data_7MDP # _model_server_result.job_id NjlBhHVdTTlCOm86JR5itQ _model_server_result.datetime_utc '2024-11-23 19:41:30' _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 7mdp # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":202}' # _entry.id 7MDP # _exptl.entry_id 7MDP _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 114.29 _cell.angle_gamma 90 _cell.entry_id 7MDP _cell.length_a 149.365 _cell.length_b 68.919 _cell.length_c 100.543 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7MDP _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 disulf ? disulf1 B SG CYS 22 H CYS 22 1_555 B SG CYS 96 H CYS 92 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? disulf ? disulf2 B SG CYS 149 H CYS 140 1_555 B SG CYS 205 H CYS 196 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 C SG CYS 21 I CYS 23 1_555 C SG CYS 88 I CYS 88 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 C SG CYS 137 I CYS 135 1_555 C SG CYS 196 I CYS 194 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc1 A OG SER 17 A SER 17 1_555 F MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? metalc ? metalc2 E O1B GDP . A GDP 202 1_555 F MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? metalc ? metalc3 F MG MG . A MG 203 1_555 V O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? metalc ? metalc4 F MG MG . A MG 203 1_555 V O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? metalc ? metalc5 F MG MG . A MG 203 1_555 V O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? metalc ? metalc6 F MG MG . A MG 203 1_555 V O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? # _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 118 n n PB O2B GDP sing 119 n n PB O3B GDP sing 120 n n PB O3A GDP sing 121 n n O2B HOB2 GDP sing 122 n n O3B HOB3 GDP sing 123 n n O3A PA GDP sing 124 n n PA O1A GDP doub 125 n n PA O2A GDP sing 126 n n PA O5' GDP sing 127 n n O2A HOA2 GDP sing 128 n n O5' C5' GDP sing 129 n n C5' C4' GDP sing 130 n n C5' H5' GDP sing 131 n n C5' "H5''" GDP sing 132 n n C4' O4' GDP sing 133 n n C4' C3' GDP sing 134 n n C4' H4' GDP sing 135 n n O4' C1' GDP sing 136 n n C3' O3' GDP sing 137 n n C3' C2' GDP sing 138 n n C3' H3' GDP sing 139 n n O3' HO3' GDP sing 140 n n C2' O2' GDP sing 141 n n C2' C1' GDP sing 142 n n C2' H2' GDP sing 143 n n O2' HO2' GDP sing 144 n n C1' N9 GDP sing 145 n n C1' H1' GDP sing 146 n n N9 C8 GDP sing 147 n y N9 C4 GDP sing 148 n y C8 N7 GDP doub 149 n y C8 H8 GDP sing 150 n n N7 C5 GDP sing 151 n y C5 C6 GDP sing 152 n n C5 C4 GDP doub 153 n y C6 O6 GDP doub 154 n n C6 N1 GDP sing 155 n n N1 C2 GDP sing 156 n n N1 HN1 GDP sing 157 n n C2 N2 GDP sing 158 n n C2 N3 GDP doub 159 n n N2 HN21 GDP sing 160 n n N2 HN22 GDP sing 161 n n N3 C4 GDP sing 162 n n # _atom_sites.entry_id 7MDP _atom_sites.fract_transf_matrix[1][1] 0.006695 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003022 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01451 _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] 0.010912 _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 4 Z07 A 1 201 1 Z07 LIG . E 5 GDP A 1 202 1 GDP GDP . F 6 MG A 1 203 1 MG MG . G 7 ACT A 1 204 102 ACT ACT . H 8 CAD H 1 301 201 CAD CAD . I 8 CAD H 1 302 202 CAD CAD . J 8 CAD H 1 303 203 CAD CAD . K 9 P15 H 1 304 204 P15 P15 . L 10 EDO H 1 305 206 EDO EDO . M 9 P15 H 1 306 209 P15 P15 . N 7 ACT H 1 307 307 ACT ACT . O 9 P15 H 1 308 311 P15 P15 . P 10 EDO H 1 309 312 EDO EDO . Q 10 EDO I 1 301 301 EDO EDO . R 10 EDO I 1 302 205 EDO EDO . S 8 CAD I 1 303 301 CAD CAD . T 11 DMS I 1 304 304 DMS DMS . U 9 P15 I 1 305 310 P15 P15 . V 12 HOH A 1 301 27 HOH HOH . V 12 HOH A 2 302 133 HOH HOH . V 12 HOH A 3 303 43 HOH HOH . V 12 HOH A 4 304 31 HOH HOH . V 12 HOH A 5 305 34 HOH HOH . V 12 HOH A 6 306 33 HOH HOH . V 12 HOH A 7 307 32 HOH HOH . W 12 HOH H 1 401 115 HOH HOH . W 12 HOH H 2 402 40 HOH HOH . W 12 HOH H 3 403 117 HOH HOH . W 12 HOH H 4 404 131 HOH HOH . W 12 HOH H 5 405 30 HOH HOH . W 12 HOH H 6 406 41 HOH HOH . W 12 HOH H 7 407 39 HOH HOH . W 12 HOH H 8 408 35 HOH HOH . W 12 HOH H 9 409 161 HOH HOH . W 12 HOH H 10 410 126 HOH HOH . W 12 HOH H 11 411 10 HOH HOH . W 12 HOH H 12 412 116 HOH HOH . W 12 HOH H 13 413 168 HOH HOH . W 12 HOH H 14 414 3 HOH HOH . W 12 HOH H 15 415 9 HOH HOH . W 12 HOH H 16 416 114 HOH HOH . W 12 HOH H 17 417 60 HOH HOH . W 12 HOH H 18 418 176 HOH HOH . W 12 HOH H 19 419 13 HOH HOH . W 12 HOH H 20 420 46 HOH HOH . W 12 HOH H 21 421 47 HOH HOH . W 12 HOH H 22 422 110 HOH HOH . W 12 HOH H 23 423 56 HOH HOH . W 12 HOH H 24 424 12 HOH HOH . W 12 HOH H 25 425 18 HOH HOH . W 12 HOH H 26 426 25 HOH HOH . W 12 HOH H 27 427 107 HOH HOH . W 12 HOH H 28 428 64 HOH HOH . W 12 HOH H 29 429 19 HOH HOH . W 12 HOH H 30 430 170 HOH HOH . W 12 HOH H 31 431 77 HOH HOH . W 12 HOH H 32 432 53 HOH HOH . W 12 HOH H 33 433 67 HOH HOH . W 12 HOH H 34 434 173 HOH HOH . W 12 HOH H 35 435 103 HOH HOH . W 12 HOH H 36 436 145 HOH HOH . W 12 HOH H 37 437 38 HOH HOH . W 12 HOH H 38 438 28 HOH HOH . W 12 HOH H 39 439 79 HOH HOH . W 12 HOH H 40 440 70 HOH HOH . W 12 HOH H 41 441 95 HOH HOH . W 12 HOH H 42 442 154 HOH HOH . W 12 HOH H 43 443 44 HOH HOH . W 12 HOH H 44 444 163 HOH HOH . W 12 HOH H 45 445 16 HOH HOH . W 12 HOH H 46 446 80 HOH HOH . W 12 HOH H 47 447 140 HOH HOH . W 12 HOH H 48 448 55 HOH HOH . W 12 HOH H 49 449 92 HOH HOH . W 12 HOH H 50 450 81 HOH HOH . W 12 HOH H 51 451 26 HOH HOH . W 12 HOH H 52 452 7 HOH HOH . W 12 HOH H 53 453 63 HOH HOH . W 12 HOH H 54 454 142 HOH HOH . W 12 HOH H 55 455 65 HOH HOH . W 12 HOH H 56 456 75 HOH HOH . W 12 HOH H 57 457 144 HOH HOH . W 12 HOH H 58 458 85 HOH HOH . W 12 HOH H 59 459 71 HOH HOH . W 12 HOH H 60 460 125 HOH HOH . W 12 HOH H 61 461 50 HOH HOH . W 12 HOH H 62 462 137 HOH HOH . W 12 HOH H 63 463 147 HOH HOH . W 12 HOH H 64 464 127 HOH HOH . W 12 HOH H 65 465 83 HOH HOH . W 12 HOH H 66 466 57 HOH HOH . W 12 HOH H 67 467 138 HOH HOH . W 12 HOH H 68 468 134 HOH HOH . X 12 HOH I 1 401 135 HOH HOH . X 12 HOH I 2 402 172 HOH HOH . X 12 HOH I 3 403 100 HOH HOH . X 12 HOH I 4 404 59 HOH HOH . X 12 HOH I 5 405 167 HOH HOH . X 12 HOH I 6 406 6 HOH HOH . X 12 HOH I 7 407 166 HOH HOH . X 12 HOH I 8 408 74 HOH HOH . X 12 HOH I 9 409 69 HOH HOH . X 12 HOH I 10 410 174 HOH HOH . X 12 HOH I 11 411 108 HOH HOH . X 12 HOH I 12 412 24 HOH HOH . X 12 HOH I 13 413 17 HOH HOH . X 12 HOH I 14 414 146 HOH HOH . X 12 HOH I 15 415 129 HOH HOH . X 12 HOH I 16 416 29 HOH HOH . X 12 HOH I 17 417 49 HOH HOH . X 12 HOH I 18 418 21 HOH HOH . X 12 HOH I 19 419 68 HOH HOH . X 12 HOH I 20 420 22 HOH HOH . X 12 HOH I 21 421 11 HOH HOH . X 12 HOH I 22 422 162 HOH HOH . X 12 HOH I 23 423 52 HOH HOH . X 12 HOH I 24 424 20 HOH HOH . X 12 HOH I 25 425 102 HOH HOH . X 12 HOH I 26 426 37 HOH HOH . X 12 HOH I 27 427 111 HOH HOH . X 12 HOH I 28 428 14 HOH HOH . X 12 HOH I 29 429 15 HOH HOH . X 12 HOH I 30 430 122 HOH HOH . X 12 HOH I 31 431 141 HOH HOH . X 12 HOH I 32 432 32 HOH HOH . X 12 HOH I 33 433 45 HOH HOH . X 12 HOH I 34 434 152 HOH HOH . X 12 HOH I 35 435 62 HOH HOH . X 12 HOH I 36 436 171 HOH HOH . X 12 HOH I 37 437 169 HOH HOH . X 12 HOH I 38 438 82 HOH HOH . X 12 HOH I 39 439 23 HOH HOH . X 12 HOH I 40 440 34 HOH HOH . X 12 HOH I 41 441 5 HOH HOH . X 12 HOH I 42 442 165 HOH HOH . X 12 HOH I 43 443 113 HOH HOH . X 12 HOH I 44 444 8 HOH HOH . X 12 HOH I 45 445 150 HOH HOH . X 12 HOH I 46 446 130 HOH HOH . X 12 HOH I 47 447 132 HOH HOH . X 12 HOH I 48 448 105 HOH HOH . X 12 HOH I 49 449 99 HOH HOH . X 12 HOH I 50 450 148 HOH HOH . X 12 HOH I 51 451 175 HOH HOH . X 12 HOH I 52 452 155 HOH HOH . X 12 HOH I 53 453 157 HOH HOH . X 12 HOH I 54 454 139 HOH HOH . X 12 HOH I 55 455 156 HOH HOH . X 12 HOH I 56 456 104 HOH HOH . X 12 HOH I 57 457 124 HOH HOH . X 12 HOH I 58 458 120 HOH HOH . X 12 HOH I 59 459 106 HOH HOH . X 12 HOH I 60 460 164 HOH HOH . X 12 HOH I 61 461 128 HOH HOH . X 12 HOH I 62 462 118 HOH HOH . X 12 HOH I 63 463 160 HOH HOH . X 12 HOH I 64 464 109 HOH HOH . X 12 HOH I 65 465 143 HOH HOH . X 12 HOH I 66 466 86 HOH HOH . X 12 HOH I 67 467 96 HOH HOH . X 12 HOH I 68 468 54 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 5 -14.688 40.557 43.731 1 64.14 ? PB GDP 202 A 1 HETATM 2 O O1B GDP . . . E 5 -13.977 40.823 42.423 1 75.33 ? O1B GDP 202 A 1 HETATM 3 O O2B GDP . . . E 5 -13.886 39.553 44.527 1 66.7 ? O2B GDP 202 A 1 HETATM 4 O O3B GDP . . . E 5 -16.096 40.045 43.487 1 58.37 ? O3B GDP 202 A 1 HETATM 5 O O3A GDP . . . E 5 -14.807 41.963 44.499 1 70.93 ? O3A GDP 202 A 1 HETATM 6 P PA GDP . . . E 5 -15.562 43.197 43.781 1 71.68 ? PA GDP 202 A 1 HETATM 7 O O1A GDP . . . E 5 -16.601 42.712 42.787 1 65.25 ? O1A GDP 202 A 1 HETATM 8 O O2A GDP . . . E 5 -14.511 44.096 43.163 1 60.71 ? O2A GDP 202 A 1 HETATM 9 O O5' GDP . . . E 5 -16.304 43.948 45.014 1 78.03 ? O5' GDP 202 A 1 HETATM 10 C C5' GDP . . . E 5 -17.733 43.894 45.129 1 74.1 ? C5' GDP 202 A 1 HETATM 11 C C4' GDP . . . E 5 -18.269 45.115 45.869 1 68.85 ? C4' GDP 202 A 1 HETATM 12 O O4' GDP . . . E 5 -17.398 45.414 46.953 1 65.45 ? O4' GDP 202 A 1 HETATM 13 C C3' GDP . . . E 5 -18.341 46.37 44.999 1 70 ? C3' GDP 202 A 1 HETATM 14 O O3' GDP . . . E 5 -19.695 46.819 44.821 1 74.3 ? O3' GDP 202 A 1 HETATM 15 C C2' GDP . . . E 5 -17.584 47.439 45.751 1 68.8 ? C2' GDP 202 A 1 HETATM 16 O O2' GDP . . . E 5 -18.417 48.587 45.912 1 75.36 ? O2' GDP 202 A 1 HETATM 17 C C1' GDP . . . E 5 -17.321 46.827 47.109 1 64.42 ? C1' GDP 202 A 1 HETATM 18 N N9 GDP . . . E 5 -15.966 47.162 47.575 1 61.5 ? N9 GDP 202 A 1 HETATM 19 C C8 GDP . . . E 5 -14.83 46.639 47.087 1 60.51 ? C8 GDP 202 A 1 HETATM 20 N N7 GDP . . . E 5 -13.75 47.14 47.743 1 59.5 ? N7 GDP 202 A 1 HETATM 21 C C5 GDP . . . E 5 -14.202 47.995 48.671 1 62.11 ? C5 GDP 202 A 1 HETATM 22 C C6 GDP . . . E 5 -13.588 48.852 49.705 1 69.36 ? C6 GDP 202 A 1 HETATM 23 O O6 GDP . . . E 5 -12.345 48.884 49.84 1 76.01 ? O6 GDP 202 A 1 HETATM 24 N N1 GDP . . . E 5 -14.403 49.584 50.479 1 67.37 ? N1 GDP 202 A 1 HETATM 25 C C2 GDP . . . E 5 -15.744 49.561 50.337 1 65.06 ? C2 GDP 202 A 1 HETATM 26 N N2 GDP . . . E 5 -16.492 50.34 51.156 1 66.01 ? N2 GDP 202 A 1 HETATM 27 N N3 GDP . . . E 5 -16.379 48.791 49.41 1 62.93 ? N3 GDP 202 A 1 HETATM 28 C C4 GDP . . . E 5 -15.668 48.002 48.566 1 62.06 ? C4 GDP 202 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 466 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #