data_8STW # _model_server_result.job_id cgVrcfpz6Ucz76gY0F9-Tw _model_server_result.datetime_utc '2024-11-22 21:37:15' _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 8stw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":501}' # _entry.id 8STW # _exptl.entry_id 8STW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "PYRIDOXAL-5'-PHOSPHATE" _entity.pdbx_number_of_molecules 6 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 106.15 _cell.angle_beta 105.49 _cell.angle_gamma 107.47 _cell.entry_id 8STW _cell.length_a 89.462 _cell.length_b 90.189 _cell.length_c 104.224 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8STW _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _pdbx_struct_assembly.details author_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 I N N ? 2 K N N ? 2 M N N ? 2 O N N ? 2 Q 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 76 A LYS 119 1_555 G C4A PLP . A PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.286 ? covale ? covale2 B NZ LYS 76 B LYS 119 1_555 I C4A PLP . B PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.274 ? covale ? covale3 C NZ LYS 76 C LYS 119 1_555 K C4A PLP . C PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.255 ? covale ? covale4 D NZ LYS 76 D LYS 119 1_555 M C4A PLP . D PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.254 ? covale ? covale5 E NZ LYS 76 E LYS 119 1_555 O C4A PLP . E PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.242 ? covale ? covale6 F NZ LYS 76 F LYS 119 1_555 Q C4A PLP . F PLP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.251 ? metalc ? metalc1 A SG CYS 9 A CYS 52 1_555 H FE HEM . A HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc2 A NE2 HIS 22 A HIS 65 1_555 H FE HEM . A HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? metalc ? metalc3 B SG CYS 9 B CYS 52 1_555 J FE HEM . B HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.405 ? metalc ? metalc4 B NE2 HIS 22 B HIS 65 1_555 J FE HEM . B HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc5 C SG CYS 9 C CYS 52 1_555 L FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.429 ? metalc ? metalc6 C NE2 HIS 22 C HIS 65 1_555 L FE HEM . C HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? metalc ? metalc7 D SG CYS 9 D CYS 52 1_555 N FE HEM . D HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc8 D NE2 HIS 22 D HIS 65 1_555 N FE HEM . D HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc9 E SG CYS 9 E CYS 52 1_555 P FE HEM . E HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc10 E NE2 HIS 22 E HIS 65 1_555 P FE HEM . E HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? metalc ? metalc11 F SG CYS 9 F CYS 52 1_555 R FE HEM . F HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.262 ? metalc ? metalc12 F NE2 HIS 22 F HIS 65 1_555 R FE HEM . F HEM 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? # _chem_comp.formula 'C8 H10 N O6 P' _chem_comp.formula_weight 247.142 _chem_comp.id PLP _chem_comp.mon_nstd_flag . _chem_comp.name "PYRIDOXAL-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'VITAMIN B6 Phosphate' # 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 PLP doub 342 n y N1 C6 PLP sing 343 n y C2 C2A PLP sing 344 n n C2 C3 PLP sing 345 n y C2A H2A1 PLP sing 346 n n C2A H2A2 PLP sing 347 n n C2A H2A3 PLP sing 348 n n C3 O3 PLP sing 349 n n C3 C4 PLP doub 350 n y O3 HO3 PLP sing 351 n n C4 C4A PLP sing 352 n n C4 C5 PLP sing 353 n y C4A O4A PLP doub 354 n n C4A H4A PLP sing 355 n n C5 C6 PLP doub 356 n y C5 C5A PLP sing 357 n n C6 H6 PLP sing 358 n n C5A O4P PLP sing 359 n n C5A H5A1 PLP sing 360 n n C5A H5A2 PLP sing 361 n n O4P P PLP sing 362 n n P O1P PLP doub 363 n n P O2P PLP sing 364 n n P O3P PLP sing 365 n n O2P HOP2 PLP sing 366 n n O3P HOP3 PLP sing 367 n n # _atom_sites.entry_id 8STW _atom_sites.fract_transf_matrix[1][1] 0.011178 _atom_sites.fract_transf_matrix[1][2] 0.003519 _atom_sites.fract_transf_matrix[1][3] 0.004854 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011624 _atom_sites.fract_transf_matrix[2][3] 0.004922 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.010812 _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 PLP A 1 501 501 PLP PLP . H 3 HEM A 1 502 502 HEM HEM . I 2 PLP B 1 501 501 PLP PLP . J 3 HEM B 1 502 502 HEM HEM . K 2 PLP C 1 501 501 PLP PLP . L 3 HEM C 1 502 502 HEM HEM . M 2 PLP D 1 501 501 PLP PLP . N 3 HEM D 1 502 502 HEM HEM . O 2 PLP E 1 501 501 PLP PLP . P 3 HEM E 1 502 502 HEM HEM . Q 2 PLP F 1 501 501 PLP PLP . R 3 HEM F 1 502 502 HEM HEM . S 4 HOH A 1 601 81 HOH HOH . S 4 HOH A 2 602 19 HOH HOH . S 4 HOH A 3 603 78 HOH HOH . S 4 HOH A 4 604 22 HOH HOH . S 4 HOH A 5 605 59 HOH HOH . S 4 HOH A 6 606 36 HOH HOH . S 4 HOH A 7 607 38 HOH HOH . S 4 HOH A 8 608 37 HOH HOH . S 4 HOH A 9 609 66 HOH HOH . S 4 HOH A 10 610 74 HOH HOH . S 4 HOH A 11 611 15 HOH HOH . S 4 HOH A 12 612 35 HOH HOH . S 4 HOH A 13 613 34 HOH HOH . S 4 HOH A 14 614 14 HOH HOH . S 4 HOH A 15 615 29 HOH HOH . S 4 HOH A 16 616 10 HOH HOH . S 4 HOH A 17 617 80 HOH HOH . S 4 HOH A 18 618 75 HOH HOH . S 4 HOH A 19 619 71 HOH HOH . T 4 HOH B 1 601 47 HOH HOH . T 4 HOH B 2 602 25 HOH HOH . T 4 HOH B 3 603 43 HOH HOH . T 4 HOH B 4 604 60 HOH HOH . T 4 HOH B 5 605 84 HOH HOH . T 4 HOH B 6 606 39 HOH HOH . T 4 HOH B 7 607 83 HOH HOH . T 4 HOH B 8 608 56 HOH HOH . T 4 HOH B 9 609 77 HOH HOH . T 4 HOH B 10 610 69 HOH HOH . U 4 HOH C 1 601 50 HOH HOH . U 4 HOH C 2 602 33 HOH HOH . U 4 HOH C 3 603 68 HOH HOH . U 4 HOH C 4 604 48 HOH HOH . U 4 HOH C 5 605 4 HOH HOH . U 4 HOH C 6 606 1 HOH HOH . U 4 HOH C 7 607 11 HOH HOH . U 4 HOH C 8 608 6 HOH HOH . U 4 HOH C 9 609 42 HOH HOH . U 4 HOH C 10 610 16 HOH HOH . U 4 HOH C 11 611 51 HOH HOH . U 4 HOH C 12 612 62 HOH HOH . U 4 HOH C 13 613 45 HOH HOH . U 4 HOH C 14 614 7 HOH HOH . U 4 HOH C 15 615 18 HOH HOH . U 4 HOH C 16 616 24 HOH HOH . V 4 HOH D 1 601 41 HOH HOH . V 4 HOH D 2 602 44 HOH HOH . V 4 HOH D 3 603 9 HOH HOH . V 4 HOH D 4 604 8 HOH HOH . V 4 HOH D 5 605 26 HOH HOH . V 4 HOH D 6 606 2 HOH HOH . V 4 HOH D 7 607 31 HOH HOH . V 4 HOH D 8 608 27 HOH HOH . V 4 HOH D 9 609 55 HOH HOH . V 4 HOH D 10 610 13 HOH HOH . W 4 HOH E 1 601 64 HOH HOH . W 4 HOH E 2 602 67 HOH HOH . W 4 HOH E 3 603 3 HOH HOH . W 4 HOH E 4 604 23 HOH HOH . W 4 HOH E 5 605 63 HOH HOH . W 4 HOH E 6 606 70 HOH HOH . X 4 HOH F 1 601 72 HOH HOH . X 4 HOH F 2 602 58 HOH HOH . X 4 HOH F 3 603 76 HOH HOH . X 4 HOH F 4 604 28 HOH HOH . X 4 HOH F 5 605 49 HOH HOH . X 4 HOH F 6 606 5 HOH HOH . X 4 HOH F 7 607 65 HOH HOH . X 4 HOH F 8 608 54 HOH HOH . X 4 HOH F 9 609 46 HOH HOH . X 4 HOH F 10 610 40 HOH HOH . X 4 HOH F 11 611 79 HOH HOH . X 4 HOH F 12 612 53 HOH HOH . X 4 HOH F 13 613 21 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 PLP . . . O 2 -15.568 -45.415 28.561 1 36.94 ? N1 PLP 501 E 1 HETATM 2 C C2 PLP . . . O 2 -14.608 -45.079 27.705 1 34.68 ? C2 PLP 501 E 1 HETATM 3 C C2A PLP . . . O 2 -13.806 -43.854 28 1 34.63 ? C2A PLP 501 E 1 HETATM 4 C C3 PLP . . . O 2 -14.307 -45.894 26.611 1 31.32 ? C3 PLP 501 E 1 HETATM 5 O O3 PLP . . . O 2 -13.281 -45.515 25.813 1 33.37 ? O3 PLP 501 E 1 HETATM 6 C C4 PLP . . . O 2 -15.062 -47.065 26.403 1 32.03 ? C4 PLP 501 E 1 HETATM 7 C C4A PLP . . . O 2 -14.81 -47.922 25.25 1 31.45 ? C4A PLP 501 E 1 HETATM 8 C C5 PLP . . . O 2 -16.081 -47.383 27.319 1 36.55 ? C5 PLP 501 E 1 HETATM 9 C C6 PLP . . . O 2 -16.284 -46.541 28.373 1 34.78 ? C6 PLP 501 E 1 HETATM 10 C C5A PLP . . . O 2 -16.955 -48.603 27.181 1 38.07 ? C5A PLP 501 E 1 HETATM 11 O O4P PLP . . . O 2 -16.266 -49.648 26.429 1 39.47 ? O4P PLP 501 E 1 HETATM 12 P P PLP . . . O 2 -17.007 -50.802 25.567 1 40.57 ? P PLP 501 E 1 HETATM 13 O O1P PLP . . . O 2 -16.754 -50.389 24.155 1 35.4 ? O1P PLP 501 E 1 HETATM 14 O O2P PLP . . . O 2 -16.316 -52.117 25.981 1 38.49 ? O2P PLP 501 E 1 HETATM 15 O O3P PLP . . . O 2 -18.493 -50.779 25.91 1 43.61 ? O3P PLP 501 E 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 20 _model_server_stats.create_model_time_ms 68 _model_server_stats.query_time_ms 580 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 15 #