25.202 1 24.74 ? N2 GDP 355 D 1 HETATM 27 N N3 GDP . . . K 5 23.642 -24.082 23.28 1 38.03 ? N3 GDP 355 D 1 HETATM 28 C C4 GDP . . . K 5 24.341 -24.057 22.113 1 43.53 ? C4 GDP 355 D 1 # _model_server_stats.io_time_ms 10 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 22 _model_server_stats.query_time_ms 310 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #