data_4R1R # _model_server_result.job_id 2bbe_jZ6uBDDqifheniTOg _model_server_result.datetime_utc '2024-11-07 12:53:26' _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 4r1r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"M","auth_seq_id":763}' # _entry.id 4R1R # _exptl.entry_id 4R1R _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 3 _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 4R1R _cell.length_a 224.02 _cell.length_b 224.02 _cell.length_c 335.97 _cell.Z_PDB 72 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4R1R _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? trimeric 3 author_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_software_defined_assembly 3 PISA pentadecameric 15 software_defined_assembly 4 PISA dodecameric 12 software_defined_assembly 5 PISA pentameric 5 software_defined_assembly 6 PISA tetrameric 4 software_defined_assembly 7 PISA dodecameric 12 software_defined_assembly 8 PISA tetrameric 4 software_defined_assembly 9 PISA dimeric 2 software_defined_assembly 10 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,G,H,I 1 1 C,D,J,K 2 1 E,F,L,M 3 1 A,B,C,D,G,H,I,J,K 4 1,2,3 E,F,L,M 5 1,4,5,6,7,8 A,B,C,D,G,H,I,J,K 6 1 E,F,L,M 7 1,8 A,B,C,D,H,I,J,K 8 1,2,3 A,B,C,D,H,I,J,K 9 1 A,B,H,I 10 1 # 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' 2_665 -y+1,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 112.01 194.007011 0 3 'crystal symmetry operation' 3_565 -x+y,-x+1,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -112.01 194.007011 0 4 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 5 'crystal symmetry operation' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 6 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 7 'crystal symmetry operation' 5_555 x-y,-y,-z 1 0 0 0 -1 0 0 0 -1 0 0 0 8 'crystal symmetry operation' 6_555 -x,-x+y,-z -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 K N N ? 4 M 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 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 4R1R _atom_sites.fract_transf_matrix[1][1] 0.004464 _atom_sites.fract_transf_matrix[1][2] 0.002577 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.005154 _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] 0.002976 _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 H 3 TTP A 1 762 1 TTP TTP . I 4 GDP A 1 763 2 GDP GDP . J 3 TTP B 1 762 1 TTP TTP . K 4 GDP B 1 763 2 GDP GDP . L 3 TTP C 1 762 1 TTP TTP . M 4 GDP C 1 763 2 GDP GDP . # 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 . . . M 4 -14.54 30.848 27.685 0.5 62.5 ? PB GDP 763 C 1 HETATM 2 O O1B GDP . . . M 4 -14.06 29.726 28.483 0.5 62.5 ? O1B GDP 763 C 1 HETATM 3 O O2B GDP . . . M 4 -14.634 32.181 28.293 0.5 62.43 ? O2B GDP 763 C 1 HETATM 4 O O3B GDP . . . M 4 -13.661 30.938 26.407 0.5 62.64 ? O3B GDP 763 C 1 HETATM 5 O O3A GDP . . . M 4 -15.984 30.523 27.048 0.5 62.57 ? O3A GDP 763 C 1 HETATM 6 P PA GDP . . . M 4 -17.351 31.367 27.164 0.5 62.61 ? PA GDP 763 C 1 HETATM 7 O O1A GDP . . . M 4 -17.729 31.5 28.602 0.5 62.76 ? O1A GDP 763 C 1 HETATM 8 O O2A GDP . . . M 4 -17.291 32.56 26.325 0.5 62.77 ? O2A GDP 763 C 1 HETATM 9 O O5' GDP . . . M 4 -18.33 30.273 26.477 0.5 62.53 ? O5' GDP 763 C 1 HETATM 10 C C5' GDP . . . M 4 -18.248 29.991 25.074 0.5 62.4 ? C5' GDP 763 C 1 HETATM 11 C C4' GDP . . . M 4 -19.28 30.818 24.298 0.5 62.38 ? C4' GDP 763 C 1 HETATM 12 O O4' GDP . . . M 4 -18.588 31.905 23.701 0.5 62.57 ? O4' GDP 763 C 1 HETATM 13 C C3' GDP . . . M 4 -19.953 30.069 23.153 0.5 62.3 ? C3' GDP 763 C 1 HETATM 14 O O3' GDP . . . M 4 -21.27 29.764 23.551 0.5 62.04 ? O3' GDP 763 C 1 HETATM 15 C C2' GDP . . . M 4 -19.937 31.008 21.943 0.5 62.4 ? C2' GDP 763 C 1 HETATM 16 O O2' GDP . . . M 4 -21.223 31.525 21.523 0.5 62.17 ? O2' GDP 763 C 1 HETATM 17 C C1' GDP . . . M 4 -18.986 32.105 22.349 0.5 62.68 ? C1' GDP 763 C 1 HETATM 18 N N9 GDP . . . M 4 -17.765 32.121 21.525 0.5 63.07 ? N9 GDP 763 C 1 HETATM 19 C C8 GDP . . . M 4 -17.6 31.893 20.191 0.5 63.18 ? C8 GDP 763 C 1 HETATM 20 N N7 GDP . . . M 4 -16.391 31.982 19.749 0.5 63.33 ? N7 GDP 763 C 1 HETATM 21 C C5 GDP . . . M 4 -15.665 32.303 20.897 0.5 63.44 ? C5 GDP 763 C 1 HETATM 22 C C6 GDP . . . M 4 -14.259 32.534 21.056 0.5 63.57 ? C6 GDP 763 C 1 HETATM 23 O O6 GDP . . . M 4 -13.373 32.5 20.203 0.5 63.65 ? O6 GDP 763 C 1 HETATM 24 N N1 GDP . . . M 4 -13.937 32.831 22.385 0.5 63.58 ? N1 GDP 763 C 1 HETATM 25 C C2 GDP . . . M 4 -14.842 32.899 23.429 0.5 63.52 ? C2 GDP 763 C 1 HETATM 26 N N2 GDP . . . M 4 -14.346 33.196 24.63 0.5 63.61 ? N2 GDP 763 C 1 HETATM 27 N N3 GDP . . . M 4 -16.159 32.684 23.29 0.5 63.41 ? N3 GDP 763 C 1 HETATM 28 C C4 GDP . . . M 4 -16.499 32.391 21.997 0.5 63.32 ? C4 GDP 763 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 23 _model_server_stats.query_time_ms 314 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #