data_3T1V # _model_server_result.job_id jDkzX8Io0-KCA0GdklQ3Ow _model_server_result.datetime_utc '2024-11-16 13:58:05' _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 3t1v # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":274}' # _entry.id 3T1V # _exptl.entry_id 3T1V _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 104.17 _cell.angle_gamma 90 _cell.entry_id 3T1V _cell.length_a 94.38 _cell.length_b 48.87 _cell.length_c 100.66 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3T1V _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # 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 PISA monomeric 1 author_and_software_defined_assembly 3 PISA monomeric 1 author_and_software_defined_assembly 4 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,E,I 1 1 B,F,J 2 1 C,G,K 3 1 D,H,L 4 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 ? 2 E N N ? 2 F N N ? 2 G N N ? 2 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 covale ? covale1 A C GLU 45 A GLU 43 1_555 A N MSE 46 A MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale2 A C MSE 46 A MSE 44 1_555 A N VAL 47 A VAL 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 A C SER 118 A SER 116 1_555 A N MSE 119 A MSE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.309 ? covale ? covale4 A C MSE 119 A MSE 117 1_555 A N ARG 120 A ARG 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 A C ASN 121 A ASN 119 1_555 A N MSE 122 A MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale6 A C MSE 122 A MSE 120 1_555 A N ARG 123 A ARG 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale7 A C GLU 154 A GLU 152 1_555 A N MSE 155 A MSE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.323 ? covale ? covale8 A C MSE 155 A MSE 153 1_555 A N VAL 156 A VAL 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale9 B C GLU 45 B GLU 43 1_555 B N MSE 46 B MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? covale ? covale10 B C MSE 46 B MSE 44 1_555 B N VAL 47 B VAL 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale11 B C SER 118 B SER 116 1_555 B N MSE 119 B MSE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale12 B C MSE 119 B MSE 117 1_555 B N ARG 120 B ARG 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale13 B C ASN 121 B ASN 119 1_555 B N MSE 122 B MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale14 B C MSE 122 B MSE 120 1_555 B N ARG 123 B ARG 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale15 B C GLU 154 B GLU 152 1_555 B N MSE 155 B MSE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale16 B C MSE 155 B MSE 153 1_555 B N VAL 156 B VAL 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.341 ? covale ? covale17 C C GLU 45 C GLU 43 1_555 C N MSE 46 C MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.311 ? covale ? covale18 C C MSE 46 C MSE 44 1_555 C N VAL 47 C VAL 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.348 ? covale ? covale19 C C SER 118 C SER 116 1_555 C N MSE 119 C MSE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale20 C C MSE 119 C MSE 117 1_555 C N ARG 120 C ARG 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale21 C C ASN 121 C ASN 119 1_555 C N MSE 122 C MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale22 C C MSE 122 C MSE 120 1_555 C N ARG 123 C ARG 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale23 C C GLU 154 C GLU 152 1_555 C N MSE 155 C MSE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale24 C C MSE 155 C MSE 153 1_555 C N VAL 156 C VAL 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale25 D C GLU 45 D GLU 43 1_555 D N MSE 46 D MSE 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.318 ? covale ? covale26 D C MSE 46 D MSE 44 1_555 D N VAL 47 D VAL 45 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale27 D C SER 118 D SER 116 1_555 D N MSE 119 D MSE 117 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.32 ? covale ? covale28 D C MSE 119 D MSE 117 1_555 D N ARG 120 D ARG 118 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.338 ? covale ? covale29 D C ASN 121 D ASN 119 1_555 D N MSE 122 D MSE 120 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale30 D C MSE 122 D MSE 120 1_555 D N ARG 123 D ARG 121 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale31 D C GLU 154 D GLU 152 1_555 D N MSE 155 D MSE 153 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale32 D C MSE 155 D MSE 153 1_555 D N VAL 156 D VAL 154 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? # _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 3T1V _atom_sites.fract_transf_matrix[1][1] 0.010595 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002675 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020462 _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] 0.010246 _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 E 2 GDP A 1 274 274 GDP GDP . F 2 GDP B 1 274 274 GDP GDP . G 2 GDP C 1 274 274 GDP GDP . H 2 GDP D 1 274 274 GDP GDP . I 3 HOH A 1 197 197 HOH HOH . I 3 HOH A 2 198 198 HOH HOH . I 3 HOH A 3 199 199 HOH HOH . I 3 HOH A 4 200 200 HOH HOH . I 3 HOH A 5 201 201 HOH HOH . I 3 HOH A 6 202 202 HOH HOH . I 3 HOH A 7 203 203 HOH HOH . I 3 HOH A 8 204 204 HOH HOH . I 3 HOH A 9 205 205 HOH HOH . I 3 HOH A 10 206 206 HOH HOH . I 3 HOH A 11 207 207 HOH HOH . I 3 HOH A 12 208 208 HOH HOH . I 3 HOH A 13 209 209 HOH HOH . I 3 HOH A 14 210 210 HOH HOH . I 3 HOH A 15 211 211 HOH HOH . I 3 HOH A 16 212 212 HOH HOH . I 3 HOH A 17 213 213 HOH HOH . I 3 HOH A 18 214 214 HOH HOH . I 3 HOH A 19 215 215 HOH HOH . I 3 HOH A 20 216 196 HOH HOH . J 3 HOH B 1 197 197 HOH HOH . J 3 HOH B 2 198 198 HOH HOH . J 3 HOH B 3 199 199 HOH HOH . J 3 HOH B 4 200 200 HOH HOH . J 3 HOH B 5 201 201 HOH HOH . J 3 HOH B 6 202 202 HOH HOH . J 3 HOH B 7 203 203 HOH HOH . J 3 HOH B 8 204 204 HOH HOH . J 3 HOH B 9 205 205 HOH HOH . J 3 HOH B 10 206 206 HOH HOH . J 3 HOH B 11 207 207 HOH HOH . J 3 HOH B 12 208 208 HOH HOH . J 3 HOH B 13 209 196 HOH HOH . K 3 HOH C 1 197 197 HOH HOH . K 3 HOH C 2 198 198 HOH HOH . K 3 HOH C 3 199 199 HOH HOH . K 3 HOH C 4 200 200 HOH HOH . K 3 HOH C 5 201 201 HOH HOH . K 3 HOH C 6 202 202 HOH HOH . K 3 HOH C 7 203 203 HOH HOH . K 3 HOH C 8 204 204 HOH HOH . K 3 HOH C 9 205 205 HOH HOH . K 3 HOH C 10 206 206 HOH HOH . K 3 HOH C 11 207 207 HOH HOH . K 3 HOH C 12 208 208 HOH HOH . K 3 HOH C 13 209 209 HOH HOH . K 3 HOH C 14 210 210 HOH HOH . K 3 HOH C 15 211 211 HOH HOH . K 3 HOH C 16 212 212 HOH HOH . K 3 HOH C 17 213 213 HOH HOH . K 3 HOH C 18 214 214 HOH HOH . K 3 HOH C 19 215 215 HOH HOH . K 3 HOH C 20 216 216 HOH HOH . K 3 HOH C 21 217 217 HOH HOH . K 3 HOH C 22 218 218 HOH HOH . L 3 HOH D 1 197 197 HOH HOH . L 3 HOH D 2 198 198 HOH HOH . L 3 HOH D 3 199 199 HOH HOH . L 3 HOH D 4 200 200 HOH HOH . L 3 HOH D 5 201 201 HOH HOH . L 3 HOH D 6 202 202 HOH HOH . L 3 HOH D 7 203 203 HOH HOH . L 3 HOH D 8 204 204 HOH HOH . L 3 HOH D 9 205 205 HOH HOH . L 3 HOH D 10 206 206 HOH HOH . L 3 HOH D 11 207 207 HOH HOH . L 3 HOH D 12 208 208 HOH HOH . L 3 HOH D 13 209 209 HOH HOH . L 3 HOH D 14 210 210 HOH HOH . L 3 HOH D 15 211 211 HOH HOH . L 3 HOH D 16 212 196 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 . . . E 2 6.914 -5.153 52.493 1 22.82 ? PB GDP 274 A 1 HETATM 2 O O1B GDP . . . E 2 6.76 -3.996 51.565 1 18.36 ? O1B GDP 274 A 1 HETATM 3 O O2B GDP . . . E 2 7.252 -4.708 53.871 1 19.99 ? O2B GDP 274 A 1 HETATM 4 O O3B GDP . . . E 2 7.8 -6.276 51.975 1 19.73 ? O3B GDP 274 A 1 HETATM 5 O O3A GDP . . . E 2 5.359 -5.572 52.494 1 26.19 ? O3A GDP 274 A 1 HETATM 6 P PA GDP . . . E 2 4.793 -7.068 52.525 1 23.94 ? PA GDP 274 A 1 HETATM 7 O O1A GDP . . . E 2 5.482 -7.759 53.648 1 20.95 ? O1A GDP 274 A 1 HETATM 8 O O2A GDP . . . E 2 4.907 -7.641 51.141 1 22.16 ? O2A GDP 274 A 1 HETATM 9 O O5' GDP . . . E 2 3.247 -6.755 52.858 1 26.19 ? O5' GDP 274 A 1 HETATM 10 C C5' GDP . . . E 2 2.796 -6.225 54.106 1 28.03 ? C5' GDP 274 A 1 HETATM 11 C C4' GDP . . . E 2 1.38 -6.72 54.392 1 28.74 ? C4' GDP 274 A 1 HETATM 12 O O4' GDP . . . E 2 0.584 -6.275 53.289 1 28.24 ? O4' GDP 274 A 1 HETATM 13 C C3' GDP . . . E 2 1.309 -8.243 54.387 1 30.42 ? C3' GDP 274 A 1 HETATM 14 O O3' GDP . . . E 2 0.454 -8.716 55.407 1 32.09 ? O3' GDP 274 A 1 HETATM 15 C C2' GDP . . . E 2 0.728 -8.585 53.016 1 32.22 ? C2' GDP 274 A 1 HETATM 16 O O2' GDP . . . E 2 -0.037 -9.787 52.905 1 32.71 ? O2' GDP 274 A 1 HETATM 17 C C1' GDP . . . E 2 -0.123 -7.388 52.712 1 30.87 ? C1' GDP 274 A 1 HETATM 18 N N9 GDP . . . E 2 -0.302 -7.213 51.24 1 33.58 ? N9 GDP 274 A 1 HETATM 19 C C8 GDP . . . E 2 0.632 -7.291 50.267 1 33.58 ? C8 GDP 274 A 1 HETATM 20 N N7 GDP . . . E 2 0.099 -7.043 49.048 1 33.2 ? N7 GDP 274 A 1 HETATM 21 C C5 GDP . . . E 2 -1.209 -6.796 49.253 1 34.76 ? C5 GDP 274 A 1 HETATM 22 C C6 GDP . . . E 2 -2.394 -6.484 48.406 1 35.98 ? C6 GDP 274 A 1 HETATM 23 O O6 GDP . . . E 2 -2.276 -6.374 47.172 1 36.22 ? O6 GDP 274 A 1 HETATM 24 N N1 GDP . . . E 2 -3.585 -6.321 49.003 1 35.61 ? N1 GDP 274 A 1 HETATM 25 C C2 GDP . . . E 2 -3.734 -6.452 50.335 1 33.98 ? C2 GDP 274 A 1 HETATM 26 N N2 GDP . . . E 2 -4.948 -6.269 50.889 1 33.08 ? N2 GDP 274 A 1 HETATM 27 N N3 GDP . . . E 2 -2.697 -6.759 51.159 1 34.85 ? N3 GDP 274 A 1 HETATM 28 C C4 GDP . . . E 2 -1.454 -6.916 50.684 1 31.93 ? C4 GDP 274 A 1 # _model_server_stats.io_time_ms 17 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #