data_2RHO # _model_server_result.job_id lKFngkGknUt7beWi3ydRtA _model_server_result.datetime_utc '2024-11-16 08:29:35' _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 2rho # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":501}' # _entry.id 2RHO # _exptl.entry_id 2RHO _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 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 2RHO _cell.length_a 82.295 _cell.length_b 97.164 _cell.length_c 134.719 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2RHO _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 2RHO _atom_sites.fract_transf_matrix[1][1] 0.012151 _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] 0.010292 _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] 0.007423 _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 GSP A 1 501 501 GSP GSP . D 3 GDP B 1 501 501 GDP GDP . E 4 HOH A 1 502 3 HOH HOH . E 4 HOH A 2 503 5 HOH HOH . E 4 HOH A 3 504 6 HOH HOH . E 4 HOH A 4 505 8 HOH HOH . E 4 HOH A 5 506 10 HOH HOH . E 4 HOH A 6 507 13 HOH HOH . E 4 HOH A 7 508 15 HOH HOH . E 4 HOH A 8 509 17 HOH HOH . E 4 HOH A 9 510 18 HOH HOH . E 4 HOH A 10 511 19 HOH HOH . E 4 HOH A 11 512 22 HOH HOH . E 4 HOH A 12 513 23 HOH HOH . E 4 HOH A 13 514 25 HOH HOH . E 4 HOH A 14 515 27 HOH HOH . E 4 HOH A 15 516 28 HOH HOH . E 4 HOH A 16 517 31 HOH HOH . E 4 HOH A 17 518 33 HOH HOH . E 4 HOH A 18 519 35 HOH HOH . E 4 HOH A 19 520 36 HOH HOH . E 4 HOH A 20 521 37 HOH HOH . E 4 HOH A 21 522 39 HOH HOH . E 4 HOH A 22 523 40 HOH HOH . E 4 HOH A 23 524 44 HOH HOH . E 4 HOH A 24 525 49 HOH HOH . E 4 HOH A 25 526 50 HOH HOH . E 4 HOH A 26 527 51 HOH HOH . E 4 HOH A 27 528 52 HOH HOH . E 4 HOH A 28 529 53 HOH HOH . E 4 HOH A 29 530 55 HOH HOH . E 4 HOH A 30 531 57 HOH HOH . E 4 HOH A 31 532 58 HOH HOH . E 4 HOH A 32 533 59 HOH HOH . E 4 HOH A 33 534 65 HOH HOH . E 4 HOH A 34 535 67 HOH HOH . E 4 HOH A 35 536 68 HOH HOH . E 4 HOH A 36 537 69 HOH HOH . E 4 HOH A 37 538 72 HOH HOH . E 4 HOH A 38 539 73 HOH HOH . E 4 HOH A 39 540 75 HOH HOH . E 4 HOH A 40 541 76 HOH HOH . E 4 HOH A 41 542 77 HOH HOH . E 4 HOH A 42 543 79 HOH HOH . E 4 HOH A 43 544 80 HOH HOH . E 4 HOH A 44 545 82 HOH HOH . E 4 HOH A 45 546 83 HOH HOH . E 4 HOH A 46 547 84 HOH HOH . E 4 HOH A 47 548 88 HOH HOH . E 4 HOH A 48 549 90 HOH HOH . E 4 HOH A 49 550 91 HOH HOH . E 4 HOH A 50 551 92 HOH HOH . E 4 HOH A 51 552 93 HOH HOH . E 4 HOH A 52 553 94 HOH HOH . E 4 HOH A 53 554 95 HOH HOH . E 4 HOH A 54 555 97 HOH HOH . E 4 HOH A 55 556 99 HOH HOH . F 4 HOH B 1 502 1 HOH HOH . F 4 HOH B 2 503 2 HOH HOH . F 4 HOH B 3 504 4 HOH HOH . F 4 HOH B 4 505 7 HOH HOH . F 4 HOH B 5 506 9 HOH HOH . F 4 HOH B 6 507 11 HOH HOH . F 4 HOH B 7 508 12 HOH HOH . F 4 HOH B 8 509 14 HOH HOH . F 4 HOH B 9 510 16 HOH HOH . F 4 HOH B 10 511 20 HOH HOH . F 4 HOH B 11 512 21 HOH HOH . F 4 HOH B 12 513 24 HOH HOH . F 4 HOH B 13 514 26 HOH HOH . F 4 HOH B 14 515 29 HOH HOH . F 4 HOH B 15 516 30 HOH HOH . F 4 HOH B 16 517 32 HOH HOH . F 4 HOH B 17 518 34 HOH HOH . F 4 HOH B 18 519 38 HOH HOH . F 4 HOH B 19 520 41 HOH HOH . F 4 HOH B 20 521 42 HOH HOH . F 4 HOH B 21 522 43 HOH HOH . F 4 HOH B 22 523 45 HOH HOH . F 4 HOH B 23 524 46 HOH HOH . F 4 HOH B 24 525 47 HOH HOH . F 4 HOH B 25 526 48 HOH HOH . F 4 HOH B 26 527 54 HOH HOH . F 4 HOH B 27 528 56 HOH HOH . F 4 HOH B 28 529 60 HOH HOH . F 4 HOH B 29 530 61 HOH HOH . F 4 HOH B 30 531 62 HOH HOH . F 4 HOH B 31 532 63 HOH HOH . F 4 HOH B 32 533 64 HOH HOH . F 4 HOH B 33 534 66 HOH HOH . F 4 HOH B 34 535 70 HOH HOH . F 4 HOH B 35 536 71 HOH HOH . F 4 HOH B 36 537 74 HOH HOH . F 4 HOH B 37 538 78 HOH HOH . F 4 HOH B 38 539 81 HOH HOH . F 4 HOH B 39 540 85 HOH HOH . F 4 HOH B 40 541 86 HOH HOH . F 4 HOH B 41 542 87 HOH HOH . F 4 HOH B 42 543 89 HOH HOH . F 4 HOH B 43 544 96 HOH HOH . F 4 HOH B 44 545 98 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 93.405 29.194 94.434 1 42.59 ? PB GDP 501 B 1 HETATM 2 O O1B GDP . . . D 3 93.139 29.201 92.952 1 42.53 ? O1B GDP 501 B 1 HETATM 3 O O2B GDP . . . D 3 92.228 29.829 95.171 1 41.03 ? O2B GDP 501 B 1 HETATM 4 O O3B GDP . . . D 3 93.649 27.784 94.911 1 42.68 ? O3B GDP 501 B 1 HETATM 5 O O3A GDP . . . D 3 94.7 30.081 94.596 1 42.34 ? O3A GDP 501 B 1 HETATM 6 P PA GDP . . . D 3 95.503 30.294 95.926 1 40.29 ? PA GDP 501 B 1 HETATM 7 O O1A GDP . . . D 3 96.663 29.327 96.002 1 45.79 ? O1A GDP 501 B 1 HETATM 8 O O2A GDP . . . D 3 94.642 30.161 97.145 1 41.63 ? O2A GDP 501 B 1 HETATM 9 O O5' GDP . . . D 3 96.051 31.779 95.686 1 42.54 ? O5' GDP 501 B 1 HETATM 10 C C5' GDP . . . D 3 95.157 32.872 95.851 1 43.96 ? C5' GDP 501 B 1 HETATM 11 C C4' GDP . . . D 3 95.744 34.031 96.645 1 42.3 ? C4' GDP 501 B 1 HETATM 12 O O4' GDP . . . D 3 95.89 33.751 98.042 1 43.26 ? O4' GDP 501 B 1 HETATM 13 C C3' GDP . . . D 3 97.125 34.413 96.149 1 42.34 ? C3' GDP 501 B 1 HETATM 14 O O3' GDP . . . D 3 97.049 35.351 95.082 1 43.13 ? O3' GDP 501 B 1 HETATM 15 C C2' GDP . . . D 3 97.776 35.038 97.364 1 42.85 ? C2' GDP 501 B 1 HETATM 16 O O2' GDP . . . D 3 97.44 36.414 97.465 1 40.56 ? O2' GDP 501 B 1 HETATM 17 C C1' GDP . . . D 3 97.134 34.287 98.502 1 43.34 ? C1' GDP 501 B 1 HETATM 18 N N9 GDP . . . D 3 97.938 33.132 98.9 1 43.83 ? N9 GDP 501 B 1 HETATM 19 C C8 GDP . . . D 3 98.742 32.333 98.174 1 43.73 ? C8 GDP 501 B 1 HETATM 20 N N7 GDP . . . D 3 99.244 31.335 98.978 1 44.51 ? N7 GDP 501 B 1 HETATM 21 C C5 GDP . . . D 3 98.766 31.504 100.227 1 43.04 ? C5 GDP 501 B 1 HETATM 22 C C6 GDP . . . D 3 98.878 30.869 101.549 1 43.99 ? C6 GDP 501 B 1 HETATM 23 O O6 GDP . . . D 3 99.596 29.851 101.755 1 44.8 ? O6 GDP 501 B 1 HETATM 24 N N1 GDP . . . D 3 98.162 31.393 102.561 1 43.67 ? N1 GDP 501 B 1 HETATM 25 C C2 GDP . . . D 3 97.391 32.481 102.422 1 43.8 ? C2 GDP 501 B 1 HETATM 26 N N2 GDP . . . D 3 96.69 32.993 103.472 1 44.12 ? N2 GDP 501 B 1 HETATM 27 N N3 GDP . . . D 3 97.257 33.101 101.24 1 43.58 ? N3 GDP 501 B 1 HETATM 28 C C4 GDP . . . D 3 97.891 32.673 100.144 1 44.18 ? C4 GDP 501 B 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 336 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #