data_5HPY # _model_server_result.job_id E3d_SbOMkaw_1mBnOoh0kA _model_server_result.datetime_utc '2024-10-11 06:21:00' _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 5hpy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":202}' # _entry.id 5HPY # _exptl.entry_id 5HPY _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 5HPY _cell.length_a 114.055 _cell.length_b 90.762 _cell.length_c 93.582 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HPY _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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,E,F,G,L,M 1 1 C,D,H,I,J,K,N,O 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 I 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 B OG1 THR 23 B THR 19 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc2 B OG1 THR 41 B THR 37 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? metalc ? metalc3 E MG MGF . B MGF 201 1_555 G O2B GDP . B GDP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc4 E MG MGF . B MGF 201 1_555 M O HOH . B HOH 318 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.407 ? metalc ? metalc5 F MG MG . B MG 202 1_555 G O3B GDP . B GDP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc6 F MG MG . B MG 202 1_555 M O HOH . B HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.091 ? metalc ? metalc7 F MG MG . B MG 202 1_555 M O HOH . B HOH 319 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc8 D OG1 THR 23 F THR 19 1_555 J MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc9 D OG1 THR 41 F THR 37 1_555 J MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? metalc ? metalc10 D OH TYR 46 F TYR 42 1_555 K MG MG . F MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.671 ? metalc ? metalc11 D OD2 ASP 63 F ASP 59 1_555 K MG MG . F MG 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.754 ? metalc ? metalc12 H MG MGF . F MGF 201 1_555 I O3B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.747 ? metalc ? metalc13 H MG MGF . F MGF 201 1_555 O O HOH . F HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.466 ? metalc ? metalc14 I O2B GDP . F GDP 202 1_555 J MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.163 ? metalc ? metalc15 J MG MG . F MG 203 1_555 O O HOH . F HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.093 ? metalc ? metalc16 J MG MG . F MG 203 1_555 O O HOH . F HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc17 K MG MG . F MG 204 1_555 O O HOH . F HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.702 ? # _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 5HPY _atom_sites.fract_transf_matrix[1][1] 0.008768 _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] 0.011018 _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] 0.010686 _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 MGF B 1 201 181 MGF MGF . F 4 MG B 1 202 182 MG MG . G 5 GDP B 1 203 183 GDP GDP . H 3 MGF F 1 201 399 MGF MGF . I 5 GDP F 1 202 182 GDP GDP . J 4 MG F 1 203 183 MG MG . K 4 MG F 1 204 184 MG MG . L 6 HOH A 1 501 422 HOH HOH . L 6 HOH A 2 502 424 HOH HOH . L 6 HOH A 3 503 412 HOH HOH . L 6 HOH A 4 504 402 HOH HOH . L 6 HOH A 5 505 410 HOH HOH . L 6 HOH A 6 506 419 HOH HOH . L 6 HOH A 7 507 414 HOH HOH . L 6 HOH A 8 508 400 HOH HOH . L 6 HOH A 9 509 2 HOH HOH . L 6 HOH A 10 510 417 HOH HOH . L 6 HOH A 11 511 403 HOH HOH . L 6 HOH A 12 512 411 HOH HOH . L 6 HOH A 13 513 399 HOH HOH . L 6 HOH A 14 514 406 HOH HOH . L 6 HOH A 15 515 1 HOH HOH . L 6 HOH A 16 516 418 HOH HOH . L 6 HOH A 17 517 409 HOH HOH . L 6 HOH A 18 518 405 HOH HOH . L 6 HOH A 19 519 427 HOH HOH . L 6 HOH A 20 520 421 HOH HOH . L 6 HOH A 21 521 408 HOH HOH . L 6 HOH A 22 522 416 HOH HOH . L 6 HOH A 23 523 413 HOH HOH . L 6 HOH A 24 524 401 HOH HOH . L 6 HOH A 25 525 415 HOH HOH . L 6 HOH A 26 526 3 HOH HOH . L 6 HOH A 27 527 426 HOH HOH . L 6 HOH A 28 528 420 HOH HOH . M 6 HOH B 1 301 6 HOH HOH . M 6 HOH B 2 302 184 HOH HOH . M 6 HOH B 3 303 207 HOH HOH . M 6 HOH B 4 304 9 HOH HOH . M 6 HOH B 5 305 190 HOH HOH . M 6 HOH B 6 306 202 HOH HOH . M 6 HOH B 7 307 407 HOH HOH . M 6 HOH B 8 308 215 HOH HOH . M 6 HOH B 9 309 217 HOH HOH . M 6 HOH B 10 310 223 HOH HOH . M 6 HOH B 11 311 187 HOH HOH . M 6 HOH B 12 312 213 HOH HOH . M 6 HOH B 13 313 189 HOH HOH . M 6 HOH B 14 314 192 HOH HOH . M 6 HOH B 15 315 7 HOH HOH . M 6 HOH B 16 316 199 HOH HOH . M 6 HOH B 17 317 208 HOH HOH . M 6 HOH B 18 318 185 HOH HOH . M 6 HOH B 19 319 188 HOH HOH . M 6 HOH B 20 320 195 HOH HOH . M 6 HOH B 21 321 191 HOH HOH . M 6 HOH B 22 322 404 HOH HOH . M 6 HOH B 23 323 222 HOH HOH . M 6 HOH B 24 324 197 HOH HOH . M 6 HOH B 25 325 198 HOH HOH . M 6 HOH B 26 326 212 HOH HOH . M 6 HOH B 27 327 214 HOH HOH . M 6 HOH B 28 328 194 HOH HOH . M 6 HOH B 29 329 218 HOH HOH . M 6 HOH B 30 330 8 HOH HOH . M 6 HOH B 31 331 196 HOH HOH . M 6 HOH B 32 332 226 HOH HOH . M 6 HOH B 33 333 216 HOH HOH . M 6 HOH B 34 334 210 HOH HOH . M 6 HOH B 35 335 211 HOH HOH . M 6 HOH B 36 336 200 HOH HOH . M 6 HOH B 37 337 201 HOH HOH . M 6 HOH B 38 338 193 HOH HOH . M 6 HOH B 39 339 224 HOH HOH . M 6 HOH B 40 340 227 HOH HOH . M 6 HOH B 41 341 229 HOH HOH . M 6 HOH B 42 342 5 HOH HOH . M 6 HOH B 43 343 206 HOH HOH . M 6 HOH B 44 344 225 HOH HOH . M 6 HOH B 45 345 203 HOH HOH . N 6 HOH D 1 501 401 HOH HOH . N 6 HOH D 2 502 407 HOH HOH . N 6 HOH D 3 503 413 HOH HOH . N 6 HOH D 4 504 410 HOH HOH . N 6 HOH D 5 505 408 HOH HOH . N 6 HOH D 6 506 415 HOH HOH . N 6 HOH D 7 507 405 HOH HOH . N 6 HOH D 8 508 411 HOH HOH . N 6 HOH D 9 509 403 HOH HOH . N 6 HOH D 10 510 409 HOH HOH . N 6 HOH D 11 511 417 HOH HOH . N 6 HOH D 12 512 421 HOH HOH . N 6 HOH D 13 513 402 HOH HOH . N 6 HOH D 14 514 400 HOH HOH . N 6 HOH D 15 515 412 HOH HOH . N 6 HOH D 16 516 422 HOH HOH . N 6 HOH D 17 517 414 HOH HOH . N 6 HOH D 18 518 418 HOH HOH . N 6 HOH D 19 519 420 HOH HOH . N 6 HOH D 20 520 416 HOH HOH . O 6 HOH F 1 301 207 HOH HOH . O 6 HOH F 2 302 226 HOH HOH . O 6 HOH F 3 303 212 HOH HOH . O 6 HOH F 4 304 224 HOH HOH . O 6 HOH F 5 305 210 HOH HOH . O 6 HOH F 6 306 225 HOH HOH . O 6 HOH F 7 307 185 HOH HOH . O 6 HOH F 8 308 404 HOH HOH . O 6 HOH F 9 309 206 HOH HOH . O 6 HOH F 10 310 215 HOH HOH . O 6 HOH F 11 311 219 HOH HOH . O 6 HOH F 12 312 193 HOH HOH . O 6 HOH F 13 313 222 HOH HOH . O 6 HOH F 14 314 195 HOH HOH . O 6 HOH F 15 315 199 HOH HOH . O 6 HOH F 16 316 196 HOH HOH . O 6 HOH F 17 317 194 HOH HOH . O 6 HOH F 18 318 186 HOH HOH . O 6 HOH F 19 319 197 HOH HOH . O 6 HOH F 20 320 198 HOH HOH . O 6 HOH F 21 321 214 HOH HOH . O 6 HOH F 22 322 188 HOH HOH . O 6 HOH F 23 323 201 HOH HOH . O 6 HOH F 24 324 208 HOH HOH . O 6 HOH F 25 325 220 HOH HOH . O 6 HOH F 26 326 202 HOH HOH . O 6 HOH F 27 327 204 HOH HOH . O 6 HOH F 28 328 203 HOH HOH . O 6 HOH F 29 329 4 HOH HOH . O 6 HOH F 30 330 205 HOH HOH . O 6 HOH F 31 331 217 HOH HOH . O 6 HOH F 32 332 209 HOH HOH . O 6 HOH F 33 333 218 HOH HOH . O 6 HOH F 34 334 227 HOH HOH . O 6 HOH F 35 335 200 HOH HOH . O 6 HOH F 36 336 406 HOH HOH . O 6 HOH F 37 337 223 HOH HOH . O 6 HOH F 38 338 190 HOH HOH . O 6 HOH F 39 339 189 HOH HOH . O 6 HOH F 40 340 191 HOH HOH . O 6 HOH F 41 341 192 HOH HOH . O 6 HOH F 42 342 221 HOH HOH . O 6 HOH F 43 343 211 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 . . . I 5 -46.678 36.237 18.218 1 43.58 ? PB GDP 202 F 1 HETATM 2 O O1B GDP . . . I 5 -46.001 35.404 17.155 1 52.78 ? O1B GDP 202 F 1 HETATM 3 O O2B GDP . . . I 5 -47.737 37.092 17.579 1 41.01 ? O2B GDP 202 F 1 HETATM 4 O O3B GDP . . . I 5 -47.266 35.364 19.292 1 39.82 ? O3B GDP 202 F 1 HETATM 5 O O3A GDP . . . I 5 -45.614 37.195 18.929 1 57.04 ? O3A GDP 202 F 1 HETATM 6 P PA GDP . . . I 5 -46.094 38.267 20.027 1 49.74 ? PA GDP 202 F 1 HETATM 7 O O1A GDP . . . I 5 -46.09 39.624 19.362 1 40.61 ? O1A GDP 202 F 1 HETATM 8 O O2A GDP . . . I 5 -47.461 37.945 20.58 1 44.99 ? O2A GDP 202 F 1 HETATM 9 O O5' GDP . . . I 5 -44.967 38.168 21.171 1 51.8 ? O5' GDP 202 F 1 HETATM 10 C C5' GDP . . . I 5 -45.115 37.231 22.245 1 50.68 ? C5' GDP 202 F 1 HETATM 11 C C4' GDP . . . I 5 -44.229 37.641 23.413 1 59.55 ? C4' GDP 202 F 1 HETATM 12 O O4' GDP . . . I 5 -42.901 37.881 22.944 1 57.91 ? O4' GDP 202 F 1 HETATM 13 C C3' GDP . . . I 5 -44.738 38.931 24.027 1 62.19 ? C3' GDP 202 F 1 HETATM 14 O O3' GDP . . . I 5 -44.974 38.745 25.425 1 68.09 ? O3' GDP 202 F 1 HETATM 15 C C2' GDP . . . I 5 -43.634 39.946 23.844 1 58.47 ? C2' GDP 202 F 1 HETATM 16 O O2' GDP . . . I 5 -43.417 40.602 25.096 1 63.6 ? O2' GDP 202 F 1 HETATM 17 C C1' GDP . . . I 5 -42.415 39.142 23.409 1 56.92 ? C1' GDP 202 F 1 HETATM 18 N N9 GDP . . . I 5 -41.69 39.855 22.321 1 54.1 ? N9 GDP 202 F 1 HETATM 19 C C8 GDP . . . I 5 -42.186 40.194 21.113 1 59.42 ? C8 GDP 202 F 1 HETATM 20 N N7 GDP . . . I 5 -41.266 40.842 20.348 1 56.19 ? N7 GDP 202 F 1 HETATM 21 C C5 GDP . . . I 5 -40.133 40.919 21.074 1 58.58 ? C5 GDP 202 F 1 HETATM 22 C C6 GDP . . . I 5 -38.767 41.473 20.877 1 60.33 ? C6 GDP 202 F 1 HETATM 23 O O6 GDP . . . I 5 -38.435 42.045 19.814 1 54.52 ? O6 GDP 202 F 1 HETATM 24 N N1 GDP . . . I 5 -37.888 41.344 21.883 1 52.77 ? N1 GDP 202 F 1 HETATM 25 C C2 GDP . . . I 5 -38.208 40.738 23.044 1 58.02 ? C2 GDP 202 F 1 HETATM 26 N N2 GDP . . . I 5 -37.267 40.645 24.016 1 62.87 ? N2 GDP 202 F 1 HETATM 27 N N3 GDP . . . I 5 -39.433 40.21 23.293 1 62.3 ? N3 GDP 202 F 1 HETATM 28 C C4 GDP . . . I 5 -40.421 40.268 22.366 1 54.28 ? C4 GDP 202 F 1 # _model_server_stats.io_time_ms 19 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 306 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #