data_3NL3 # _model_server_result.job_id WaBl_jOVgpfqxDlIHY6E9g _model_server_result.datetime_utc '2024-11-15 07:34:42' _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 3nl3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"T","auth_seq_id":2006}' # _entry.id 3NL3 # _exptl.entry_id 3NL3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 345.334 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIAMIN PHOSPHATE' _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 102.55 _cell.angle_gamma 90 _cell.entry_id 3NL3 _cell.length_a 104.543 _cell.length_b 154.292 _cell.length_c 148.627 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3NL3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 G N N ? 2 K N N ? 2 M N N ? 2 P N N ? 2 T N N ? 2 V 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 51 A THR 51 1_555 N MG MG . C MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.587 ? metalc ? metalc2 A OD2 ASP 76 A ASP 76 1_555 H MG MG . A MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.849 ? metalc ? metalc3 A OD1 ASP 95 A ASP 95 1_555 H MG MG . A MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc4 A O PRO 341 A PRO 341 1_555 J MG MG . A MG 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc5 A OE2 GLU 372 A GLU 372 1_555 J MG MG . A MG 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.701 ? metalc ? metalc6 A OE1 GLU 372 A GLU 372 1_555 J MG MG . A MG 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.719 ? metalc ? metalc7 A OD2 ASP 424 A ASP 424 1_555 I MG MG . A MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc8 H MG MG . A MG 541 1_555 C OG1 THR 51 C THR 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.689 ? metalc ? metalc9 B OG1 THR 51 B THR 51 1_555 W MG MG . F MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc10 B O PRO 341 B PRO 341 1_555 L MG MG . B MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.679 ? metalc ? metalc11 B OE2 GLU 372 B GLU 372 1_555 L MG MG . B MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.5 ? metalc ? metalc12 B OE1 GLU 372 B GLU 372 1_555 L MG MG . B MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.805 ? metalc ? metalc13 C OD2 ASP 340 C ASP 340 1_555 O MG MG . C MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc14 C O PRO 341 C PRO 341 1_555 O MG MG . C MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc15 C OE2 GLU 372 C GLU 372 1_555 O MG MG . C MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.575 ? metalc ? metalc16 C OE1 GLU 372 C GLU 372 1_555 O MG MG . C MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.586 ? metalc ? metalc17 D O ALA 49 D ALA 49 1_555 R MG MG . D MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.735 ? metalc ? metalc18 D OG1 THR 51 D THR 51 1_555 R MG MG . D MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.942 ? metalc ? metalc19 D OD2 ASP 76 D ASP 76 1_555 Q MG MG . D MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.814 ? metalc ? metalc20 D O PRO 341 D PRO 341 1_555 S MG MG . D MG 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc21 D OE2 GLU 372 D GLU 372 1_555 S MG MG . D MG 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.453 ? metalc ? metalc22 D OE1 GLU 372 D GLU 372 1_555 S MG MG . D MG 543 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.654 ? metalc ? metalc23 Q MG MG . D MG 541 1_555 E OG1 THR 51 E THR 51 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.652 ? metalc ? metalc24 R MG MG . D MG 542 1_555 E OD2 ASP 76 E ASP 76 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.778 ? metalc ? metalc25 E O PRO 341 E PRO 341 1_555 U MG MG . E MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.772 ? metalc ? metalc26 E OE2 GLU 372 E GLU 372 1_555 U MG MG . E MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? metalc ? metalc27 E OE1 GLU 372 E GLU 372 1_555 U MG MG . E MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.535 ? metalc ? metalc28 F OD2 ASP 76 F ASP 76 1_555 W MG MG . F MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.788 ? metalc ? metalc29 F OD1 ASP 95 F ASP 95 1_555 W MG MG . F MG 541 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.526 ? metalc ? metalc30 F O PRO 341 F PRO 341 1_555 X MG MG . F MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.581 ? metalc ? metalc31 F OE2 GLU 372 F GLU 372 1_555 X MG MG . F MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.514 ? metalc ? metalc32 F OE1 GLU 372 F GLU 372 1_555 X MG MG . F MG 542 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.516 ? # _chem_comp.formula 'C12 H18 N4 O4 P S 1' _chem_comp.formula_weight 345.334 _chem_comp.id TPS _chem_comp.mon_nstd_flag . _chem_comp.name 'THIAMIN PHOSPHATE' _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 CM2 C2A TPS sing 304 n n CM2 HM21 TPS sing 305 n n CM2 HM22 TPS sing 306 n n CM2 HM23 TPS sing 307 n n N3 C2 TPS doub 308 n y N3 C4 TPS sing 309 n y N3 C7A TPS sing 310 n n C2 S1 TPS sing 311 n y C2 H2 TPS sing 312 n n S1 C5 TPS sing 313 n y C5 C4 TPS doub 314 n y C5 C6 TPS sing 315 n n C4 CM4 TPS sing 316 n n CM4 HM41 TPS sing 317 n n CM4 HM42 TPS sing 318 n n CM4 HM43 TPS sing 319 n n C6 C7 TPS sing 320 n n C6 H61 TPS sing 321 n n C6 H62 TPS sing 322 n n C7 O7 TPS sing 323 n n C7 H71 TPS sing 324 n n C7 H72 TPS sing 325 n n O7 P1 TPS sing 326 n n N1A C2A TPS doub 327 n y N1A C6A TPS sing 328 n y C2A N3A TPS sing 329 n y N3A C4A TPS doub 330 n y C4A N4A TPS sing 331 n n C4A C5A TPS sing 332 n y N4A H41N TPS sing 333 n n N4A H42N TPS sing 334 n n C5A C6A TPS doub 335 n y C5A C7A TPS sing 336 n n C6A H6A TPS sing 337 n n C7A H7A1 TPS sing 338 n n C7A H7A2 TPS sing 339 n n P1 O1 TPS doub 340 n n P1 O2 TPS sing 341 n n P1 O3 TPS sing 342 n n O2 HO2 TPS sing 343 n n O3 HO3 TPS sing 344 n n # _atom_sites.entry_id 3NL3 _atom_sites.fract_transf_matrix[1][1] 0.009565 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002129 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.006481 _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] 0.006893 _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 2 TPS A 1 2001 2001 TPS TPS . H 3 MG A 1 541 2 MG MG . I 3 MG A 1 542 3 MG MG . J 3 MG A 1 543 7 MG MG . K 2 TPS B 1 2005 2005 TPS TPS . L 3 MG B 1 541 11 MG MG . M 2 TPS C 1 2004 2004 TPS TPS . N 3 MG C 1 541 1 MG MG . O 3 MG C 1 542 10 MG MG . P 2 TPS D 1 2003 2003 TPS TPS . Q 3 MG D 1 541 5 MG MG . R 3 MG D 1 542 6 MG MG . S 3 MG D 1 543 9 MG MG . T 2 TPS E 1 2006 2006 TPS TPS . U 3 MG E 1 541 12 MG MG . V 2 TPS F 1 2002 2002 TPS TPS . W 3 MG F 1 541 4 MG MG . X 3 MG F 1 542 8 MG MG . # 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 C CM2 TPS . . . T 2 6.538 40.093 51.527 1 60.96 ? CM2 TPS 2006 E 1 HETATM 2 N N3 TPS . . . T 2 9.443 34.471 50.864 1 76.26 ? N3 TPS 2006 E 1 HETATM 3 C C2 TPS . . . T 2 9.566 33.659 52.182 1 81.92 ? C2 TPS 2006 E 1 HETATM 4 S S1 TPS . . . T 2 8.396 32.46 52.172 1 66.59 ? S1 TPS 2006 E 1 HETATM 5 C C5 TPS . . . T 2 7.676 32.606 50.607 1 57.27 ? C5 TPS 2006 E 1 HETATM 6 C C4 TPS . . . T 2 8.434 33.707 49.865 1 61.62 ? C4 TPS 2006 E 1 HETATM 7 C CM4 TPS . . . T 2 7.891 34.32 48.587 1 74.78 ? CM4 TPS 2006 E 1 HETATM 8 C C6 TPS . . . T 2 6.773 31.573 49.955 1 64.91 ? C6 TPS 2006 E 1 HETATM 9 C C7 TPS . . . T 2 5.5 31.155 50.68 1 53.18 ? C7 TPS 2006 E 1 HETATM 10 O O7 TPS . . . T 2 4.498 30.591 49.884 1 59.46 ? O7 TPS 2006 E 1 HETATM 11 N N1A TPS . . . T 2 8.133 38.292 52.388 1 67.46 ? N1A TPS 2006 E 1 HETATM 12 C C2A TPS . . . T 2 7.536 38.965 51.294 1 64.07 ? C2A TPS 2006 E 1 HETATM 13 N N3A TPS . . . T 2 7.822 38.594 49.994 1 51.84 ? N3A TPS 2006 E 1 HETATM 14 C C4A TPS . . . T 2 8.642 37.615 49.762 1 48.14 ? C4A TPS 2006 E 1 HETATM 15 N N4A TPS . . . T 2 8.95 37.235 48.394 1 76.48 ? N4A TPS 2006 E 1 HETATM 16 C C5A TPS . . . T 2 9.269 36.923 50.877 1 45.29 ? C5A TPS 2006 E 1 HETATM 17 C C6A TPS . . . T 2 8.997 37.271 52.134 1 66.73 ? C6A TPS 2006 E 1 HETATM 18 C C7A TPS . . . T 2 10.148 35.716 50.586 1 63.2 ? C7A TPS 2006 E 1 HETATM 19 P P1 TPS . . . T 2 3.255 29.797 50.617 1 61.98 ? P1 TPS 2006 E 1 HETATM 20 O O1 TPS . . . T 2 3.786 28.786 51.544 1 48.85 ? O1 TPS 2006 E 1 HETATM 21 O O2 TPS . . . T 2 2.357 29.045 49.463 1 79 ? O2 TPS 2006 E 1 HETATM 22 O O3 TPS . . . T 2 2.286 30.913 51.359 1 60.16 ? O3 TPS 2006 E 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 45 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 9 _model_server_stats.element_count 22 #