data_6S6D # _model_server_result.job_id vR3aZyippI7Wl4K4ycVC7g _model_server_result.datetime_utc '2024-12-27 00:47:41' _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 6s6d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":401}' # _entry.id 6S6D # _exptl.entry_id 6S6D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 523.18 _entity.id 3 _entity.src_method man _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-TRIPHOSPHATE" _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 90 _cell.entry_id 6S6D _cell.length_a 71.504 _cell.length_b 81.439 _cell.length_c 246.033 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6S6D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,M,N 1 1 C,D,H,I,J,K,L,O,P 2 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 E 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 OG1 THR 21 A THR 21 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? metalc ? metalc2 A OG1 THR 42 A THR 42 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? metalc ? metalc3 E O1G GTP . A GTP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.149 ? metalc ? metalc4 E O1B GTP . A GTP 401 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.076 ? metalc ? metalc5 F MG MG . A MG 402 1_555 M O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc6 F MG MG . A MG 402 1_555 M O HOH . A HOH 507 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc7 C OG1 THR 21 B THR 21 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.989 ? metalc ? metalc8 C OG1 THR 42 B THR 42 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.472 ? metalc ? metalc9 H O1G GTP . B GTP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.295 ? metalc ? metalc10 H O1B GTP . B GTP 401 1_555 I MG MG . B MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.454 ? metalc ? metalc11 I MG MG . B MG 402 1_555 O O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc12 I MG MG . B MG 402 1_555 O O HOH . B HOH 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? # _chem_comp.formula 'C10 H16 N5 O14 P3' _chem_comp.formula_weight 523.18 _chem_comp.id GTP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-TRIPHOSPHATE" _chem_comp.type non-polymer _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 PG O1G GTP doub 192 n n PG O2G GTP sing 193 n n PG O3G GTP sing 194 n n PG O3B GTP sing 195 n n O2G HOG2 GTP sing 196 n n O3G HOG3 GTP sing 197 n n O3B PB GTP sing 198 n n PB O1B GTP doub 199 n n PB O2B GTP sing 200 n n PB O3A GTP sing 201 n n O2B HOB2 GTP sing 202 n n O3A PA GTP sing 203 n n PA O1A GTP doub 204 n n PA O2A GTP sing 205 n n PA O5' GTP sing 206 n n O2A HOA2 GTP sing 207 n n O5' C5' GTP sing 208 n n C5' C4' GTP sing 209 n n C5' H5' GTP sing 210 n n C5' "H5''" GTP sing 211 n n C4' O4' GTP sing 212 n n C4' C3' GTP sing 213 n n C4' H4' GTP sing 214 n n O4' C1' GTP sing 215 n n C3' O3' GTP sing 216 n n C3' C2' GTP sing 217 n n C3' H3' GTP sing 218 n n O3' HO3' GTP sing 219 n n C2' O2' GTP sing 220 n n C2' C1' GTP sing 221 n n C2' H2' GTP sing 222 n n O2' HO2' GTP sing 223 n n C1' N9 GTP sing 224 n n C1' H1' GTP sing 225 n n N9 C8 GTP sing 226 n y N9 C4 GTP sing 227 n y C8 N7 GTP doub 228 n y C8 H8 GTP sing 229 n n N7 C5 GTP sing 230 n y C5 C6 GTP sing 231 n n C5 C4 GTP doub 232 n y C6 O6 GTP doub 233 n n C6 N1 GTP sing 234 n n N1 C2 GTP sing 235 n n N1 HN1 GTP sing 236 n n C2 N2 GTP sing 237 n n C2 N3 GTP doub 238 n n N2 HN21 GTP sing 239 n n N2 HN22 GTP sing 240 n n N3 C4 GTP sing 241 n n # _atom_sites.entry_id 6S6D _atom_sites.fract_transf_matrix[1][1] 0.013985 _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] 0.012279 _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] 0.004064 _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 3 GTP A 1 401 1 GTP GTP . F 4 MG A 1 402 1 MG MG . G 5 GDP C 1 401 3 GDP GDP . H 3 GTP B 1 401 2 GTP GTP . I 4 MG B 1 402 2 MG MG . J 6 9JE B 1 403 1 9JE PEN . K 6 9JE B 1 404 2 9JE PEN . L 5 GDP D 1 401 4 GDP GDP . M 7 HOH A 1 501 113 HOH HOH . M 7 HOH A 2 502 117 HOH HOH . M 7 HOH A 3 503 119 HOH HOH . M 7 HOH A 4 504 112 HOH HOH . M 7 HOH A 5 505 111 HOH HOH . M 7 HOH A 6 506 19 HOH HOH . M 7 HOH A 7 507 118 HOH HOH . M 7 HOH A 8 508 72 HOH HOH . M 7 HOH A 9 509 102 HOH HOH . M 7 HOH A 10 510 88 HOH HOH . M 7 HOH A 11 511 21 HOH HOH . M 7 HOH A 12 512 17 HOH HOH . M 7 HOH A 13 513 28 HOH HOH . M 7 HOH A 14 514 12 HOH HOH . N 7 HOH C 1 501 25 HOH HOH . N 7 HOH C 2 502 116 HOH HOH . N 7 HOH C 3 503 9 HOH HOH . N 7 HOH C 4 504 110 HOH HOH . N 7 HOH C 5 505 53 HOH HOH . N 7 HOH C 6 506 68 HOH HOH . N 7 HOH C 7 507 64 HOH HOH . N 7 HOH C 8 508 20 HOH HOH . N 7 HOH C 9 509 24 HOH HOH . N 7 HOH C 10 510 37 HOH HOH . N 7 HOH C 11 511 49 HOH HOH . N 7 HOH C 12 512 115 HOH HOH . N 7 HOH C 13 513 1 HOH HOH . N 7 HOH C 14 514 114 HOH HOH . N 7 HOH C 15 515 40 HOH HOH . O 7 HOH B 1 501 2 HOH HOH . O 7 HOH B 2 502 3 HOH HOH . O 7 HOH B 3 503 43 HOH HOH . O 7 HOH B 4 504 4 HOH HOH . O 7 HOH B 5 505 41 HOH HOH . O 7 HOH B 6 506 78 HOH HOH . O 7 HOH B 7 507 27 HOH HOH . O 7 HOH B 8 508 50 HOH HOH . O 7 HOH B 9 509 60 HOH HOH . O 7 HOH B 10 510 18 HOH HOH . O 7 HOH B 11 511 101 HOH HOH . O 7 HOH B 12 512 42 HOH HOH . O 7 HOH B 13 513 16 HOH HOH . O 7 HOH B 14 514 31 HOH HOH . O 7 HOH B 15 515 23 HOH HOH . O 7 HOH B 16 516 104 HOH HOH . O 7 HOH B 17 517 22 HOH HOH . O 7 HOH B 18 518 6 HOH HOH . P 7 HOH D 1 501 26 HOH HOH . P 7 HOH D 2 502 65 HOH HOH . P 7 HOH D 3 503 5 HOH HOH . P 7 HOH D 4 504 30 HOH HOH . P 7 HOH D 5 505 8 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 PG GTP . . . E 3 7.139 6.383 21.005 1 42.34 ? PG GTP 401 A 1 HETATM 2 O O1G GTP . . . E 3 5.624 6.185 20.949 1 41.56 ? O1G GTP 401 A 1 HETATM 3 O O2G GTP . . . E 3 7.534 7.54 22 1 44.89 -1 O2G GTP 401 A 1 HETATM 4 O O3G GTP . . . E 3 7.837 5.104 21.325 1 41.84 ? O3G GTP 401 A 1 HETATM 5 O O3B GTP . . . E 3 7.671 6.809 19.557 1 39.98 ? O3B GTP 401 A 1 HETATM 6 P PB GTP . . . E 3 7.395 6.056 18.164 1 41.87 ? PB GTP 401 A 1 HETATM 7 O O1B GTP . . . E 3 6.049 5.44 18.281 1 33.2 -1 O1B GTP 401 A 1 HETATM 8 O O2B GTP . . . E 3 8.603 5.223 17.824 1 36.29 ? O2B GTP 401 A 1 HETATM 9 O O3A GTP . . . E 3 7.448 7.221 17.068 1 36.18 ? O3A GTP 401 A 1 HETATM 10 P PA GTP . . . E 3 6.387 7.874 16.081 1 41.5 ? PA GTP 401 A 1 HETATM 11 O O1A GTP . . . E 3 5.49 8.697 16.947 1 42.72 -1 O1A GTP 401 A 1 HETATM 12 O O2A GTP . . . E 3 5.751 6.838 15.21 1 40.48 ? O2A GTP 401 A 1 HETATM 13 O O5' GTP . . . E 3 7.25 8.803 15.092 1 40.46 ? O5' GTP 401 A 1 HETATM 14 C C5' GTP . . . E 3 7.969 9.948 15.543 1 44.44 ? C5' GTP 401 A 1 HETATM 15 C C4' GTP . . . E 3 8.187 10.89 14.382 1 43.82 ? C4' GTP 401 A 1 HETATM 16 O O4' GTP . . . E 3 9.065 10.265 13.413 1 39.85 ? O4' GTP 401 A 1 HETATM 17 C C3' GTP . . . E 3 6.922 11.311 13.609 1 43.21 ? C3' GTP 401 A 1 HETATM 18 O O3' GTP . . . E 3 7.058 12.678 13.286 1 51.78 ? O3' GTP 401 A 1 HETATM 19 C C2' GTP . . . E 3 7.019 10.529 12.308 1 45.92 ? C2' GTP 401 A 1 HETATM 20 O O2' GTP . . . E 3 6.371 11.111 11.195 1 40.89 ? O2' GTP 401 A 1 HETATM 21 C C1' GTP . . . E 3 8.536 10.501 12.123 1 40.14 ? C1' GTP 401 A 1 HETATM 22 N N9 GTP . . . E 3 8.924 9.398 11.264 1 42.68 ? N9 GTP 401 A 1 HETATM 23 C C8 GTP . . . E 3 8.487 8.095 11.401 1 41.74 ? C8 GTP 401 A 1 HETATM 24 N N7 GTP . . . E 3 8.959 7.291 10.479 1 45.4 ? N7 GTP 401 A 1 HETATM 25 C C5 GTP . . . E 3 9.759 8.12 9.697 1 44.48 ? C5 GTP 401 A 1 HETATM 26 C C6 GTP . . . E 3 10.522 7.814 8.549 1 44.86 ? C6 GTP 401 A 1 HETATM 27 O O6 GTP . . . E 3 10.642 6.735 7.957 1 56.55 ? O6 GTP 401 A 1 HETATM 28 N N1 GTP . . . E 3 11.19 8.93 8.079 1 45.54 ? N1 GTP 401 A 1 HETATM 29 C C2 GTP . . . E 3 11.138 10.185 8.616 1 42.84 ? C2 GTP 401 A 1 HETATM 30 N N2 GTP . . . E 3 11.881 11.109 7.985 1 42.15 ? N2 GTP 401 A 1 HETATM 31 N N3 GTP . . . E 3 10.399 10.499 9.679 1 44.66 ? N3 GTP 401 A 1 HETATM 32 C C4 GTP . . . E 3 9.742 9.419 10.164 1 44.22 ? C4 GTP 401 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 331 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #