data_4JVS # _model_server_result.job_id D4oa9I7NZZyj5jzVGeWoPA _model_server_result.datetime_utc '2024-10-12 19:22:26' _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 4jvs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":400}' # _entry.id 4JVS # _exptl.entry_id 4JVS _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 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 120 _cell.entry_id 4JVS _cell.length_a 95.561 _cell.length_b 95.561 _cell.length_c 197.724 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4JVS _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 4 _struct_asym.id D _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 B OG SER 29 B SER 25 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.7 ? metalc ? metalc2 B OG1 THR 47 B THR 43 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc3 D O2B GDP . B GDP 400 1_555 F MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.052 ? # _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 93 n n PB O2B GDP sing 94 n n PB O3B GDP sing 95 n n PB O3A GDP sing 96 n n O2B HOB2 GDP sing 97 n n O3B HOB3 GDP sing 98 n n O3A PA GDP sing 99 n n PA O1A GDP doub 100 n n PA O2A GDP sing 101 n n PA O5' GDP sing 102 n n O2A HOA2 GDP sing 103 n n O5' C5' GDP sing 104 n n C5' C4' GDP sing 105 n n C5' H5' GDP sing 106 n n C5' "H5''" GDP sing 107 n n C4' O4' GDP sing 108 n n C4' C3' GDP sing 109 n n C4' H4' GDP sing 110 n n O4' C1' GDP sing 111 n n C3' O3' GDP sing 112 n n C3' C2' GDP sing 113 n n C3' H3' GDP sing 114 n n O3' HO3' GDP sing 115 n n C2' O2' GDP sing 116 n n C2' C1' GDP sing 117 n n C2' H2' GDP sing 118 n n O2' HO2' GDP sing 119 n n C1' N9 GDP sing 120 n n C1' H1' GDP sing 121 n n N9 C8 GDP sing 122 n y N9 C4 GDP sing 123 n y C8 N7 GDP doub 124 n y C8 H8 GDP sing 125 n n N7 C5 GDP sing 126 n y C5 C6 GDP sing 127 n n C5 C4 GDP doub 128 n y C6 O6 GDP doub 129 n n C6 N1 GDP sing 130 n n N1 C2 GDP sing 131 n n N1 HN1 GDP sing 132 n n C2 N2 GDP sing 133 n n C2 N3 GDP doub 134 n n N2 HN21 GDP sing 135 n n N2 HN22 GDP sing 136 n n N3 C4 GDP sing 137 n n # _atom_sites.entry_id 4JVS _atom_sites.fract_transf_matrix[1][1] 0.010465 _atom_sites.fract_transf_matrix[1][2] 0.006042 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012083 _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] 0.005058 _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 3 ACY A 1 701 1433 ACY ACY . D 4 GDP B 1 400 400 GDP GDP . E 5 AF3 B 1 401 401 AF3 AF3 . F 6 MG B 1 402 402 MG MG . G 7 HOH A 1 801 1 HOH HOH . H 7 HOH B 1 501 2 HOH HOH . H 7 HOH B 2 502 4 HOH HOH . H 7 HOH B 3 503 5 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 4 22.371 -33.626 10.08 1 34.27 ? PB GDP 400 B 1 HETATM 2 O O1B GDP . . . D 4 22.323 -33.548 8.545 1 38.71 ? O1B GDP 400 B 1 HETATM 3 O O2B GDP . . . D 4 23.82 -33.336 10.516 1 36.23 ? O2B GDP 400 B 1 HETATM 4 O O3B GDP . . . D 4 21.87 -34.958 10.581 1 29.19 ? O3B GDP 400 B 1 HETATM 5 O O3A GDP . . . D 4 21.419 -32.501 10.627 1 35.7 ? O3A GDP 400 B 1 HETATM 6 P PA GDP . . . D 4 21.298 -32.152 12.157 1 38.03 ? PA GDP 400 B 1 HETATM 7 O O1A GDP . . . D 4 21.844 -30.771 12.419 1 37.26 ? O1A GDP 400 B 1 HETATM 8 O O2A GDP . . . D 4 22.048 -33.128 13.011 1 34.1 ? O2A GDP 400 B 1 HETATM 9 O O5' GDP . . . D 4 19.761 -32.227 12.44 1 37.55 ? O5' GDP 400 B 1 HETATM 10 C C5' GDP . . . D 4 19.313 -31.261 13.313 1 43.32 ? C5' GDP 400 B 1 HETATM 11 C C4' GDP . . . D 4 17.986 -30.66 12.916 1 40.22 ? C4' GDP 400 B 1 HETATM 12 O O4' GDP . . . D 4 16.919 -31.571 13.057 1 40.31 ? O4' GDP 400 B 1 HETATM 13 C C3' GDP . . . D 4 17.851 -29.599 13.932 1 43.2 ? C3' GDP 400 B 1 HETATM 14 O O3' GDP . . . D 4 18.002 -28.357 13.357 1 47.39 ? O3' GDP 400 B 1 HETATM 15 C C2' GDP . . . D 4 16.567 -29.874 14.618 1 42.63 ? C2' GDP 400 B 1 HETATM 16 O O2' GDP . . . D 4 15.57 -29.007 14.209 1 48.11 ? O2' GDP 400 B 1 HETATM 17 C C1' GDP . . . D 4 16.264 -31.296 14.266 1 39.51 ? C1' GDP 400 B 1 HETATM 18 N N9 GDP . . . D 4 16.566 -32.295 15.298 1 40.84 ? N9 GDP 400 B 1 HETATM 19 C C8 GDP . . . D 4 17.728 -32.962 15.48 1 39.22 ? C8 GDP 400 B 1 HETATM 20 N N7 GDP . . . D 4 17.647 -33.818 16.502 1 36.88 ? N7 GDP 400 B 1 HETATM 21 C C5 GDP . . . D 4 16.416 -33.747 17.022 1 37.3 ? C5 GDP 400 B 1 HETATM 22 C C6 GDP . . . D 4 15.762 -34.429 18.133 1 39.75 ? C6 GDP 400 B 1 HETATM 23 O O6 GDP . . . D 4 16.345 -35.262 18.81 1 38.16 ? O6 GDP 400 B 1 HETATM 24 N N1 GDP . . . D 4 14.438 -34.095 18.409 1 41.91 ? N1 GDP 400 B 1 HETATM 25 C C2 GDP . . . D 4 13.68 -33.137 17.676 1 37.63 ? C2 GDP 400 B 1 HETATM 26 N N2 GDP . . . D 4 12.312 -32.845 18.008 1 37.88 ? N2 GDP 400 B 1 HETATM 27 N N3 GDP . . . D 4 14.284 -32.502 16.642 1 38.19 ? N3 GDP 400 B 1 HETATM 28 C C4 GDP . . . D 4 15.695 -32.792 16.283 1 38.9 ? C4 GDP 400 B 1 # _model_server_stats.io_time_ms 0 _model_server_stats.parse_time_ms 129 _model_server_stats.create_model_time_ms 21 _model_server_stats.query_time_ms 517 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 28 #