data_6EFH # _model_server_result.job_id HVBy1rpK8TkPXpOzfztDAQ _model_server_result.datetime_utc '2024-11-22 21:22:02' _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 6efh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":602}' # _entry.id 6EFH # _exptl.entry_id 6EFH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 425.314 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'THIAMINE DIPHOSPHATE' _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 6EFH _cell.length_a 172.765 _cell.length_b 172.765 _cell.length_c 210.083 _cell.Z_PDB 32 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6EFH _symmetry.cell_setting ? _symmetry.Int_Tables_number 97 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 4 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,I,J,K _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 ? 3 D 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 covale ? covale1 A SG CYS 221 A CYS 221 1_555 C C2 PY0 . A PY0 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? covale ? covale2 B SG CYS 221 B CYS 221 1_555 G C2 PY0 . B PY0 600 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? metalc ? metalc1 A OD1 ASP 444 A ASP 444 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.452 ? metalc ? metalc2 A OD1 ASN 471 A ASN 471 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc3 A O GLY 473 A GLY 473 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc4 D O1A TPP . A TPP 602 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.232 ? metalc ? metalc5 D O1B TPP . A TPP 602 1_555 E MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc6 B OD1 ASP 444 B ASP 444 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.257 ? metalc ? metalc7 B OD1 ASN 471 B ASN 471 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc8 B O GLY 473 B GLY 473 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.811 ? metalc ? metalc9 H O1A TPP . B TPP 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.936 ? metalc ? metalc10 H O3B TPP . B TPP 601 1_555 I MG MG . B MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.966 ? # _chem_comp.formula 'C12 H19 N4 O7 P2 S 1' _chem_comp.formula_weight 425.314 _chem_comp.id TPP _chem_comp.mon_nstd_flag . _chem_comp.name 'THIAMINE DIPHOSPHATE' _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 N1' C2' TPP doub 357 n y N1' C6' TPP sing 358 n y C2' CM2 TPP sing 359 n n C2' N3' TPP sing 360 n y CM2 HM21 TPP sing 361 n n CM2 HM22 TPP sing 362 n n CM2 HM23 TPP sing 363 n n N3' C4' TPP doub 364 n y C4' N4' TPP sing 365 n n C4' C5' TPP sing 366 n y N4' HN41 TPP sing 367 n n N4' HN42 TPP sing 368 n n C5' C6' TPP doub 369 n y C5' C7' TPP sing 370 n n C6' H6' TPP sing 371 n n C7' N3 TPP sing 372 n n C7' "H7'1" TPP sing 373 n n C7' "H7'2" TPP sing 374 n n N3 C2 TPP doub 375 n y N3 C4 TPP sing 376 n y C2 S1 TPP sing 377 n y C2 H2 TPP sing 378 n n S1 C5 TPP sing 379 n y C5 C4 TPP doub 380 n y C5 C6 TPP sing 381 n n C4 CM4 TPP sing 382 n n CM4 HM41 TPP sing 383 n n CM4 HM42 TPP sing 384 n n CM4 HM43 TPP sing 385 n n C6 C7 TPP sing 386 n n C6 H61 TPP sing 387 n n C6 H62 TPP sing 388 n n C7 O7 TPP sing 389 n n C7 H71 TPP sing 390 n n C7 H72 TPP sing 391 n n O7 PA TPP sing 392 n n PA O1A TPP doub 393 n n PA O2A TPP sing 394 n n PA O3A TPP sing 395 n n O2A HOA2 TPP sing 396 n n O3A PB TPP sing 397 n n PB O1B TPP doub 398 n n PB O2B TPP sing 399 n n PB O3B TPP sing 400 n n O2B HOB2 TPP sing 401 n n O3B HOB3 TPP sing 402 n n # _atom_sites.entry_id 6EFH _atom_sites.fract_transf_matrix[1][1] 0.005788 _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] 0.005788 _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] 0.00476 _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 2 PY0 A 1 601 600 PY0 PY0 . D 3 TPP A 1 602 601 TPP TPP . E 4 MG A 1 603 602 MG MG . F 5 1PE A 1 604 1 1PE 1PE . G 2 PY0 B 1 600 600 PY0 PY0 . H 3 TPP B 1 601 601 TPP TPP . I 4 MG B 1 602 602 MG MG . J 6 HOH A 1 701 4 HOH HOH . J 6 HOH A 2 702 6 HOH HOH . J 6 HOH A 3 703 28 HOH HOH . J 6 HOH A 4 704 26 HOH HOH . J 6 HOH A 5 705 1 HOH HOH . J 6 HOH A 6 706 3 HOH HOH . J 6 HOH A 7 707 18 HOH HOH . J 6 HOH A 8 708 40 HOH HOH . J 6 HOH A 9 709 29 HOH HOH . J 6 HOH A 10 710 33 HOH HOH . J 6 HOH A 11 711 9 HOH HOH . J 6 HOH A 12 712 30 HOH HOH . J 6 HOH A 13 713 34 HOH HOH . J 6 HOH A 14 714 15 HOH HOH . J 6 HOH A 15 715 17 HOH HOH . J 6 HOH A 16 716 20 HOH HOH . J 6 HOH A 17 717 11 HOH HOH . J 6 HOH A 18 718 13 HOH HOH . J 6 HOH A 19 719 14 HOH HOH . J 6 HOH A 20 720 38 HOH HOH . J 6 HOH A 21 721 39 HOH HOH . J 6 HOH A 22 722 7 HOH HOH . J 6 HOH A 23 723 12 HOH HOH . J 6 HOH A 24 724 27 HOH HOH . J 6 HOH A 25 725 36 HOH HOH . J 6 HOH A 26 726 22 HOH HOH . J 6 HOH A 27 727 16 HOH HOH . J 6 HOH A 28 728 21 HOH HOH . J 6 HOH A 29 729 23 HOH HOH . J 6 HOH A 30 730 19 HOH HOH . K 6 HOH B 1 701 2 HOH HOH . K 6 HOH B 2 702 5 HOH HOH . K 6 HOH B 3 703 24 HOH HOH . K 6 HOH B 4 704 32 HOH HOH . K 6 HOH B 5 705 31 HOH HOH . K 6 HOH B 6 706 37 HOH HOH . K 6 HOH B 7 707 35 HOH HOH . K 6 HOH B 8 708 10 HOH HOH . K 6 HOH B 9 709 8 HOH HOH . K 6 HOH B 10 710 41 HOH HOH . K 6 HOH B 11 711 25 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 N1' TPP . . . D 3 -44.018 -44.948 24.134 1 56.74 ? N1' TPP 602 A 1 HETATM 2 C C2' TPP . . . D 3 -44.964 -45.271 25.073 1 58.3 ? C2' TPP 602 A 1 HETATM 3 C CM2 TPP . . . D 3 -44.868 -46.473 25.996 1 56.92 ? CM2 TPP 602 A 1 HETATM 4 N N3' TPP . . . D 3 -46.061 -44.503 25.217 1 60.51 ? N3' TPP 602 A 1 HETATM 5 C C4' TPP . . . D 3 -46.255 -43.406 24.459 1 64.33 ? C4' TPP 602 A 1 HETATM 6 N N4' TPP . . . D 3 -47.376 -42.707 24.685 1 66.99 ? N4' TPP 602 A 1 HETATM 7 C C5' TPP . . . D 3 -45.256 -43.015 23.416 1 70.76 ? C5' TPP 602 A 1 HETATM 8 C C6' TPP . . . D 3 -44.134 -43.865 23.329 1 61.76 ? C6' TPP 602 A 1 HETATM 9 C C7' TPP . . . D 3 -45.474 -41.773 22.505 1 77.67 ? C7' TPP 602 A 1 HETATM 10 N N3 TPP . . . D 3 -46.593 -41.941 21.517 1 76.66 ? N3 TPP 602 A 1 HETATM 11 C C2 TPP . . . D 3 -47.851 -41.502 21.768 1 74.4 ? C2 TPP 602 A 1 HETATM 12 S S1 TPP . . . D 3 -49.076 -41.774 20.558 1 78.4 ? S1 TPP 602 A 1 HETATM 13 C C5 TPP . . . D 3 -47.844 -42.527 19.604 1 73.58 ? C5 TPP 602 A 1 HETATM 14 C C4 TPP . . . D 3 -46.515 -42.533 20.278 1 73.21 ? C4 TPP 602 A 1 HETATM 15 C CM4 TPP . . . D 3 -45.302 -43.145 19.619 1 67.4 ? CM4 TPP 602 A 1 HETATM 16 C C6 TPP . . . D 3 -48.322 -43.048 18.268 1 74.22 ? C6 TPP 602 A 1 HETATM 17 C C7 TPP . . . D 3 -49.337 -44.185 18.457 1 71.69 ? C7 TPP 602 A 1 HETATM 18 O O7 TPP . . . D 3 -49.469 -44.998 17.281 1 66.76 ? O7 TPP 602 A 1 HETATM 19 P PA TPP . . . D 3 -50.899 -45.318 16.565 1 62.71 ? PA TPP 602 A 1 HETATM 20 O O1A TPP . . . D 3 -50.605 -45.882 15.179 1 59.84 ? O1A TPP 602 A 1 HETATM 21 O O2A TPP . . . D 3 -51.734 -46.114 17.589 1 58.18 ? O2A TPP 602 A 1 HETATM 22 O O3A TPP . . . D 3 -51.604 -43.864 16.239 1 62.53 ? O3A TPP 602 A 1 HETATM 23 P PB TPP . . . D 3 -52.741 -43.452 15.106 1 56.97 ? PB TPP 602 A 1 HETATM 24 O O1B TPP . . . D 3 -52.044 -43.579 13.769 1 59.92 ? O1B TPP 602 A 1 HETATM 25 O O2B TPP . . . D 3 -53.017 -42.077 15.667 1 52.95 ? O2B TPP 602 A 1 HETATM 26 O O3B TPP . . . D 3 -53.945 -44.355 15.113 1 51.61 ? O3B TPP 602 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 294 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 26 #