data_4LRW # _model_server_result.job_id Kce0jOnVBt21fOfDmF31ug _model_server_result.datetime_utc '2024-11-25 23:55:28' _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 4lrw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":203}' # _entry.id 4LRW # _exptl.entry_id 4LRW _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 90 _cell.angle_gamma 120 _cell.entry_id 4LRW _cell.length_a 82.862 _cell.length_b 82.862 _cell.length_c 38.397 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LRW _symmetry.cell_setting ? _symmetry.Int_Tables_number 143 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 PISA monomeric 1 software_defined_assembly 2 PISA monomeric 1 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F,G,H,I,J 1 1 A,C,D,E,I 2 1 B,F,G,H,J 3 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 H 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 A OG SER 18 A SER 17 1_555 C MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.103 ? metalc ? metalc2 C MG MG . A MG 201 1_555 D O1B GDP . A GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.107 ? metalc ? metalc3 C MG MG . A MG 201 1_555 I O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.06 ? metalc ? metalc4 C MG MG . A MG 201 1_555 I O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc5 C MG MG . A MG 201 1_555 I O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc6 C MG MG . A MG 201 1_555 I O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? metalc ? metalc7 E MG MG . A MG 203 1_555 I O HOH . A HOH 325 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.167 ? metalc ? metalc8 E MG MG . A MG 203 1_555 I O HOH . A HOH 326 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.154 ? metalc ? metalc9 B OG SER 18 B SER 17 1_555 G MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.122 ? metalc ? metalc10 F MG MG . B MG 201 1_555 J O HOH . B HOH 322 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc11 F MG MG . B MG 201 1_555 J O HOH . B HOH 323 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.271 ? metalc ? metalc12 G MG MG . B MG 202 1_555 H O1B GDP . B GDP 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc13 G MG MG . B MG 202 1_555 J O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.102 ? metalc ? metalc14 G MG MG . B MG 202 1_555 J O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc15 G MG MG . B MG 202 1_555 J O HOH . B HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? metalc ? metalc16 G MG MG . B MG 202 1_555 J O HOH . B HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.903 ? # _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 4LRW _atom_sites.fract_transf_matrix[1][1] 0.012068 _atom_sites.fract_transf_matrix[1][2] 0.006968 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013935 _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] 0.026044 _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 1 201 200 MG MG . D 3 GDP A 1 202 220 GDP GDP . E 2 MG A 1 203 205 MG MG . F 2 MG B 1 201 205 MG MG . G 2 MG B 1 202 200 MG MG . H 3 GDP B 1 203 220 GDP GDP . I 4 HOH A 1 301 1 HOH HOH . I 4 HOH A 2 302 2 HOH HOH . I 4 HOH A 3 303 5 HOH HOH . I 4 HOH A 4 304 9 HOH HOH . I 4 HOH A 5 305 11 HOH HOH . I 4 HOH A 6 306 12 HOH HOH . I 4 HOH A 7 307 13 HOH HOH . I 4 HOH A 8 308 16 HOH HOH . I 4 HOH A 9 309 18 HOH HOH . I 4 HOH A 10 310 20 HOH HOH . I 4 HOH A 11 311 24 HOH HOH . I 4 HOH A 12 312 26 HOH HOH . I 4 HOH A 13 313 27 HOH HOH . I 4 HOH A 14 314 28 HOH HOH . I 4 HOH A 15 315 30 HOH HOH . I 4 HOH A 16 316 31 HOH HOH . I 4 HOH A 17 317 32 HOH HOH . I 4 HOH A 18 318 35 HOH HOH . I 4 HOH A 19 319 36 HOH HOH . I 4 HOH A 20 320 38 HOH HOH . I 4 HOH A 21 321 41 HOH HOH . I 4 HOH A 22 322 42 HOH HOH . I 4 HOH A 23 323 44 HOH HOH . I 4 HOH A 24 324 45 HOH HOH . I 4 HOH A 25 325 46 HOH HOH . I 4 HOH A 26 326 47 HOH HOH . J 4 HOH B 1 301 3 HOH HOH . J 4 HOH B 2 302 4 HOH HOH . J 4 HOH B 3 303 6 HOH HOH . J 4 HOH B 4 304 7 HOH HOH . J 4 HOH B 5 305 8 HOH HOH . J 4 HOH B 6 306 10 HOH HOH . J 4 HOH B 7 307 14 HOH HOH . J 4 HOH B 8 308 15 HOH HOH . J 4 HOH B 9 309 17 HOH HOH . J 4 HOH B 10 310 19 HOH HOH . J 4 HOH B 11 311 21 HOH HOH . J 4 HOH B 12 312 22 HOH HOH . J 4 HOH B 13 313 23 HOH HOH . J 4 HOH B 14 314 25 HOH HOH . J 4 HOH B 15 315 29 HOH HOH . J 4 HOH B 16 316 33 HOH HOH . J 4 HOH B 17 317 34 HOH HOH . J 4 HOH B 18 318 37 HOH HOH . J 4 HOH B 19 319 39 HOH HOH . J 4 HOH B 20 320 40 HOH HOH . J 4 HOH B 21 321 43 HOH HOH . J 4 HOH B 22 322 48 HOH HOH . J 4 HOH B 23 323 49 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 . . . H 3 25.96 -20.921 -22.767 1 15.76 ? PB GDP 203 B 1 HETATM 2 O O1B GDP . . . H 3 24.662 -20.737 -22.022 1 20.01 ? O1B GDP 203 B 1 HETATM 3 O O2B GDP . . . H 3 27.014 -21.482 -21.844 1 20.63 ? O2B GDP 203 B 1 HETATM 4 O O3B GDP . . . H 3 25.762 -21.881 -23.912 1 14.54 ? O3B GDP 203 B 1 HETATM 5 O O3A GDP . . . H 3 26.473 -19.52 -23.364 1 16.76 ? O3A GDP 203 B 1 HETATM 6 P PA GDP . . . H 3 25.687 -18.138 -23.115 1 13.65 ? PA GDP 203 B 1 HETATM 7 O O1A GDP . . . H 3 25.643 -17.803 -21.645 1 12.06 ? O1A GDP 203 B 1 HETATM 8 O O2A GDP . . . H 3 24.294 -18.175 -23.695 1 16.65 ? O2A GDP 203 B 1 HETATM 9 O O5' GDP . . . H 3 26.614 -17.094 -23.914 1 15.62 ? O5' GDP 203 B 1 HETATM 10 C C5' GDP . . . H 3 27.828 -16.635 -23.323 1 13.73 ? C5' GDP 203 B 1 HETATM 11 C C4' GDP . . . H 3 28.182 -15.27 -23.891 1 14.03 ? C4' GDP 203 B 1 HETATM 12 O O4' GDP . . . H 3 28.191 -15.323 -25.318 1 14.65 ? O4' GDP 203 B 1 HETATM 13 C C3' GDP . . . H 3 27.141 -14.245 -23.482 1 16.46 ? C3' GDP 203 B 1 HETATM 14 O O3' GDP . . . H 3 27.752 -13.231 -22.681 1 20.39 ? O3' GDP 203 B 1 HETATM 15 C C2' GDP . . . H 3 26.621 -13.645 -24.772 1 17.37 ? C2' GDP 203 B 1 HETATM 16 O O2' GDP . . . H 3 26.665 -12.217 -24.705 1 25.75 ? O2' GDP 203 B 1 HETATM 17 C C1' GDP . . . H 3 27.545 -14.17 -25.861 1 13.86 ? C1' GDP 203 B 1 HETATM 18 N N9 GDP . . . H 3 26.761 -14.543 -27.064 1 13.35 ? N9 GDP 203 B 1 HETATM 19 C C8 GDP . . . H 3 25.829 -15.512 -27.126 1 15.45 ? C8 GDP 203 B 1 HETATM 20 N N7 GDP . . . H 3 25.3 -15.604 -28.372 1 20.1 ? N7 GDP 203 B 1 HETATM 21 C C5 GDP . . . H 3 25.907 -14.679 -29.138 1 17.27 ? C5 GDP 203 B 1 HETATM 22 C C6 GDP . . . H 3 25.825 -14.242 -30.552 1 14.39 ? C6 GDP 203 B 1 HETATM 23 O O6 GDP . . . H 3 25.031 -14.785 -31.348 1 15.46 ? O6 GDP 203 B 1 HETATM 24 N N1 GDP . . . H 3 26.627 -13.248 -30.95 1 14.47 ? N1 GDP 203 B 1 HETATM 25 C C2 GDP . . . H 3 27.493 -12.645 -30.114 1 18.54 ? C2 GDP 203 B 1 HETATM 26 N N2 GDP . . . H 3 28.269 -11.646 -30.597 1 18.63 ? N2 GDP 203 B 1 HETATM 27 N N3 GDP . . . H 3 27.621 -12.993 -28.807 1 18.86 ? N3 GDP 203 B 1 HETATM 28 C C4 GDP . . . H 3 26.87 -13.985 -28.272 1 17.83 ? C4 GDP 203 B 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 309 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #