data_2ZJY # _model_server_result.job_id 2tHAfnFjqc9ljGXnI7zwNw _model_server_result.datetime_utc '2024-11-13 05:05:18' _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 2zjy # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":355}' # _entry.id 2ZJY # _exptl.entry_id 2ZJY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 4 _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 120 _cell.entry_id 2ZJY _cell.length_a 79.375 _cell.length_b 79.375 _cell.length_c 105.297 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ZJY _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 4 _struct_asym.id D _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 metalc ? metalc1 A OG SER 49 A SER 47 1_555 C MG MG . A MG 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.483 ? metalc ? metalc2 A OG1 THR 183 A THR 181 1_555 C MG MG . A MG 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc3 D O2B GDP . A GDP 355 1_555 C MG MG . A MG 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.444 ? metalc ? metalc4 C MG MG . A MG 357 1_555 E O HOH . A HOH 533 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? # _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 87 n n PB O2B GDP sing 88 n n PB O3B GDP sing 89 n n PB O3A GDP sing 90 n n O2B HOB2 GDP sing 91 n n O3B HOB3 GDP sing 92 n n O3A PA GDP sing 93 n n PA O1A GDP doub 94 n n PA O2A GDP sing 95 n n PA O5' GDP sing 96 n n O2A HOA2 GDP sing 97 n n O5' C5' GDP sing 98 n n C5' C4' GDP sing 99 n n C5' H5' GDP sing 100 n n C5' "H5''" GDP sing 101 n n C4' O4' GDP sing 102 n n C4' C3' GDP sing 103 n n C4' H4' GDP sing 104 n n O4' C1' GDP sing 105 n n C3' O3' GDP sing 106 n n C3' C2' GDP sing 107 n n C3' H3' GDP sing 108 n n O3' HO3' GDP sing 109 n n C2' O2' GDP sing 110 n n C2' C1' GDP sing 111 n n C2' H2' GDP sing 112 n n O2' HO2' GDP sing 113 n n C1' N9 GDP sing 114 n n C1' H1' GDP sing 115 n n N9 C8 GDP sing 116 n y N9 C4 GDP sing 117 n y C8 N7 GDP doub 118 n y C8 H8 GDP sing 119 n n N7 C5 GDP sing 120 n y C5 C6 GDP sing 121 n n C5 C4 GDP doub 122 n y C6 O6 GDP doub 123 n n C6 N1 GDP sing 124 n n N1 C2 GDP sing 125 n n N1 HN1 GDP sing 126 n n C2 N2 GDP sing 127 n n C2 N3 GDP doub 128 n n N2 HN21 GDP sing 129 n n N2 HN22 GDP sing 130 n n N3 C4 GDP sing 131 n n # _atom_sites.entry_id 2ZJY _atom_sites.fract_transf_matrix[1][1] 0.012598 _atom_sites.fract_transf_matrix[1][2] 0.007274 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014547 _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] 0.009497 _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 ALF A 1 356 356 ALF ALF . C 3 MG A 1 357 357 MG MG . D 4 GDP A 1 355 355 GDP GDP . E 5 HOH A 1 403 403 HOH HOH . E 5 HOH A 2 406 406 HOH HOH . E 5 HOH A 3 407 407 HOH HOH . E 5 HOH A 4 408 408 HOH HOH . E 5 HOH A 5 409 409 HOH HOH . E 5 HOH A 6 410 410 HOH HOH . E 5 HOH A 7 411 411 HOH HOH . E 5 HOH A 8 412 412 HOH HOH . E 5 HOH A 9 413 413 HOH HOH . E 5 HOH A 10 414 414 HOH HOH . E 5 HOH A 11 415 415 HOH HOH . E 5 HOH A 12 416 416 HOH HOH . E 5 HOH A 13 417 417 HOH HOH . E 5 HOH A 14 418 418 HOH HOH . E 5 HOH A 15 419 419 HOH HOH . E 5 HOH A 16 421 421 HOH HOH . E 5 HOH A 17 422 422 HOH HOH . E 5 HOH A 18 423 423 HOH HOH . E 5 HOH A 19 424 424 HOH HOH . E 5 HOH A 20 425 425 HOH HOH . E 5 HOH A 21 426 426 HOH HOH . E 5 HOH A 22 427 427 HOH HOH . E 5 HOH A 23 428 428 HOH HOH . E 5 HOH A 24 429 429 HOH HOH . E 5 HOH A 25 430 430 HOH HOH . E 5 HOH A 26 431 431 HOH HOH . E 5 HOH A 27 433 433 HOH HOH . E 5 HOH A 28 434 434 HOH HOH . E 5 HOH A 29 435 435 HOH HOH . E 5 HOH A 30 436 436 HOH HOH . E 5 HOH A 31 438 438 HOH HOH . E 5 HOH A 32 439 439 HOH HOH . E 5 HOH A 33 440 440 HOH HOH . E 5 HOH A 34 442 442 HOH HOH . E 5 HOH A 35 444 444 HOH HOH . E 5 HOH A 36 446 446 HOH HOH . E 5 HOH A 37 447 447 HOH HOH . E 5 HOH A 38 448 448 HOH HOH . E 5 HOH A 39 449 449 HOH HOH . E 5 HOH A 40 452 452 HOH HOH . E 5 HOH A 41 453 453 HOH HOH . E 5 HOH A 42 454 454 HOH HOH . E 5 HOH A 43 455 455 HOH HOH . E 5 HOH A 44 456 456 HOH HOH . E 5 HOH A 45 457 457 HOH HOH . E 5 HOH A 46 458 458 HOH HOH . E 5 HOH A 47 459 459 HOH HOH . E 5 HOH A 48 461 461 HOH HOH . E 5 HOH A 49 462 462 HOH HOH . E 5 HOH A 50 463 463 HOH HOH . E 5 HOH A 51 464 464 HOH HOH . E 5 HOH A 52 465 465 HOH HOH . E 5 HOH A 53 466 466 HOH HOH . E 5 HOH A 54 467 467 HOH HOH . E 5 HOH A 55 468 468 HOH HOH . E 5 HOH A 56 469 469 HOH HOH . E 5 HOH A 57 470 470 HOH HOH . E 5 HOH A 58 477 477 HOH HOH . E 5 HOH A 59 478 478 HOH HOH . E 5 HOH A 60 479 479 HOH HOH . E 5 HOH A 61 481 481 HOH HOH . E 5 HOH A 62 482 482 HOH HOH . E 5 HOH A 63 483 483 HOH HOH . E 5 HOH A 64 487 487 HOH HOH . E 5 HOH A 65 488 488 HOH HOH . E 5 HOH A 66 491 491 HOH HOH . E 5 HOH A 67 492 492 HOH HOH . E 5 HOH A 68 494 494 HOH HOH . E 5 HOH A 69 497 497 HOH HOH . E 5 HOH A 70 498 498 HOH HOH . E 5 HOH A 71 499 499 HOH HOH . E 5 HOH A 72 500 500 HOH HOH . E 5 HOH A 73 501 501 HOH HOH . E 5 HOH A 74 502 502 HOH HOH . E 5 HOH A 75 504 504 HOH HOH . E 5 HOH A 76 505 505 HOH HOH . E 5 HOH A 77 509 509 HOH HOH . E 5 HOH A 78 510 510 HOH HOH . E 5 HOH A 79 511 511 HOH HOH . E 5 HOH A 80 512 512 HOH HOH . E 5 HOH A 81 517 517 HOH HOH . E 5 HOH A 82 518 518 HOH HOH . E 5 HOH A 83 519 519 HOH HOH . E 5 HOH A 84 521 521 HOH HOH . E 5 HOH A 85 522 522 HOH HOH . E 5 HOH A 86 523 523 HOH HOH . E 5 HOH A 87 524 524 HOH HOH . E 5 HOH A 88 525 525 HOH HOH . E 5 HOH A 89 526 526 HOH HOH . E 5 HOH A 90 531 531 HOH HOH . E 5 HOH A 91 532 532 HOH HOH . E 5 HOH A 92 533 533 HOH HOH . E 5 HOH A 93 534 534 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 4 43.449 30.516 9.997 1 18.1 ? PB GDP 355 A 1 HETATM 2 O O1B GDP . . . D 4 43.332 31.693 9.178 1 19.25 ? O1B GDP 355 A 1 HETATM 3 O O2B GDP . . . D 4 44.815 30.141 10.36 1 28.58 ? O2B GDP 355 A 1 HETATM 4 O O3B GDP . . . D 4 42.445 30.572 11.073 1 22.1 ? O3B GDP 355 A 1 HETATM 5 O O3A GDP . . . D 4 42.959 29.306 9.1 1 22.13 ? O3A GDP 355 A 1 HETATM 6 P PA GDP . . . D 4 42.433 27.831 9.36 1 14.85 ? PA GDP 355 A 1 HETATM 7 O O1A GDP . . . D 4 43.449 26.904 8.837 1 17.6 ? O1A GDP 355 A 1 HETATM 8 O O2A GDP . . . D 4 42.059 27.679 10.849 1 12.4 ? O2A GDP 355 A 1 HETATM 9 O O5' GDP . . . D 4 41.192 27.742 8.395 1 12.05 ? O5' GDP 355 A 1 HETATM 10 C C5' GDP . . . D 4 39.78 27.835 8.776 1 14.55 ? C5' GDP 355 A 1 HETATM 11 C C4' GDP . . . D 4 38.907 26.708 8.25 1 2.22 ? C4' GDP 355 A 1 HETATM 12 O O4' GDP . . . D 4 38.897 26.665 6.762 1 6.09 ? O4' GDP 355 A 1 HETATM 13 C C3' GDP . . . D 4 39.398 25.344 8.732 1 2.22 ? C3' GDP 355 A 1 HETATM 14 O O3' GDP . . . D 4 38.325 24.499 9.13 1 2.22 ? O3' GDP 355 A 1 HETATM 15 C C2' GDP . . . D 4 40.11 24.793 7.458 1 5.89 ? C2' GDP 355 A 1 HETATM 16 O O2' GDP . . . D 4 40.179 23.373 7.363 1 12.34 ? O2' GDP 355 A 1 HETATM 17 C C1' GDP . . . D 4 39.341 25.378 6.277 1 9.55 ? C1' GDP 355 A 1 HETATM 18 N N9 GDP . . . D 4 40.225 25.613 5.15 1 3.42 ? N9 GDP 355 A 1 HETATM 19 C C8 GDP . . . D 4 41.46 26.245 5.07 1 7.94 ? C8 GDP 355 A 1 HETATM 20 N N7 GDP . . . D 4 41.998 26.294 3.859 1 12.4 ? N7 GDP 355 A 1 HETATM 21 C C5 GDP . . . D 4 41.004 25.62 3.076 1 8.18 ? C5 GDP 355 A 1 HETATM 22 C C6 GDP . . . D 4 40.924 25.295 1.617 1 9.63 ? C6 GDP 355 A 1 HETATM 23 O O6 GDP . . . D 4 41.721 25.54 0.727 1 13.02 ? O6 GDP 355 A 1 HETATM 24 N N1 GDP . . . D 4 39.761 24.606 1.234 1 10.37 ? N1 GDP 355 A 1 HETATM 25 C C2 GDP . . . D 4 38.746 24.243 2.118 1 12.26 ? C2 GDP 355 A 1 HETATM 26 N N2 GDP . . . D 4 37.705 23.597 1.68 1 9.36 ? N2 GDP 355 A 1 HETATM 27 N N3 GDP . . . D 4 38.806 24.54 3.445 1 8.73 ? N3 GDP 355 A 1 HETATM 28 C C4 GDP . . . D 4 39.946 25.218 3.87 1 3.42 ? C4 GDP 355 A 1 # _model_server_stats.io_time_ms 54 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 286 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #