data_1JBQ # _model_server_result.job_id i4cJzUEVu99LaaNb3ZGgCA _model_server_result.datetime_utc '2024-11-01 02:17:44' _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 1jbq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":1001}' # _entry.id 1JBQ # _exptl.entry_id 1JBQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 247.142 _entity.id 3 _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 90 _cell.angle_beta 90 _cell.angle_gamma 120 _cell.entry_id 1JBQ _cell.length_a 144.52 _cell.length_b 144.52 _cell.length_c 108.16 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1JBQ _symmetry.cell_setting trigonal _symmetry.Int_Tables_number 144 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 31' # 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 PISA dimeric 2 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,B,G,H,I,J,S,T 1 1 C,D,K,L,M,N,U,V 2 1 E,F,O,P,Q,R,W,X 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 ? 3 H N N ? 3 J N N ? 3 L N N ? 3 N N N ? 3 P N N ? 3 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 disulf ? disulf1 A SG CYS 294 A CYS 272 1_555 A SG CYS 297 A CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 B SG CYS 294 B CYS 272 1_555 B SG CYS 297 B CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 C SG CYS 294 C CYS 272 1_555 C SG CYS 297 C CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 D SG CYS 294 D CYS 272 1_555 D SG CYS 297 D CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf5 E SG CYS 294 E CYS 272 1_555 E SG CYS 297 E CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf6 F SG CYS 294 F CYS 272 1_555 F SG CYS 297 F CYS 275 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? covale ? covale1 A NZ LYS 141 A LYS 119 1_555 H C4A PLP . A PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale2 B NZ LYS 141 B LYS 119 1_555 J C4A PLP . B PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? covale ? covale3 C NZ LYS 141 C LYS 119 1_555 L C4A PLP . C PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.269 ? covale ? covale4 D NZ LYS 141 D LYS 119 1_555 N C4A PLP . D PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.265 ? covale ? covale5 E NZ LYS 141 E LYS 119 1_555 P C4A PLP . E PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.263 ? covale ? covale6 F NZ LYS 141 F LYS 119 1_555 R C4A PLP . F PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.275 ? metalc ? metalc1 A SG CYS 74 A CYS 52 1_555 G FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc2 A NE2 HIS 87 A HIS 65 1_555 G FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? metalc ? metalc3 B SG CYS 74 B CYS 52 1_555 I FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc4 B NE2 HIS 87 B HIS 65 1_555 I FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc5 C SG CYS 74 C CYS 52 1_555 K FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.218 ? metalc ? metalc6 C NE2 HIS 87 C HIS 65 1_555 K FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc7 D SG CYS 74 D CYS 52 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc8 D NE2 HIS 87 D HIS 65 1_555 M FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.171 ? metalc ? metalc9 E SG CYS 74 E CYS 52 1_555 O FE HEM . E HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc10 E NE2 HIS 87 E HIS 65 1_555 O FE HEM . E HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc11 F SG CYS 74 F CYS 52 1_555 Q FE HEM . F HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc12 F NE2 HIS 87 F HIS 65 1_555 Q FE HEM . F HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _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 1JBQ _atom_sites.fract_transf_matrix[1][1] 0.006919 _atom_sites.fract_transf_matrix[1][2] 0.003995 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00799 _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] 0.009246 _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 HEM A 1 501 501 HEM HEM . H 3 PLP A 1 1001 1001 PLP PLP . I 2 HEM B 1 501 501 HEM HEM . J 3 PLP B 1 1001 1001 PLP PLP . K 2 HEM C 1 501 501 HEM HEM . L 3 PLP C 1 1001 1001 PLP PLP . M 2 HEM D 1 501 501 HEM HEM . N 3 PLP D 1 1001 1001 PLP PLP . O 2 HEM E 1 501 501 HEM HEM . P 3 PLP E 1 1001 1001 PLP PLP . Q 2 HEM F 1 501 501 HEM HEM . R 3 PLP F 1 1001 1001 PLP PLP . S 4 HOH A 1 1002 1 HOH HOH . S 4 HOH A 2 1003 6 HOH HOH . S 4 HOH A 3 1004 13 HOH HOH . S 4 HOH A 4 1005 19 HOH HOH . S 4 HOH A 5 1006 26 HOH HOH . S 4 HOH A 6 1007 33 HOH HOH . S 4 HOH A 7 1008 42 HOH HOH . S 4 HOH A 8 1009 54 HOH HOH . S 4 HOH A 9 1010 60 HOH HOH . S 4 HOH A 10 1011 66 HOH HOH . S 4 HOH A 11 1012 73 HOH HOH . S 4 HOH A 12 1013 91 HOH HOH . S 4 HOH A 13 1014 102 HOH HOH . S 4 HOH A 14 1015 114 HOH HOH . S 4 HOH A 15 1016 119 HOH HOH . S 4 HOH A 16 1017 131 HOH HOH . S 4 HOH A 17 1018 133 HOH HOH . S 4 HOH A 18 1019 139 HOH HOH . S 4 HOH A 19 1020 140 HOH HOH . S 4 HOH A 20 1021 141 HOH HOH . S 4 HOH A 21 1022 157 HOH HOH . S 4 HOH A 22 1023 158 HOH HOH . T 4 HOH B 1 1002 7 HOH HOH . T 4 HOH B 2 1003 14 HOH HOH . T 4 HOH B 3 1004 34 HOH HOH . T 4 HOH B 4 1005 39 HOH HOH . T 4 HOH B 5 1006 43 HOH HOH . T 4 HOH B 6 1007 47 HOH HOH . T 4 HOH B 7 1008 55 HOH HOH . T 4 HOH B 8 1009 61 HOH HOH . T 4 HOH B 9 1010 67 HOH HOH . T 4 HOH B 10 1011 71 HOH HOH . T 4 HOH B 11 1012 74 HOH HOH . T 4 HOH B 12 1013 78 HOH HOH . T 4 HOH B 13 1014 81 HOH HOH . T 4 HOH B 14 1015 84 HOH HOH . T 4 HOH B 15 1016 85 HOH HOH . T 4 HOH B 16 1017 89 HOH HOH . T 4 HOH B 17 1018 95 HOH HOH . T 4 HOH B 18 1019 97 HOH HOH . T 4 HOH B 19 1020 98 HOH HOH . T 4 HOH B 20 1021 99 HOH HOH . T 4 HOH B 21 1022 106 HOH HOH . T 4 HOH B 22 1023 107 HOH HOH . T 4 HOH B 23 1024 112 HOH HOH . T 4 HOH B 24 1025 118 HOH HOH . T 4 HOH B 25 1026 127 HOH HOH . T 4 HOH B 26 1027 134 HOH HOH . T 4 HOH B 27 1028 142 HOH HOH . T 4 HOH B 28 1029 143 HOH HOH . T 4 HOH B 29 1030 159 HOH HOH . T 4 HOH B 30 1031 160 HOH HOH . U 4 HOH C 1 1002 8 HOH HOH . U 4 HOH C 2 1003 12 HOH HOH . U 4 HOH C 3 1004 15 HOH HOH . U 4 HOH C 4 1005 29 HOH HOH . U 4 HOH C 5 1006 35 HOH HOH . U 4 HOH C 6 1007 44 HOH HOH . U 4 HOH C 7 1008 48 HOH HOH . U 4 HOH C 8 1009 51 HOH HOH . U 4 HOH C 9 1010 56 HOH HOH . U 4 HOH C 10 1011 62 HOH HOH . U 4 HOH C 11 1012 68 HOH HOH . U 4 HOH C 12 1013 79 HOH HOH . U 4 HOH C 13 1014 82 HOH HOH . U 4 HOH C 14 1015 86 HOH HOH . U 4 HOH C 15 1016 92 HOH HOH . U 4 HOH C 16 1017 93 HOH HOH . U 4 HOH C 17 1018 96 HOH HOH . U 4 HOH C 18 1019 103 HOH HOH . U 4 HOH C 19 1020 115 HOH HOH . U 4 HOH C 20 1021 124 HOH HOH . U 4 HOH C 21 1022 135 HOH HOH . U 4 HOH C 22 1023 145 HOH HOH . U 4 HOH C 23 1024 146 HOH HOH . U 4 HOH C 24 1025 147 HOH HOH . U 4 HOH C 25 1026 161 HOH HOH . V 4 HOH D 1 1002 9 HOH HOH . V 4 HOH D 2 1003 16 HOH HOH . V 4 HOH D 3 1004 20 HOH HOH . V 4 HOH D 4 1005 30 HOH HOH . V 4 HOH D 5 1006 36 HOH HOH . V 4 HOH D 6 1007 40 HOH HOH . V 4 HOH D 7 1008 57 HOH HOH . V 4 HOH D 8 1009 63 HOH HOH . V 4 HOH D 9 1010 69 HOH HOH . V 4 HOH D 10 1011 72 HOH HOH . V 4 HOH D 11 1012 75 HOH HOH . V 4 HOH D 12 1013 77 HOH HOH . V 4 HOH D 13 1014 100 HOH HOH . V 4 HOH D 14 1015 104 HOH HOH . V 4 HOH D 15 1016 108 HOH HOH . V 4 HOH D 16 1017 109 HOH HOH . V 4 HOH D 17 1018 120 HOH HOH . V 4 HOH D 18 1019 125 HOH HOH . V 4 HOH D 19 1020 128 HOH HOH . V 4 HOH D 20 1021 136 HOH HOH . V 4 HOH D 21 1022 148 HOH HOH . V 4 HOH D 22 1023 149 HOH HOH . V 4 HOH D 23 1024 150 HOH HOH . V 4 HOH D 24 1025 162 HOH HOH . W 4 HOH E 1 1002 10 HOH HOH . W 4 HOH E 2 1003 17 HOH HOH . W 4 HOH E 3 1004 18 HOH HOH . W 4 HOH E 4 1005 31 HOH HOH . W 4 HOH E 5 1006 37 HOH HOH . W 4 HOH E 6 1007 41 HOH HOH . W 4 HOH E 7 1008 45 HOH HOH . W 4 HOH E 8 1009 49 HOH HOH . W 4 HOH E 9 1010 52 HOH HOH . W 4 HOH E 10 1011 58 HOH HOH . W 4 HOH E 11 1012 64 HOH HOH . W 4 HOH E 12 1013 70 HOH HOH . W 4 HOH E 13 1014 76 HOH HOH . W 4 HOH E 14 1015 83 HOH HOH . W 4 HOH E 15 1016 90 HOH HOH . W 4 HOH E 16 1017 94 HOH HOH . W 4 HOH E 17 1018 101 HOH HOH . W 4 HOH E 18 1019 110 HOH HOH . W 4 HOH E 19 1020 111 HOH HOH . W 4 HOH E 20 1021 113 HOH HOH . W 4 HOH E 21 1022 116 HOH HOH . W 4 HOH E 22 1023 117 HOH HOH . W 4 HOH E 23 1024 126 HOH HOH . W 4 HOH E 24 1025 129 HOH HOH . W 4 HOH E 25 1026 132 HOH HOH . W 4 HOH E 26 1027 137 HOH HOH . W 4 HOH E 27 1028 151 HOH HOH . W 4 HOH E 28 1029 152 HOH HOH . W 4 HOH E 29 1030 153 HOH HOH . W 4 HOH E 30 1031 163 HOH HOH . W 4 HOH E 31 1032 164 HOH HOH . X 4 HOH F 1 1002 11 HOH HOH . X 4 HOH F 2 1003 27 HOH HOH . X 4 HOH F 3 1004 32 HOH HOH . X 4 HOH F 4 1005 38 HOH HOH . X 4 HOH F 5 1006 46 HOH HOH . X 4 HOH F 6 1007 53 HOH HOH . X 4 HOH F 7 1008 59 HOH HOH . X 4 HOH F 8 1009 65 HOH HOH . X 4 HOH F 9 1010 80 HOH HOH . X 4 HOH F 10 1011 87 HOH HOH . X 4 HOH F 11 1012 88 HOH HOH . X 4 HOH F 12 1013 105 HOH HOH . X 4 HOH F 13 1014 121 HOH HOH . X 4 HOH F 14 1015 122 HOH HOH . X 4 HOH F 15 1016 123 HOH HOH . X 4 HOH F 16 1017 130 HOH HOH . X 4 HOH F 17 1018 138 HOH HOH . X 4 HOH F 18 1019 154 HOH HOH . X 4 HOH F 19 1020 155 HOH HOH . X 4 HOH F 20 1021 156 HOH HOH . X 4 HOH F 21 1022 165 HOH HOH . X 4 HOH F 22 1023 166 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 . . . L 3 61.084 102.846 45.843 1 25.72 ? N1 PLP 1001 C 1 HETATM 2 C C2 PLP . . . L 3 59.932 103.555 45.651 1 19.23 ? C2 PLP 1001 C 1 HETATM 3 C C2A PLP . . . L 3 58.839 103.51 46.723 1 11.18 ? C2A PLP 1001 C 1 HETATM 4 C C3 PLP . . . L 3 59.742 104.251 44.467 1 22.49 ? C3 PLP 1001 C 1 HETATM 5 O O3 PLP . . . L 3 58.616 105.02 44.286 1 23.15 ? O3 PLP 1001 C 1 HETATM 6 C C4 PLP . . . L 3 60.71 104.201 43.474 1 22.99 ? C4 PLP 1001 C 1 HETATM 7 C C4A PLP . . . L 3 60.453 104.891 42.13 1 25.7 ? C4A PLP 1001 C 1 HETATM 8 C C5 PLP . . . L 3 61.87 103.468 43.681 1 17.86 ? C5 PLP 1001 C 1 HETATM 9 C C6 PLP . . . L 3 62.045 102.809 44.867 1 28.59 ? C6 PLP 1001 C 1 HETATM 10 C C5A PLP . . . L 3 62.88 103.229 42.557 1 12.33 ? C5A PLP 1001 C 1 HETATM 11 O O4P PLP . . . L 3 63.625 104.395 42.208 1 25.51 ? O4P PLP 1001 C 1 HETATM 12 P P PLP . . . L 3 64.179 104.567 40.694 1 23.87 ? P PLP 1001 C 1 HETATM 13 O O1P PLP . . . L 3 64.949 105.815 40.627 1 18.33 ? O1P PLP 1001 C 1 HETATM 14 O O2P PLP . . . L 3 65.204 103.356 40.55 1 13.4 ? O2P PLP 1001 C 1 HETATM 15 O O3P PLP . . . L 3 63.047 104.332 39.776 1 25.11 ? O3P PLP 1001 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 19 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #