data_4FMD # _model_server_result.job_id QhTCX2qVyXFNPo_BiwWVhA _model_server_result.datetime_utc '2024-11-25 13:49:44' _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 4fmd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":202}' # _entry.id 4FMD # _exptl.entry_id 4FMD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 5 _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 90 _cell.entry_id 4FMD _cell.length_a 106.568 _cell.length_b 153.221 _cell.length_c 230.805 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4FMD _symmetry.cell_setting ? _symmetry.Int_Tables_number 23 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 2 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 PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 PISA dimeric 2 author_and_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,G,H,I,R,S 1 1 C,D,J,K,L,M,T,U 2 1 E,F,N,O,P,Q,V,W 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 ? 5 H N N ? 5 L N N ? 5 P 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 R O HOH . A HOH 401 1_555 G AL AF3 . B AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.97 ? metalc ? metalc2 B OG SER 20 B SER 25 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? metalc ? metalc3 B OG1 THR 38 B THR 43 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.311 ? metalc ? metalc4 G AL AF3 . B AF3 201 1_555 H O2B GDP . B GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? metalc ? metalc5 H O3B GDP . B GDP 202 1_555 I MG MG . B MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.939 ? metalc ? metalc6 I MG MG . B MG 203 1_555 S O HOH . B HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.138 ? metalc ? metalc7 I MG MG . B MG 203 1_555 S O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.343 ? metalc ? metalc8 T O HOH . C HOH 501 1_555 K AL AF3 . D AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.798 ? metalc ? metalc9 D OG SER 20 D SER 25 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.388 ? metalc ? metalc10 D OG1 THR 38 D THR 43 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.79 ? metalc ? metalc11 K AL AF3 . D AF3 201 1_555 L O3B GDP . D GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? metalc ? metalc12 L O3B GDP . D GDP 202 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.135 ? metalc ? metalc13 L O1B GDP . D GDP 202 1_555 M MG MG . D MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.819 ? metalc ? metalc14 M MG MG . D MG 203 1_555 U O HOH . D HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.8 ? metalc ? metalc15 M MG MG . D MG 203 1_555 U O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc16 V O HOH . E HOH 501 1_555 O AL AF3 . F AF3 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.845 ? metalc ? metalc17 F OG SER 13 F SER 25 1_555 Q MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.904 ? metalc ? metalc18 F OG1 THR 31 F THR 43 1_555 Q MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.958 ? metalc ? metalc19 O AL AF3 . F AF3 201 1_555 P O1B GDP . F GDP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? metalc ? metalc20 P O3B GDP . F GDP 202 1_555 Q MG MG . F MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? metalc ? metalc21 Q MG MG . F MG 203 1_555 W O HOH . F HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.579 ? # _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 86 n n PB O2B GDP sing 87 n n PB O3B GDP sing 88 n n PB O3A GDP sing 89 n n O2B HOB2 GDP sing 90 n n O3B HOB3 GDP sing 91 n n O3A PA GDP sing 92 n n PA O1A GDP doub 93 n n PA O2A GDP sing 94 n n PA O5' GDP sing 95 n n O2A HOA2 GDP sing 96 n n O5' C5' GDP sing 97 n n C5' C4' GDP sing 98 n n C5' H5' GDP sing 99 n n C5' "H5''" GDP sing 100 n n C4' O4' GDP sing 101 n n C4' C3' GDP sing 102 n n C4' H4' GDP sing 103 n n O4' C1' GDP sing 104 n n C3' O3' GDP sing 105 n n C3' C2' GDP sing 106 n n C3' H3' GDP sing 107 n n O3' HO3' GDP sing 108 n n C2' O2' GDP sing 109 n n C2' C1' GDP sing 110 n n C2' H2' GDP sing 111 n n O2' HO2' GDP sing 112 n n C1' N9 GDP sing 113 n n C1' H1' GDP sing 114 n n N9 C8 GDP sing 115 n y N9 C4 GDP sing 116 n y C8 N7 GDP doub 117 n y C8 H8 GDP sing 118 n n N7 C5 GDP sing 119 n y C5 C6 GDP sing 120 n n C5 C4 GDP doub 121 n y C6 O6 GDP doub 122 n n C6 N1 GDP sing 123 n n N1 C2 GDP sing 124 n n N1 HN1 GDP sing 125 n n C2 N2 GDP sing 126 n n C2 N3 GDP doub 127 n n N2 HN21 GDP sing 128 n n N2 HN22 GDP sing 129 n n N3 C4 GDP sing 130 n n # _atom_sites.entry_id 4FMD _atom_sites.fract_transf_matrix[1][1] 0.009384 _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] 0.006527 _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] 0.004333 _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 G 4 AF3 B 1 201 506 AF3 AF3 . H 5 GDP B 1 202 501 GDP GDP . I 6 MG B 1 203 502 MG MG . J 7 PGE C 1 401 1 PGE PEG . K 4 AF3 D 1 201 506 AF3 AF3 . L 5 GDP D 1 202 501 GDP GDP . M 6 MG D 1 203 502 MG MG . N 8 PEG E 1 401 2 PEG PEG . O 4 AF3 F 1 201 505 AF3 AF3 . P 5 GDP F 1 202 501 GDP GDP . Q 6 MG F 1 203 502 MG MG . R 9 HOH A 1 401 505 HOH HOH . S 9 HOH B 1 301 503 HOH HOH . S 9 HOH B 2 302 504 HOH HOH . T 9 HOH C 1 501 501 HOH HOH . U 9 HOH D 1 301 503 HOH HOH . U 9 HOH D 2 302 504 HOH HOH . V 9 HOH E 1 501 501 HOH HOH . W 9 HOH F 1 301 503 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 5 -15.618 -42.805 50.9 1 61.49 ? PB GDP 202 B 1 HETATM 2 O O1B GDP . . . H 5 -15.171 -41.601 49.95 1 57.63 ? O1B GDP 202 B 1 HETATM 3 O O2B GDP . . . H 5 -16.136 -43.96 50.093 1 65.95 ? O2B GDP 202 B 1 HETATM 4 O O3B GDP . . . H 5 -16.684 -42.241 51.961 1 61.18 ? O3B GDP 202 B 1 HETATM 5 O O3A GDP . . . H 5 -14.316 -43.363 51.674 1 62.86 ? O3A GDP 202 B 1 HETATM 6 P PA GDP . . . H 5 -14.442 -43.551 53.281 1 61.78 ? PA GDP 202 B 1 HETATM 7 O O1A GDP . . . H 5 -15.615 -44.53 53.759 1 61.73 ? O1A GDP 202 B 1 HETATM 8 O O2A GDP . . . H 5 -14.595 -42.26 53.956 1 61.61 ? O2A GDP 202 B 1 HETATM 9 O O5' GDP . . . H 5 -13.006 -44.117 53.675 1 64.25 ? O5' GDP 202 B 1 HETATM 10 C C5' GDP . . . H 5 -13.028 -45.527 53.497 1 67.6 ? C5' GDP 202 B 1 HETATM 11 C C4' GDP . . . H 5 -11.9 -46.14 54.314 1 70.58 ? C4' GDP 202 B 1 HETATM 12 O O4' GDP . . . H 5 -10.657 -45.523 53.966 1 69.78 ? O4' GDP 202 B 1 HETATM 13 C C3' GDP . . . H 5 -12.095 -45.91 55.804 1 72.26 ? C3' GDP 202 B 1 HETATM 14 O O3' GDP . . . H 5 -12.653 -47.06 56.443 1 75.15 ? O3' GDP 202 B 1 HETATM 15 C C2' GDP . . . H 5 -10.707 -45.633 56.33 1 73.23 ? C2' GDP 202 B 1 HETATM 16 O O2' GDP . . . H 5 -10.187 -46.789 56.978 1 77.27 ? O2' GDP 202 B 1 HETATM 17 C C1' GDP . . . H 5 -9.84 -45.339 55.123 1 72.06 ? C1' GDP 202 B 1 HETATM 18 N N9 GDP . . . H 5 -9.344 -43.943 55.252 1 71.86 ? N9 GDP 202 B 1 HETATM 19 C C8 GDP . . . H 5 -10.032 -42.838 54.926 1 70.62 ? C8 GDP 202 B 1 HETATM 20 N N7 GDP . . . H 5 -9.286 -41.745 55.171 1 69.89 ? N7 GDP 202 B 1 HETATM 21 C C5 GDP . . . H 5 -8.117 -42.183 55.672 1 71.9 ? C5 GDP 202 B 1 HETATM 22 C C6 GDP . . . H 5 -6.89 -41.492 56.137 1 73.18 ? C6 GDP 202 B 1 HETATM 23 O O6 GDP . . . H 5 -6.817 -40.13 56.107 1 72.69 ? O6 GDP 202 B 1 HETATM 24 N N1 GDP . . . H 5 -5.86 -42.244 56.585 1 74.6 ? N1 GDP 202 B 1 HETATM 25 C C2 GDP . . . H 5 -5.94 -43.591 56.608 1 75.17 ? C2 GDP 202 B 1 HETATM 26 N N2 GDP . . . H 5 -4.874 -44.292 57.064 1 77.08 ? N2 GDP 202 B 1 HETATM 27 N N3 GDP . . . H 5 -7.06 -44.234 56.191 1 74.82 ? N3 GDP 202 B 1 HETATM 28 C C4 GDP . . . H 5 -8.15 -43.562 55.726 1 72.87 ? C4 GDP 202 B 1 # _model_server_stats.io_time_ms 27 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #