data_5GP1 # _model_server_result.job_id i-Pe3zZis8Zjx960BEXSgw _model_server_result.datetime_utc '2024-11-08 03:16:56' _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 5gp1 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"R","auth_seq_id":304}' # _entry.id 5GP1 # _exptl.entry_id 5GP1 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _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 120 _cell.entry_id 5GP1 _cell.length_a 123.77 _cell.length_b 123.77 _cell.length_c 119.36 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5GP1 _symmetry.cell_setting ? _symmetry.Int_Tables_number 169 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 61' # 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 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,D,E,F,G,H,I,J,S 1 1 B,K,L,M,N,T 2 1 C,O,P,Q,R,U 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 ? 4 J N N ? 4 N N N ? 4 R 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 NZ LYS 30 A LYS 29 1_555 D O3 SO4 . A SO4 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.295 ? covale ? covale2 A NE ARG 42 A ARG 41 1_555 E O3 SO4 . A SO4 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag n _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _chem_comp.type 'l-peptide linking' _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 5GP1 _atom_sites.fract_transf_matrix[1][1] 0.00808 _atom_sites.fract_transf_matrix[1][2] 0.004665 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009329 _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] 0.008378 _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 D 2 SO4 A 1 301 267 SO4 SO4 . E 2 SO4 A 1 302 268 SO4 SO4 . F 2 SO4 A 1 303 269 SO4 SO4 . G 2 SO4 A 1 304 270 SO4 SO4 . H 2 SO4 A 1 305 297 SO4 SO4 . I 3 GTA A 1 306 266 GTA GTA . J 4 SAH A 1 307 298 SAH SAH . K 2 SO4 B 1 301 267 SO4 SO4 . L 2 SO4 B 1 302 285 SO4 SO4 . M 3 GTA B 1 303 266 GTA GTA . N 4 SAH B 1 304 286 SAH SAH . O 2 SO4 C 1 301 266 SO4 SO4 . P 5 NI C 1 302 288 NI NI . Q 3 GTA C 1 303 265 GTA GTA . R 4 SAH C 1 304 289 SAH SAH . S 6 HOH A 1 401 286 HOH HOH . S 6 HOH A 2 402 287 HOH HOH . S 6 HOH A 3 403 282 HOH HOH . S 6 HOH A 4 404 281 HOH HOH . S 6 HOH A 5 405 302 HOH HOH . S 6 HOH A 6 406 283 HOH HOH . S 6 HOH A 7 407 272 HOH HOH . S 6 HOH A 8 408 292 HOH HOH . S 6 HOH A 9 409 277 HOH HOH . S 6 HOH A 10 410 278 HOH HOH . S 6 HOH A 11 411 274 HOH HOH . S 6 HOH A 12 412 285 HOH HOH . S 6 HOH A 13 413 299 HOH HOH . S 6 HOH A 14 414 279 HOH HOH . S 6 HOH A 15 415 291 HOH HOH . S 6 HOH A 16 416 294 HOH HOH . S 6 HOH A 17 417 289 HOH HOH . S 6 HOH A 18 418 295 HOH HOH . S 6 HOH A 19 419 290 HOH HOH . S 6 HOH A 20 420 284 HOH HOH . S 6 HOH A 21 421 288 HOH HOH . S 6 HOH A 22 422 276 HOH HOH . S 6 HOH A 23 423 293 HOH HOH . S 6 HOH A 24 424 296 HOH HOH . S 6 HOH A 25 425 280 HOH HOH . S 6 HOH A 26 426 300 HOH HOH . S 6 HOH A 27 427 273 HOH HOH . S 6 HOH A 28 428 271 HOH HOH . S 6 HOH A 29 429 303 HOH HOH . S 6 HOH A 30 430 301 HOH HOH . S 6 HOH A 31 431 275 HOH HOH . T 6 HOH B 1 401 275 HOH HOH . T 6 HOH B 2 402 278 HOH HOH . T 6 HOH B 3 403 270 HOH HOH . T 6 HOH B 4 404 287 HOH HOH . T 6 HOH B 5 405 284 HOH HOH . T 6 HOH B 6 406 277 HOH HOH . T 6 HOH B 7 407 272 HOH HOH . T 6 HOH B 8 408 279 HOH HOH . T 6 HOH B 9 409 268 HOH HOH . T 6 HOH B 10 410 273 HOH HOH . T 6 HOH B 11 411 287 HOH HOH . T 6 HOH B 12 412 276 HOH HOH . T 6 HOH B 13 413 280 HOH HOH . T 6 HOH B 14 414 281 HOH HOH . T 6 HOH B 15 415 271 HOH HOH . T 6 HOH B 16 416 282 HOH HOH . T 6 HOH B 17 417 283 HOH HOH . T 6 HOH B 18 418 274 HOH HOH . T 6 HOH B 19 419 288 HOH HOH . U 6 HOH C 1 401 269 HOH HOH . U 6 HOH C 2 402 271 HOH HOH . U 6 HOH C 3 403 282 HOH HOH . U 6 HOH C 4 404 270 HOH HOH . U 6 HOH C 5 405 284 HOH HOH . U 6 HOH C 6 406 279 HOH HOH . U 6 HOH C 7 407 290 HOH HOH . U 6 HOH C 8 408 276 HOH HOH . U 6 HOH C 9 409 268 HOH HOH . U 6 HOH C 10 410 267 HOH HOH . U 6 HOH C 11 411 278 HOH HOH . U 6 HOH C 12 412 286 HOH HOH . U 6 HOH C 13 413 280 HOH HOH . U 6 HOH C 14 414 285 HOH HOH . U 6 HOH C 15 415 274 HOH HOH . U 6 HOH C 16 416 277 HOH HOH . U 6 HOH C 17 417 291 HOH HOH . U 6 HOH C 18 418 281 HOH HOH . U 6 HOH C 19 419 272 HOH HOH . U 6 HOH C 20 420 283 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 N N SAH . . . R 4 63.783 145.439 29.055 1 31.52 ? N SAH 304 C 1 HETATM 2 C CA SAH . . . R 4 63.703 143.991 28.902 1 30.96 ? CA SAH 304 C 1 HETATM 3 C CB SAH . . . R 4 63.572 143.617 27.429 1 37.93 ? CB SAH 304 C 1 HETATM 4 C CG SAH . . . R 4 63.318 144.793 26.494 1 38.38 ? CG SAH 304 C 1 HETATM 5 S SD SAH . . . R 4 61.679 145.507 26.777 1 46.89 ? SD SAH 304 C 1 HETATM 6 C C SAH . . . R 4 64.905 143.281 29.512 1 26.56 ? C SAH 304 C 1 HETATM 7 O O SAH . . . R 4 64.924 142.055 29.614 1 29.05 ? O SAH 304 C 1 HETATM 8 O OXT SAH . . . R 4 65.884 143.906 29.918 1 26.45 -1 OXT SAH 304 C 1 HETATM 9 C C5' SAH . . . R 4 61.095 144.904 25.174 1 40.57 ? C5' SAH 304 C 1 HETATM 10 C C4' SAH . . . R 4 59.978 143.874 25.304 1 30.45 ? C4' SAH 304 C 1 HETATM 11 O O4' SAH . . . R 4 58.697 144.474 25.37 1 21.67 ? O4' SAH 304 C 1 HETATM 12 C C3' SAH . . . R 4 59.949 142.94 24.106 1 35.16 ? C3' SAH 304 C 1 HETATM 13 O O3' SAH . . . R 4 60.4 141.664 24.495 1 39.84 ? O3' SAH 304 C 1 HETATM 14 C C2' SAH . . . R 4 58.499 142.863 23.682 1 28.01 ? C2' SAH 304 C 1 HETATM 15 O O2' SAH . . . R 4 58.075 141.525 23.593 1 39.08 ? O2' SAH 304 C 1 HETATM 16 C C1' SAH . . . R 4 57.768 143.566 24.807 1 25.83 ? C1' SAH 304 C 1 HETATM 17 N N9 SAH . . . R 4 56.537 144.203 24.308 1 30.49 ? N9 SAH 304 C 1 HETATM 18 C C8 SAH . . . R 4 56.387 144.969 23.184 1 40.22 ? C8 SAH 304 C 1 HETATM 19 N N7 SAH . . . R 4 55.089 145.345 23.091 1 39.97 ? N7 SAH 304 C 1 HETATM 20 C C5 SAH . . . R 4 54.412 144.823 24.136 1 36.01 ? C5 SAH 304 C 1 HETATM 21 C C6 SAH . . . R 4 53.081 144.891 24.524 1 38.72 ? C6 SAH 304 C 1 HETATM 22 N N6 SAH . . . R 4 52.204 145.58 23.801 1 42.04 ? N6 SAH 304 C 1 HETATM 23 N N1 SAH . . . R 4 52.673 144.239 25.667 1 37.17 ? N1 SAH 304 C 1 HETATM 24 C C2 SAH . . . R 4 53.586 143.527 26.415 1 31.57 ? C2 SAH 304 C 1 HETATM 25 N N3 SAH . . . R 4 54.905 143.463 26.025 1 29.43 ? N3 SAH 304 C 1 HETATM 26 C C4 SAH . . . R 4 55.311 144.101 24.905 1 29.97 ? C4 SAH 304 C 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 31 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 26 #