data_1HUR # _model_server_result.job_id Ixc6jF-cDufybC62TId_WQ _model_server_result.datetime_utc '2024-11-26 22:50:26' _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 1hur # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 1HUR # _exptl.entry_id 1HUR _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _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 133.51 _cell.angle_gamma 90 _cell.entry_id 1HUR _cell.length_a 121.01 _cell.length_b 45.92 _cell.length_c 91.78 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1HUR _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 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,H _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 D N N ? 3 F 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 D O1B GDP . A GDP 1 1_555 C MG MG . A MG 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc2 A OG1 THR 30 A THR 31 1_555 C MG MG . A MG 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.354 ? metalc ? metalc3 A OE2 GLU 53 A GLU 54 1_555 C MG MG . A MG 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc4 C MG MG . A MG 182 1_555 G O HOH . A HOH 443 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc5 C MG MG . A MG 182 1_555 G O HOH . A HOH 452 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.547 ? metalc ? metalc6 C MG MG . A MG 182 1_555 G O HOH . A HOH 466 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.73 ? metalc ? metalc7 C MG MG . A MG 182 1_555 G O HOH . A HOH 505 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.601 ? metalc ? metalc8 F O1B GDP . B GDP 1 1_555 E MG MG . B MG 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.561 ? metalc ? metalc9 B OG1 THR 30 B THR 31 1_555 E MG MG . B MG 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.389 ? metalc ? metalc10 B OE2 GLU 53 B GLU 54 1_555 E MG MG . B MG 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.629 ? metalc ? metalc11 E MG MG . B MG 182 1_555 H O HOH . B HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.49 ? metalc ? metalc12 E MG MG . B MG 182 1_555 H O HOH . B HOH 423 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.467 ? metalc ? metalc13 E MG MG . B MG 182 1_555 H O HOH . B HOH 476 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.508 ? metalc ? metalc14 E MG MG . B MG 182 1_555 H O HOH . B HOH 500 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? # _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 1HUR _atom_sites.fract_transf_matrix[1][1] 0.008264 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.007845 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021777 _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] 0.015023 _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 C 2 MG A 1 182 2 MG MG . D 3 GDP A 1 1 1 GDP GDP . E 2 MG B 1 182 2 MG MG . F 3 GDP B 1 1 1 GDP GDP . G 4 HOH A 1 405 405 HOH HOH . G 4 HOH A 2 431 431 HOH HOH . G 4 HOH A 3 433 433 HOH HOH . G 4 HOH A 4 434 434 HOH HOH . G 4 HOH A 5 436 436 HOH HOH . G 4 HOH A 6 437 437 HOH HOH . G 4 HOH A 7 438 438 HOH HOH . G 4 HOH A 8 439 439 HOH HOH . G 4 HOH A 9 440 440 HOH HOH . G 4 HOH A 10 441 441 HOH HOH . G 4 HOH A 11 442 442 HOH HOH . G 4 HOH A 12 443 443 HOH HOH . G 4 HOH A 13 444 444 HOH HOH . G 4 HOH A 14 445 445 HOH HOH . G 4 HOH A 15 447 447 HOH HOH . G 4 HOH A 16 449 449 HOH HOH . G 4 HOH A 17 450 450 HOH HOH . G 4 HOH A 18 451 451 HOH HOH . G 4 HOH A 19 452 452 HOH HOH . G 4 HOH A 20 453 453 HOH HOH . G 4 HOH A 21 454 454 HOH HOH . G 4 HOH A 22 455 455 HOH HOH . G 4 HOH A 23 456 456 HOH HOH . G 4 HOH A 24 457 457 HOH HOH . G 4 HOH A 25 458 458 HOH HOH . G 4 HOH A 26 462 462 HOH HOH . G 4 HOH A 27 463 463 HOH HOH . G 4 HOH A 28 464 464 HOH HOH . G 4 HOH A 29 465 465 HOH HOH . G 4 HOH A 30 466 466 HOH HOH . G 4 HOH A 31 467 467 HOH HOH . G 4 HOH A 32 468 468 HOH HOH . G 4 HOH A 33 469 469 HOH HOH . G 4 HOH A 34 470 470 HOH HOH . G 4 HOH A 35 471 471 HOH HOH . G 4 HOH A 36 474 474 HOH HOH . G 4 HOH A 37 488 488 HOH HOH . G 4 HOH A 38 498 498 HOH HOH . G 4 HOH A 39 499 499 HOH HOH . G 4 HOH A 40 501 501 HOH HOH . G 4 HOH A 41 502 502 HOH HOH . G 4 HOH A 42 504 504 HOH HOH . G 4 HOH A 43 505 505 HOH HOH . H 4 HOH B 1 401 401 HOH HOH . H 4 HOH B 2 402 402 HOH HOH . H 4 HOH B 3 403 403 HOH HOH . H 4 HOH B 4 404 404 HOH HOH . H 4 HOH B 5 406 406 HOH HOH . H 4 HOH B 6 407 407 HOH HOH . H 4 HOH B 7 408 408 HOH HOH . H 4 HOH B 8 409 409 HOH HOH . H 4 HOH B 9 410 410 HOH HOH . H 4 HOH B 10 411 411 HOH HOH . H 4 HOH B 11 412 412 HOH HOH . H 4 HOH B 12 413 413 HOH HOH . H 4 HOH B 13 414 414 HOH HOH . H 4 HOH B 14 415 415 HOH HOH . H 4 HOH B 15 416 416 HOH HOH . H 4 HOH B 16 417 417 HOH HOH . H 4 HOH B 17 418 418 HOH HOH . H 4 HOH B 18 419 419 HOH HOH . H 4 HOH B 19 420 420 HOH HOH . H 4 HOH B 20 421 421 HOH HOH . H 4 HOH B 21 422 422 HOH HOH . H 4 HOH B 22 423 423 HOH HOH . H 4 HOH B 23 424 424 HOH HOH . H 4 HOH B 24 425 425 HOH HOH . H 4 HOH B 25 426 426 HOH HOH . H 4 HOH B 26 428 428 HOH HOH . H 4 HOH B 27 429 429 HOH HOH . H 4 HOH B 28 432 432 HOH HOH . H 4 HOH B 29 446 446 HOH HOH . H 4 HOH B 30 475 475 HOH HOH . H 4 HOH B 31 476 476 HOH HOH . H 4 HOH B 32 477 477 HOH HOH . H 4 HOH B 33 478 478 HOH HOH . H 4 HOH B 34 479 479 HOH HOH . H 4 HOH B 35 480 480 HOH HOH . H 4 HOH B 36 481 481 HOH HOH . H 4 HOH B 37 482 482 HOH HOH . H 4 HOH B 38 483 483 HOH HOH . H 4 HOH B 39 484 484 HOH HOH . H 4 HOH B 40 485 485 HOH HOH . H 4 HOH B 41 486 486 HOH HOH . H 4 HOH B 42 489 489 HOH HOH . H 4 HOH B 43 490 490 HOH HOH . H 4 HOH B 44 491 491 HOH HOH . H 4 HOH B 45 492 492 HOH HOH . H 4 HOH B 46 493 493 HOH HOH . H 4 HOH B 47 494 494 HOH HOH . H 4 HOH B 48 495 495 HOH HOH . H 4 HOH B 49 496 496 HOH HOH . H 4 HOH B 50 497 497 HOH HOH . H 4 HOH B 51 500 500 HOH HOH . H 4 HOH B 52 503 503 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 3 57.222 19.668 15.533 1 22.67 ? PB GDP 1 A 1 HETATM 2 O O1B GDP . . . D 3 57.223 18.171 15.681 1 12.59 ? O1B GDP 1 A 1 HETATM 3 O O2B GDP . . . D 3 56.1 20.38 16.32 1 24.46 ? O2B GDP 1 A 1 HETATM 4 O O3B GDP . . . D 3 58.429 20.543 15.831 1 27.51 ? O3B GDP 1 A 1 HETATM 5 O O3A GDP . . . D 3 56.764 20.094 14.091 1 24.49 ? O3A GDP 1 A 1 HETATM 6 P PA GDP . . . D 3 56.358 19.404 12.846 1 24.87 ? PA GDP 1 A 1 HETATM 7 O O1A GDP . . . D 3 57.382 18.377 12.34 1 28.72 ? O1A GDP 1 A 1 HETATM 8 O O2A GDP . . . D 3 55.063 18.592 12.999 1 31.38 ? O2A GDP 1 A 1 HETATM 9 O O5' GDP . . . D 3 56.253 20.542 11.905 1 28.24 ? O5' GDP 1 A 1 HETATM 10 C C5' GDP . . . D 3 55.449 21.658 12.234 1 26.86 ? C5' GDP 1 A 1 HETATM 11 C C4' GDP . . . D 3 55.026 22.4 10.933 1 26.03 ? C4' GDP 1 A 1 HETATM 12 O O4' GDP . . . D 3 56.147 23.04 10.367 1 31.32 ? O4' GDP 1 A 1 HETATM 13 C C3' GDP . . . D 3 54.443 21.428 9.878 1 27.04 ? C3' GDP 1 A 1 HETATM 14 O O3' GDP . . . D 3 53.391 22.201 9.281 1 34.43 ? O3' GDP 1 A 1 HETATM 15 C C2' GDP . . . D 3 55.62 21.297 8.903 1 27.66 ? C2' GDP 1 A 1 HETATM 16 O O2' GDP . . . D 3 55.271 20.978 7.545 1 25.15 ? O2' GDP 1 A 1 HETATM 17 C C1' GDP . . . D 3 56.23 22.709 8.98 1 28.62 ? C1' GDP 1 A 1 HETATM 18 N N9 GDP . . . D 3 57.683 22.643 8.66 1 35.19 ? N9 GDP 1 A 1 HETATM 19 C C8 GDP . . . D 3 58.65 21.792 9.164 1 31.74 ? C8 GDP 1 A 1 HETATM 20 N N7 GDP . . . D 3 59.856 22.01 8.625 1 31.55 ? N7 GDP 1 A 1 HETATM 21 C C5 GDP . . . D 3 59.705 23.147 7.737 1 28.11 ? C5 GDP 1 A 1 HETATM 22 C C6 GDP . . . D 3 60.637 23.989 6.857 1 28.36 ? C6 GDP 1 A 1 HETATM 23 O O6 GDP . . . D 3 61.857 23.829 6.882 1 31.43 ? O6 GDP 1 A 1 HETATM 24 N N1 GDP . . . D 3 60.187 25.013 6.089 1 29.93 ? N1 GDP 1 A 1 HETATM 25 C C2 GDP . . . D 3 58.857 25.433 6.108 1 32.51 ? C2 GDP 1 A 1 HETATM 26 N N2 GDP . . . D 3 58.446 26.482 5.383 1 35.38 ? N2 GDP 1 A 1 HETATM 27 N N3 GDP . . . D 3 57.988 24.673 6.919 1 29.01 ? N3 GDP 1 A 1 HETATM 28 C C4 GDP . . . D 3 58.419 23.51 7.754 1 30.66 ? C4 GDP 1 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #