data_2RHL # _model_server_result.job_id mg_deCVpMOCgJzLwsZPE7A _model_server_result.datetime_utc '2024-12-21 14:32:02' _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 2rhl # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 2RHL # _exptl.entry_id 2RHL _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 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 2RHL _cell.length_a 82.294 _cell.length_b 97.577 _cell.length_c 135.451 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RHL _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 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,C,E 1 1 B,D,F 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 ? 2 C N N ? 2 D N N # _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 70 n n PB O2B GDP sing 71 n n PB O3B GDP sing 72 n n PB O3A GDP sing 73 n n O2B HOB2 GDP sing 74 n n O3B HOB3 GDP sing 75 n n O3A PA GDP sing 76 n n PA O1A GDP doub 77 n n PA O2A GDP sing 78 n n PA O5' GDP sing 79 n n O2A HOA2 GDP sing 80 n n O5' C5' GDP sing 81 n n C5' C4' GDP sing 82 n n C5' H5' GDP sing 83 n n C5' "H5''" GDP sing 84 n n C4' O4' GDP sing 85 n n C4' C3' GDP sing 86 n n C4' H4' GDP sing 87 n n O4' C1' GDP sing 88 n n C3' O3' GDP sing 89 n n C3' C2' GDP sing 90 n n C3' H3' GDP sing 91 n n O3' HO3' GDP sing 92 n n C2' O2' GDP sing 93 n n C2' C1' GDP sing 94 n n C2' H2' GDP sing 95 n n O2' HO2' GDP sing 96 n n C1' N9 GDP sing 97 n n C1' H1' GDP sing 98 n n N9 C8 GDP sing 99 n y N9 C4 GDP sing 100 n y C8 N7 GDP doub 101 n y C8 H8 GDP sing 102 n n N7 C5 GDP sing 103 n y C5 C6 GDP sing 104 n n C5 C4 GDP doub 105 n y C6 O6 GDP doub 106 n n C6 N1 GDP sing 107 n n N1 C2 GDP sing 108 n n N1 HN1 GDP sing 109 n n C2 N2 GDP sing 110 n n C2 N3 GDP doub 111 n n N2 HN21 GDP sing 112 n n N2 HN22 GDP sing 113 n n N3 C4 GDP sing 114 n n # _atom_sites.entry_id 2RHL _atom_sites.fract_transf_matrix[1][1] 0.012152 _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] 0.010248 _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] 0.007383 _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 GDP A 1 1 1 GDP GDP . D 2 GDP B 1 1 1 GDP GDP . E 3 HOH A 1 336 5 HOH HOH . E 3 HOH A 2 337 6 HOH HOH . E 3 HOH A 3 338 8 HOH HOH . E 3 HOH A 4 339 9 HOH HOH . E 3 HOH A 5 340 11 HOH HOH . E 3 HOH A 6 341 12 HOH HOH . E 3 HOH A 7 342 15 HOH HOH . E 3 HOH A 8 343 18 HOH HOH . E 3 HOH A 9 344 21 HOH HOH . E 3 HOH A 10 345 22 HOH HOH . E 3 HOH A 11 346 23 HOH HOH . E 3 HOH A 12 347 25 HOH HOH . E 3 HOH A 13 348 28 HOH HOH . E 3 HOH A 14 349 30 HOH HOH . E 3 HOH A 15 350 31 HOH HOH . E 3 HOH A 16 351 32 HOH HOH . E 3 HOH A 17 352 33 HOH HOH . E 3 HOH A 18 353 34 HOH HOH . E 3 HOH A 19 354 37 HOH HOH . E 3 HOH A 20 355 40 HOH HOH . E 3 HOH A 21 356 41 HOH HOH . E 3 HOH A 22 357 42 HOH HOH . E 3 HOH A 23 358 43 HOH HOH . E 3 HOH A 24 359 44 HOH HOH . E 3 HOH A 25 360 47 HOH HOH . E 3 HOH A 26 361 48 HOH HOH . E 3 HOH A 27 362 51 HOH HOH . E 3 HOH A 28 363 56 HOH HOH . E 3 HOH A 29 364 61 HOH HOH . E 3 HOH A 30 365 62 HOH HOH . E 3 HOH A 31 366 63 HOH HOH . E 3 HOH A 32 367 64 HOH HOH . E 3 HOH A 33 368 65 HOH HOH . E 3 HOH A 34 369 66 HOH HOH . E 3 HOH A 35 370 69 HOH HOH . E 3 HOH A 36 371 70 HOH HOH . E 3 HOH A 37 372 72 HOH HOH . E 3 HOH A 38 373 74 HOH HOH . E 3 HOH A 39 374 78 HOH HOH . E 3 HOH A 40 375 80 HOH HOH . E 3 HOH A 41 376 81 HOH HOH . E 3 HOH A 42 377 83 HOH HOH . E 3 HOH A 43 378 85 HOH HOH . E 3 HOH A 44 379 86 HOH HOH . E 3 HOH A 45 380 87 HOH HOH . E 3 HOH A 46 381 89 HOH HOH . E 3 HOH A 47 382 90 HOH HOH . E 3 HOH A 48 383 91 HOH HOH . E 3 HOH A 49 384 93 HOH HOH . E 3 HOH A 50 385 94 HOH HOH . E 3 HOH A 51 386 97 HOH HOH . F 3 HOH B 1 336 88 HOH HOH . F 3 HOH B 2 337 1 HOH HOH . F 3 HOH B 3 338 2 HOH HOH . F 3 HOH B 4 339 3 HOH HOH . F 3 HOH B 5 340 4 HOH HOH . F 3 HOH B 6 341 7 HOH HOH . F 3 HOH B 7 342 10 HOH HOH . F 3 HOH B 8 343 13 HOH HOH . F 3 HOH B 9 344 14 HOH HOH . F 3 HOH B 10 345 16 HOH HOH . F 3 HOH B 11 346 17 HOH HOH . F 3 HOH B 12 347 19 HOH HOH . F 3 HOH B 13 348 20 HOH HOH . F 3 HOH B 14 349 24 HOH HOH . F 3 HOH B 15 350 26 HOH HOH . F 3 HOH B 16 351 27 HOH HOH . F 3 HOH B 17 352 29 HOH HOH . F 3 HOH B 18 353 35 HOH HOH . F 3 HOH B 19 354 36 HOH HOH . F 3 HOH B 20 355 38 HOH HOH . F 3 HOH B 21 356 39 HOH HOH . F 3 HOH B 22 357 45 HOH HOH . F 3 HOH B 23 358 46 HOH HOH . F 3 HOH B 24 359 49 HOH HOH . F 3 HOH B 25 360 50 HOH HOH . F 3 HOH B 26 361 52 HOH HOH . F 3 HOH B 27 362 53 HOH HOH . F 3 HOH B 28 363 54 HOH HOH . F 3 HOH B 29 364 55 HOH HOH . F 3 HOH B 30 365 57 HOH HOH . F 3 HOH B 31 366 58 HOH HOH . F 3 HOH B 32 367 59 HOH HOH . F 3 HOH B 33 368 60 HOH HOH . F 3 HOH B 34 369 67 HOH HOH . F 3 HOH B 35 370 68 HOH HOH . F 3 HOH B 36 371 71 HOH HOH . F 3 HOH B 37 372 73 HOH HOH . F 3 HOH B 38 373 75 HOH HOH . F 3 HOH B 39 374 76 HOH HOH . F 3 HOH B 40 375 77 HOH HOH . F 3 HOH B 41 376 79 HOH HOH . F 3 HOH B 42 377 82 HOH HOH . F 3 HOH B 43 378 84 HOH HOH . F 3 HOH B 44 379 92 HOH HOH . F 3 HOH B 45 380 95 HOH HOH . F 3 HOH B 46 381 96 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 2 -11.108 -19.312 -27.033 1 51.51 ? PB GDP 1 B 1 HETATM 2 O O1B GDP . . . D 2 -10.8 -19.4 -25.553 1 51.82 ? O1B GDP 1 B 1 HETATM 3 O O2B GDP . . . D 2 -9.943 -18.689 -27.761 1 51.51 ? O2B GDP 1 B 1 HETATM 4 O O3B GDP . . . D 2 -11.406 -20.686 -27.592 1 51.31 ? O3B GDP 1 B 1 HETATM 5 O O3A GDP . . . D 2 -12.354 -18.331 -27.121 1 51.43 ? O3A GDP 1 B 1 HETATM 6 P PA GDP . . . D 2 -13.163 -18.134 -28.437 1 50.35 ? PA GDP 1 B 1 HETATM 7 O O1A GDP . . . D 2 -14.335 -19.067 -28.478 1 55.16 ? O1A GDP 1 B 1 HETATM 8 O O2A GDP . . . D 2 -12.337 -18.442 -29.651 1 52.17 ? O2A GDP 1 B 1 HETATM 9 O O5' GDP . . . D 2 -13.658 -16.62 -28.289 1 52.25 ? O5' GDP 1 B 1 HETATM 10 C C5' GDP . . . D 2 -12.747 -15.543 -28.403 1 52.99 ? C5' GDP 1 B 1 HETATM 11 C C4' GDP . . . D 2 -13.368 -14.365 -29.132 1 51.94 ? C4' GDP 1 B 1 HETATM 12 O O4' GDP . . . D 2 -13.563 -14.675 -30.514 1 52.98 ? O4' GDP 1 B 1 HETATM 13 C C3' GDP . . . D 2 -14.75 -13.986 -28.596 1 51.7 ? C3' GDP 1 B 1 HETATM 14 O O3' GDP . . . D 2 -14.667 -13.04 -27.535 1 51.34 ? O3' GDP 1 B 1 HETATM 15 C C2' GDP . . . D 2 -15.444 -13.38 -29.794 1 52.22 ? C2' GDP 1 B 1 HETATM 16 O O2' GDP . . . D 2 -15.049 -12.021 -29.959 1 51.28 ? O2' GDP 1 B 1 HETATM 17 C C1' GDP . . . D 2 -14.852 -14.17 -30.942 1 55.11 ? C1' GDP 1 B 1 HETATM 18 N N9 GDP . . . D 2 -15.685 -15.324 -31.351 1 55.1 ? N9 GDP 1 B 1 HETATM 19 C C8 GDP . . . D 2 -16.499 -16.104 -30.61 1 54.9 ? C8 GDP 1 B 1 HETATM 20 N N7 GDP . . . D 2 -17.035 -17.08 -31.413 1 56.47 ? N7 GDP 1 B 1 HETATM 21 C C5 GDP . . . D 2 -16.573 -16.929 -32.682 1 54.7 ? C5 GDP 1 B 1 HETATM 22 C C6 GDP . . . D 2 -16.721 -17.572 -34.016 1 55.63 ? C6 GDP 1 B 1 HETATM 23 O O6 GDP . . . D 2 -17.451 -18.575 -34.224 1 56.1 ? O6 GDP 1 B 1 HETATM 24 N N1 GDP . . . D 2 -16.011 -17.08 -35.053 1 55.13 ? N1 GDP 1 B 1 HETATM 25 C C2 GDP . . . D 2 -15.215 -16.005 -34.929 1 55.53 ? C2 GDP 1 B 1 HETATM 26 N N2 GDP . . . D 2 -14.542 -15.552 -36.02 1 55.36 ? N2 GDP 1 B 1 HETATM 27 N N3 GDP . . . D 2 -15.054 -15.345 -33.736 1 55.12 ? N3 GDP 1 B 1 HETATM 28 C C4 GDP . . . D 2 -15.672 -15.765 -32.611 1 55.67 ? C4 GDP 1 B 1 # _model_server_stats.io_time_ms 65 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 259 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #