data_7ULE # _model_server_result.job_id yUCDnZaFvxOoec4056_1gA _model_server_result.datetime_utc '2024-10-20 19:35:44' _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 7ule # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 7ULE # _exptl.entry_id 7ULE _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 1 _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 7ULE _cell.length_a 69.082 _cell.length_b 69.082 _cell.length_c 92.352 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ULE _symmetry.cell_setting ? _symmetry.Int_Tables_number 91 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 5_557 -x,y,-z+2 -1 0 0 0 1 0 0 0 -1 0 0 184.704 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 A SG CYS 157 A CYS 155 1_555 A SG CYS 157 A CYS 155 5_557 ? ? ? ? ? ? ? ? ? ? ? ? 2.228 ? disulf ? disulf2 A SG CYS 246 A CYS 244 1_555 A SG CYS 246 A CYS 244 5_557 ? A ? ? A ? ? ? ? ? ? ? 2.132 ? disulf ? disulf3 A SG CYS 246 A CYS 244 1_555 A SG CYS 250 A CYS 248 5_557 ? A ? ? ? ? ? ? ? ? ? ? 2.765 ? metalc ? metalc1 A OD2 ASP 111 A ASP 109 1_555 E MN MN . A MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc2 A OD1 ASP 111 A ASP 109 1_555 F NA NA . A NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc3 A OD1 ASP 152 A ASP 150 1_555 E MN MN . A MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.009 ? metalc ? metalc4 A OG1 THR 153 A THR 151 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc5 A OE1 GLU 210 A GLU 208 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.997 ? metalc ? metalc6 B O1B GDP . A GDP 301 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc7 B O1A GDP . A GDP 301 1_555 D MN MN . A MN 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc8 B O2B GDP . A GDP 301 1_555 E MN MN . A MN 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.986 ? metalc ? metalc9 C O2P F4I . A F4I 302 1_555 F NA NA . A NA 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc10 D MN MN . A MN 303 1_555 G O HOH . A HOH 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.981 ? metalc ? metalc11 D MN MN . A MN 303 1_555 G O HOH . A HOH 444 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc12 E MN MN . A MN 304 1_555 G O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.952 ? metalc ? metalc13 E MN MN . A MN 304 1_555 G O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc14 E MN MN . A MN 304 1_555 G O HOH . A HOH 449 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.98 ? metalc ? metalc15 F NA NA . A NA 305 1_555 G O HOH . A HOH 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? metalc ? metalc16 F NA NA . A NA 305 1_555 G O HOH . A HOH 446 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc17 F NA NA . A NA 305 1_555 G O HOH . A HOH 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? metalc ? metalc18 F NA NA . A NA 305 1_555 G O HOH . A HOH 463 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? # _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 158 n n PB O2B GDP sing 159 n n PB O3B GDP sing 160 n n PB O3A GDP sing 161 n n O2B HOB2 GDP sing 162 n n O3B HOB3 GDP sing 163 n n O3A PA GDP sing 164 n n PA O1A GDP doub 165 n n PA O2A GDP sing 166 n n PA O5' GDP sing 167 n n O2A HOA2 GDP sing 168 n n O5' C5' GDP sing 169 n n C5' C4' GDP sing 170 n n C5' H5' GDP sing 171 n n C5' "H5''" GDP sing 172 n n C4' O4' GDP sing 173 n n C4' C3' GDP sing 174 n n C4' H4' GDP sing 175 n n O4' C1' GDP sing 176 n n C3' O3' GDP sing 177 n n C3' C2' GDP sing 178 n n C3' H3' GDP sing 179 n n O3' HO3' GDP sing 180 n n C2' O2' GDP sing 181 n n C2' C1' GDP sing 182 n n C2' H2' GDP sing 183 n n O2' HO2' GDP sing 184 n n C1' N9 GDP sing 185 n n C1' H1' GDP sing 186 n n N9 C8 GDP sing 187 n y N9 C4 GDP sing 188 n y C8 N7 GDP doub 189 n y C8 H8 GDP sing 190 n n N7 C5 GDP sing 191 n y C5 C6 GDP sing 192 n n C5 C4 GDP doub 193 n y C6 O6 GDP doub 194 n n C6 N1 GDP sing 195 n n N1 C2 GDP sing 196 n n N1 HN1 GDP sing 197 n n C2 N2 GDP sing 198 n n C2 N3 GDP doub 199 n n N2 HN21 GDP sing 200 n n N2 HN22 GDP sing 201 n n N3 C4 GDP sing 202 n n # _atom_sites.entry_id 7ULE _atom_sites.fract_transf_matrix[1][1] 0.014476 _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] 0.014476 _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] 0.010828 _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 B 2 GDP A 1 301 1 GDP GDP . C 3 F4I A 1 302 1 F4I F4I . D 4 MN A 1 303 1 MN MN . E 4 MN A 1 304 2 MN MN . F 5 NA A 1 305 3 NA NA . G 6 HOH A 1 401 4 HOH HOH . G 6 HOH A 2 402 39 HOH HOH . G 6 HOH A 3 403 70 HOH HOH . G 6 HOH A 4 404 103 HOH HOH . G 6 HOH A 5 405 6 HOH HOH . G 6 HOH A 6 406 91 HOH HOH . G 6 HOH A 7 407 8 HOH HOH . G 6 HOH A 8 408 63 HOH HOH . G 6 HOH A 9 409 98 HOH HOH . G 6 HOH A 10 410 60 HOH HOH . G 6 HOH A 11 411 9 HOH HOH . G 6 HOH A 12 412 27 HOH HOH . G 6 HOH A 13 413 76 HOH HOH . G 6 HOH A 14 414 112 HOH HOH . G 6 HOH A 15 415 10 HOH HOH . G 6 HOH A 16 416 96 HOH HOH . G 6 HOH A 17 417 49 HOH HOH . G 6 HOH A 18 418 36 HOH HOH . G 6 HOH A 19 419 100 HOH HOH . G 6 HOH A 20 420 71 HOH HOH . G 6 HOH A 21 421 11 HOH HOH . G 6 HOH A 22 422 85 HOH HOH . G 6 HOH A 23 423 25 HOH HOH . G 6 HOH A 24 424 107 HOH HOH . G 6 HOH A 25 425 75 HOH HOH . G 6 HOH A 26 426 19 HOH HOH . G 6 HOH A 27 427 33 HOH HOH . G 6 HOH A 28 428 113 HOH HOH . G 6 HOH A 29 429 21 HOH HOH . G 6 HOH A 30 430 136 HOH HOH . G 6 HOH A 31 431 69 HOH HOH . G 6 HOH A 32 432 108 HOH HOH . G 6 HOH A 33 433 79 HOH HOH . G 6 HOH A 34 434 65 HOH HOH . G 6 HOH A 35 435 26 HOH HOH . G 6 HOH A 36 436 82 HOH HOH . G 6 HOH A 37 437 30 HOH HOH . G 6 HOH A 38 438 14 HOH HOH . G 6 HOH A 39 439 128 HOH HOH . G 6 HOH A 40 440 24 HOH HOH . G 6 HOH A 41 441 32 HOH HOH . G 6 HOH A 42 442 95 HOH HOH . G 6 HOH A 43 443 90 HOH HOH . G 6 HOH A 44 444 7 HOH HOH . G 6 HOH A 45 445 101 HOH HOH . G 6 HOH A 46 446 3 HOH HOH . G 6 HOH A 47 447 35 HOH HOH . G 6 HOH A 48 448 116 HOH HOH . G 6 HOH A 49 449 5 HOH HOH . G 6 HOH A 50 450 94 HOH HOH . G 6 HOH A 51 451 110 HOH HOH . G 6 HOH A 52 452 1 HOH HOH . G 6 HOH A 53 453 29 HOH HOH . G 6 HOH A 54 454 102 HOH HOH . G 6 HOH A 55 455 18 HOH HOH . G 6 HOH A 56 456 53 HOH HOH . G 6 HOH A 57 457 88 HOH HOH . G 6 HOH A 58 458 72 HOH HOH . G 6 HOH A 59 459 66 HOH HOH . G 6 HOH A 60 460 73 HOH HOH . G 6 HOH A 61 461 97 HOH HOH . G 6 HOH A 62 462 99 HOH HOH . G 6 HOH A 63 463 2 HOH HOH . G 6 HOH A 64 464 130 HOH HOH . G 6 HOH A 65 465 137 HOH HOH . G 6 HOH A 66 466 58 HOH HOH . G 6 HOH A 67 467 52 HOH HOH . G 6 HOH A 68 468 17 HOH HOH . G 6 HOH A 69 469 104 HOH HOH . G 6 HOH A 70 470 80 HOH HOH . G 6 HOH A 71 471 119 HOH HOH . G 6 HOH A 72 472 114 HOH HOH . G 6 HOH A 73 473 87 HOH HOH . G 6 HOH A 74 474 15 HOH HOH . G 6 HOH A 75 475 64 HOH HOH . G 6 HOH A 76 476 74 HOH HOH . G 6 HOH A 77 477 31 HOH HOH . G 6 HOH A 78 478 51 HOH HOH . G 6 HOH A 79 479 67 HOH HOH . G 6 HOH A 80 480 117 HOH HOH . G 6 HOH A 81 481 16 HOH HOH . G 6 HOH A 82 482 12 HOH HOH . G 6 HOH A 83 483 44 HOH HOH . G 6 HOH A 84 484 43 HOH HOH . G 6 HOH A 85 485 47 HOH HOH . G 6 HOH A 86 486 46 HOH HOH . G 6 HOH A 87 487 81 HOH HOH . G 6 HOH A 88 488 106 HOH HOH . G 6 HOH A 89 489 54 HOH HOH . G 6 HOH A 90 490 89 HOH HOH . G 6 HOH A 91 491 122 HOH HOH . G 6 HOH A 92 492 20 HOH HOH . G 6 HOH A 93 493 86 HOH HOH . G 6 HOH A 94 494 28 HOH HOH . G 6 HOH A 95 495 68 HOH HOH . G 6 HOH A 96 496 92 HOH HOH . G 6 HOH A 97 497 126 HOH HOH . G 6 HOH A 98 498 61 HOH HOH . G 6 HOH A 99 499 77 HOH HOH . G 6 HOH A 100 500 120 HOH HOH . G 6 HOH A 101 501 62 HOH HOH . G 6 HOH A 102 502 109 HOH HOH . G 6 HOH A 103 503 37 HOH HOH . G 6 HOH A 104 504 115 HOH HOH . G 6 HOH A 105 505 45 HOH HOH . G 6 HOH A 106 506 38 HOH HOH . G 6 HOH A 107 507 42 HOH HOH . G 6 HOH A 108 508 78 HOH HOH . G 6 HOH A 109 509 84 HOH HOH . G 6 HOH A 110 510 83 HOH HOH . G 6 HOH A 111 511 13 HOH HOH . G 6 HOH A 112 512 129 HOH HOH . G 6 HOH A 113 513 59 HOH HOH . G 6 HOH A 114 514 105 HOH HOH . G 6 HOH A 115 515 139 HOH HOH . G 6 HOH A 116 516 50 HOH HOH . G 6 HOH A 117 517 140 HOH HOH . G 6 HOH A 118 518 41 HOH HOH . G 6 HOH A 119 519 125 HOH HOH . G 6 HOH A 120 520 111 HOH HOH . G 6 HOH A 121 521 131 HOH HOH . G 6 HOH A 122 522 135 HOH HOH . G 6 HOH A 123 523 134 HOH HOH . G 6 HOH A 124 524 34 HOH HOH . G 6 HOH A 125 525 40 HOH HOH . G 6 HOH A 126 526 22 HOH HOH . G 6 HOH A 127 527 57 HOH HOH . G 6 HOH A 128 528 56 HOH HOH . G 6 HOH A 129 529 93 HOH HOH . G 6 HOH A 130 530 55 HOH HOH . G 6 HOH A 131 531 123 HOH HOH . G 6 HOH A 132 532 127 HOH HOH . G 6 HOH A 133 533 132 HOH HOH . G 6 HOH A 134 534 133 HOH HOH . G 6 HOH A 135 535 23 HOH HOH . G 6 HOH A 136 536 138 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 . . . B 2 14.802 29.861 93.831 1 32.29 0 PB GDP 301 A 1 HETATM 2 O O1B GDP . . . B 2 13.525 30.172 93.06 1 33.92 0 O1B GDP 301 A 1 HETATM 3 O O2B GDP . . . B 2 15.351 28.448 93.541 1 32.42 0 O2B GDP 301 A 1 HETATM 4 O O3B GDP . . . B 2 14.844 30.161 95.307 1 32.17 0 O3B GDP 301 A 1 HETATM 5 O O3A GDP . . . B 2 15.833 31.009 93.325 1 33.5 0 O3A GDP 301 A 1 HETATM 6 P PA GDP . . . B 2 16.231 31.387 91.808 1 35.38 0 PA GDP 301 A 1 HETATM 7 O O1A GDP . . . B 2 15.051 31.003 90.917 1 33.25 0 O1A GDP 301 A 1 HETATM 8 O O2A GDP . . . B 2 17.615 30.824 91.561 1 33.31 0 O2A GDP 301 A 1 HETATM 9 O O5' GDP . . . B 2 16.418 32.974 91.805 1 33.54 0 O5' GDP 301 A 1 HETATM 10 C C5' GDP . . . B 2 15.3 33.847 91.937 1 33.9 0 C5' GDP 301 A 1 HETATM 11 C C4' GDP . . . B 2 15.725 35.284 91.659 1 33.63 0 C4' GDP 301 A 1 HETATM 12 O O4' GDP . . . B 2 16.683 35.69 92.646 1 33.36 0 O4' GDP 301 A 1 HETATM 13 C C3' GDP . . . B 2 16.415 35.492 90.322 1 33.62 0 C3' GDP 301 A 1 HETATM 14 O O3' GDP . . . B 2 16.057 36.778 89.792 1 32.31 0 O3' GDP 301 A 1 HETATM 15 C C2' GDP . . . B 2 17.891 35.481 90.653 1 33.36 0 C2' GDP 301 A 1 HETATM 16 O O2' GDP . . . B 2 18.689 36.172 89.687 1 34.75 0 O2' GDP 301 A 1 HETATM 17 C C1' GDP . . . B 2 17.87 36.166 92.005 1 33.01 0 C1' GDP 301 A 1 HETATM 18 N N9 GDP . . . B 2 19.044 35.856 92.838 1 32.5 0 N9 GDP 301 A 1 HETATM 19 C C8 GDP . . . B 2 19.497 34.644 93.203 1 33.03 0 C8 GDP 301 A 1 HETATM 20 N N7 GDP . . . B 2 20.598 34.765 93.995 1 33.54 0 N7 GDP 301 A 1 HETATM 21 C C5 GDP . . . B 2 20.839 36.076 94.152 1 33.31 0 C5 GDP 301 A 1 HETATM 22 C C6 GDP . . . B 2 21.843 36.908 94.863 1 34.32 0 C6 GDP 301 A 1 HETATM 23 O O6 GDP . . . B 2 22.746 36.369 95.539 1 35.41 0 O6 GDP 301 A 1 HETATM 24 N N1 GDP . . . B 2 21.731 38.238 94.767 1 32.41 0 N1 GDP 301 A 1 HETATM 25 C C2 GDP . . . B 2 20.755 38.833 94.048 1 33.37 0 C2 GDP 301 A 1 HETATM 26 N N2 GDP . . . B 2 20.689 40.182 93.981 1 33.47 0 N2 GDP 301 A 1 HETATM 27 N N3 GDP . . . B 2 19.806 38.135 93.375 1 33.55 0 N3 GDP 301 A 1 HETATM 28 C C4 GDP . . . B 2 19.806 36.785 93.398 1 33.54 0 C4 GDP 301 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 28 #