data_5LR8
#
_model_server_result.job_id            rYi_8gt_sOvVYOBSus2jXg 
_model_server_result.datetime_utc      '2024-10-12 22:16:07' 
_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          5lr8 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1001}' 
#
_entry.id    5LR8 
#
_exptl.entry_id    5LR8 
_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    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          115.21 
_cell.angle_gamma         90 
_cell.entry_id            5LR8 
_cell.length_a            229.21 
_cell.length_b            63.48 
_cell.length_c            148.82 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5LR8 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
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 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,C,D,F 1 1,2 
B,E,G 2 1,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 2_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 165.822025 0 134.645301 
3 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E 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 772 A LYS 814 1_555 C C4A PLP . A PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.266 ? 
covale ? covale2 B NZ LYS 772 B LYS 814 1_555 E C4A PLP . B PLP 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.263 ? 
#
_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 280 n y 
N1 C6 PLP sing 281 n y 
C2 C2A PLP sing 282 n n 
C2 C3 PLP sing 283 n y 
C2A H2A1 PLP sing 284 n n 
C2A H2A2 PLP sing 285 n n 
C2A H2A3 PLP sing 286 n n 
C3 O3 PLP sing 287 n n 
C3 C4 PLP doub 288 n y 
O3 HO3 PLP sing 289 n n 
C4 C4A PLP sing 290 n n 
C4 C5 PLP sing 291 n y 
C4A O4A PLP doub 292 n n 
C4A H4A PLP sing 293 n n 
C5 C6 PLP doub 294 n y 
C5 C5A PLP sing 295 n n 
C6 H6 PLP sing 296 n n 
C5A O4P PLP sing 297 n n 
C5A H5A1 PLP sing 298 n n 
C5A H5A2 PLP sing 299 n n 
O4P P PLP sing 300 n n 
P O1P PLP doub 301 n n 
P O2P PLP sing 302 n n 
P O3P PLP sing 303 n n 
O2P HOP2 PLP sing 304 n n 
O3P HOP3 PLP sing 305 n n 
#
_atom_sites.entry_id                     5LR8 
_atom_sites.fract_transf_matrix[1][1]    0.004363 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.002054 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.015753 
_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]    0.007427 
_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 PLP A 1 1001 1001 PLP PLP . 
D 3 CIT A 1 1002 1002 CIT CIT . 
E 2 PLP B 1 1001 1001 PLP PLP . 
F 4 HOH A 1 1101 1145 HOH HOH . 
F 4 HOH A 2 1102 1168 HOH HOH . 
F 4 HOH A 3 1103 1101 HOH HOH . 
F 4 HOH A 4 1104 1133 HOH HOH . 
F 4 HOH A 5 1105 1157 HOH HOH . 
F 4 HOH A 6 1106 1137 HOH HOH . 
F 4 HOH A 7 1107 1160 HOH HOH . 
F 4 HOH A 8 1108 1102 HOH HOH . 
F 4 HOH A 9 1109 1103 HOH HOH . 
F 4 HOH A 10 1110 1115 HOH HOH . 
F 4 HOH A 11 1111 1122 HOH HOH . 
F 4 HOH A 12 1112 1119 HOH HOH . 
F 4 HOH A 13 1113 1154 HOH HOH . 
F 4 HOH A 14 1114 1144 HOH HOH . 
F 4 HOH A 15 1115 1125 HOH HOH . 
F 4 HOH A 16 1116 1104 HOH HOH . 
F 4 HOH A 17 1117 1105 HOH HOH . 
F 4 HOH A 18 1118 1106 HOH HOH . 
F 4 HOH A 19 1119 1123 HOH HOH . 
F 4 HOH A 20 1120 1117 HOH HOH . 
F 4 HOH A 21 1121 1129 HOH HOH . 
F 4 HOH A 22 1122 1136 HOH HOH . 
F 4 HOH A 23 1123 1132 HOH HOH . 
F 4 HOH A 24 1124 1150 HOH HOH . 
F 4 HOH A 25 1125 1107 HOH HOH . 
F 4 HOH A 26 1126 1138 HOH HOH . 
F 4 HOH A 27 1127 1127 HOH HOH . 
F 4 HOH A 28 1128 1108 HOH HOH . 
F 4 HOH A 29 1129 1140 HOH HOH . 
F 4 HOH A 30 1130 1121 HOH HOH . 
F 4 HOH A 31 1131 1124 HOH HOH . 
F 4 HOH A 32 1132 1148 HOH HOH . 
F 4 HOH A 33 1133 1159 HOH HOH . 
F 4 HOH A 34 1134 1147 HOH HOH . 
F 4 HOH A 35 1135 1134 HOH HOH . 
F 4 HOH A 36 1136 1156 HOH HOH . 
F 4 HOH A 37 1137 1130 HOH HOH . 
F 4 HOH A 38 1138 1126 HOH HOH . 
F 4 HOH A 39 1139 1120 HOH HOH . 
F 4 HOH A 40 1140 1109 HOH HOH . 
F 4 HOH A 41 1141 1110 HOH HOH . 
F 4 HOH A 42 1142 1116 HOH HOH . 
F 4 HOH A 43 1143 1141 HOH HOH . 
F 4 HOH A 44 1144 1118 HOH HOH . 
F 4 HOH A 45 1145 1151 HOH HOH . 
F 4 HOH A 46 1146 1139 HOH HOH . 
F 4 HOH A 47 1147 1153 HOH HOH . 
F 4 HOH A 48 1148 1169 HOH HOH . 
F 4 HOH A 49 1149 1165 HOH HOH . 
F 4 HOH A 50 1150 1161 HOH HOH . 
F 4 HOH A 51 1151 1158 HOH HOH . 
F 4 HOH A 52 1152 1155 HOH HOH . 
F 4 HOH A 53 1153 1143 HOH HOH . 
F 4 HOH A 54 1154 1131 HOH HOH . 
F 4 HOH A 55 1155 1164 HOH HOH . 
F 4 HOH A 56 1156 1111 HOH HOH . 
F 4 HOH A 57 1157 1162 HOH HOH . 
F 4 HOH A 58 1158 1149 HOH HOH . 
F 4 HOH A 59 1159 1135 HOH HOH . 
F 4 HOH A 60 1160 1142 HOH HOH . 
F 4 HOH A 61 1161 1112 HOH HOH . 
F 4 HOH A 62 1162 1152 HOH HOH . 
F 4 HOH A 63 1163 1113 HOH HOH . 
F 4 HOH A 64 1164 1128 HOH HOH . 
F 4 HOH A 65 1165 1163 HOH HOH . 
F 4 HOH A 66 1166 1146 HOH HOH . 
F 4 HOH A 67 1167 1167 HOH HOH . 
F 4 HOH A 68 1168 1114 HOH HOH . 
F 4 HOH A 69 1169 1166 HOH HOH . 
G 4 HOH B 1 1101 1101 HOH HOH . 
G 4 HOH B 2 1102 1102 HOH HOH . 
G 4 HOH B 3 1103 1152 HOH HOH . 
G 4 HOH B 4 1104 1131 HOH HOH . 
G 4 HOH B 5 1105 1168 HOH HOH . 
G 4 HOH B 6 1106 1139 HOH HOH . 
G 4 HOH B 7 1107 1159 HOH HOH . 
G 4 HOH B 8 1108 1171 HOH HOH . 
G 4 HOH B 9 1109 1121 HOH HOH . 
G 4 HOH B 10 1110 1156 HOH HOH . 
G 4 HOH B 11 1111 1148 HOH HOH . 
G 4 HOH B 12 1112 1130 HOH HOH . 
G 4 HOH B 13 1113 1120 HOH HOH . 
G 4 HOH B 14 1114 1103 HOH HOH . 
G 4 HOH B 15 1115 1118 HOH HOH . 
G 4 HOH B 16 1116 1119 HOH HOH . 
G 4 HOH B 17 1117 1155 HOH HOH . 
G 4 HOH B 18 1118 1144 HOH HOH . 
G 4 HOH B 19 1119 1135 HOH HOH . 
G 4 HOH B 20 1120 1179 HOH HOH . 
G 4 HOH B 21 1121 1138 HOH HOH . 
G 4 HOH B 22 1122 1136 HOH HOH . 
G 4 HOH B 23 1123 1174 HOH HOH . 
G 4 HOH B 24 1124 1122 HOH HOH . 
G 4 HOH B 25 1125 1112 HOH HOH . 
G 4 HOH B 26 1126 1169 HOH HOH . 
G 4 HOH B 27 1127 1178 HOH HOH . 
G 4 HOH B 28 1128 1132 HOH HOH . 
G 4 HOH B 29 1129 1162 HOH HOH . 
G 4 HOH B 30 1130 1147 HOH HOH . 
G 4 HOH B 31 1131 1173 HOH HOH . 
G 4 HOH B 32 1132 1133 HOH HOH . 
G 4 HOH B 33 1133 1104 HOH HOH . 
G 4 HOH B 34 1134 1123 HOH HOH . 
G 4 HOH B 35 1135 1146 HOH HOH . 
G 4 HOH B 36 1136 1113 HOH HOH . 
G 4 HOH B 37 1137 1175 HOH HOH . 
G 4 HOH B 38 1138 1105 HOH HOH . 
G 4 HOH B 39 1139 1154 HOH HOH . 
G 4 HOH B 40 1140 1129 HOH HOH . 
G 4 HOH B 41 1141 1117 HOH HOH . 
G 4 HOH B 42 1142 1161 HOH HOH . 
G 4 HOH B 43 1143 1158 HOH HOH . 
G 4 HOH B 44 1144 1106 HOH HOH . 
G 4 HOH B 45 1145 1107 HOH HOH . 
G 4 HOH B 46 1146 1125 HOH HOH . 
G 4 HOH B 47 1147 1111 HOH HOH . 
G 4 HOH B 48 1148 1153 HOH HOH . 
G 4 HOH B 49 1149 1108 HOH HOH . 
G 4 HOH B 50 1150 1170 HOH HOH . 
G 4 HOH B 51 1151 1114 HOH HOH . 
G 4 HOH B 52 1152 1140 HOH HOH . 
G 4 HOH B 53 1153 1109 HOH HOH . 
G 4 HOH B 54 1154 1128 HOH HOH . 
G 4 HOH B 55 1155 1115 HOH HOH . 
G 4 HOH B 56 1156 1145 HOH HOH . 
G 4 HOH B 57 1157 1126 HOH HOH . 
G 4 HOH B 58 1158 1141 HOH HOH . 
G 4 HOH B 59 1159 1176 HOH HOH . 
G 4 HOH B 60 1160 1163 HOH HOH . 
G 4 HOH B 61 1161 1137 HOH HOH . 
G 4 HOH B 62 1162 1172 HOH HOH . 
G 4 HOH B 63 1163 1149 HOH HOH . 
G 4 HOH B 64 1164 1142 HOH HOH . 
G 4 HOH B 65 1165 1167 HOH HOH . 
G 4 HOH B 66 1166 1116 HOH HOH . 
G 4 HOH B 67 1167 1134 HOH HOH . 
G 4 HOH B 68 1168 1177 HOH HOH . 
G 4 HOH B 69 1169 1150 HOH HOH . 
G 4 HOH B 70 1170 1166 HOH HOH . 
G 4 HOH B 71 1171 1127 HOH HOH . 
G 4 HOH B 72 1172 1164 HOH HOH . 
G 4 HOH B 73 1173 1143 HOH HOH . 
G 4 HOH B 74 1174 1160 HOH HOH . 
G 4 HOH B 75 1175 1110 HOH HOH . 
G 4 HOH B 76 1176 1124 HOH HOH . 
G 4 HOH B 77 1177 1165 HOH HOH . 
G 4 HOH B 78 1178 1157 HOH HOH . 
G 4 HOH B 79 1179 1151 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 . . . E 2 26.07 4.863 11.112 1 48.24 ? N1 PLP 1001 B 1 
HETATM 2 C C2 PLP . . . E 2 26.023 3.589 10.672 1 46.54 ? C2 PLP 1001 B 1 
HETATM 3 C C2A PLP . . . E 2 25.571 3.317 9.268 1 46.7 ? C2A PLP 1001 B 1 
HETATM 4 C C3 PLP . . . E 2 26.41 2.471 11.56 1 46.6 ? C3 PLP 1001 B 1 
HETATM 5 O O3 PLP . . . E 2 26.367 1.181 11.139 1 47.54 ? O3 PLP 1001 B 1 
HETATM 6 C C4 PLP . . . E 2 26.844 2.799 12.929 1 48.44 ? C4 PLP 1001 B 1 
HETATM 7 C C4A PLP . . . E 2 27.241 1.716 13.858 1 46.65 ? C4A PLP 1001 B 1 
HETATM 8 C C5 PLP . . . E 2 26.855 4.241 13.29 1 51.41 ? C5 PLP 1001 B 1 
HETATM 9 C C6 PLP . . . E 2 26.465 5.194 12.349 1 50.45 ? C6 PLP 1001 B 1 
HETATM 10 C C5A PLP . . . E 2 27.284 4.728 14.653 1 53.97 ? C5A PLP 1001 B 1 
HETATM 11 O O4P PLP . . . E 2 28.682 5.005 14.614 1 57.27 ? O4P PLP 1001 B 1 
HETATM 12 P P PLP . . . E 2 29.322 6.058 15.649 1 59.74 ? P PLP 1001 B 1 
HETATM 13 O O1P PLP . . . E 2 29.06 7.386 14.982 1 58 ? O1P PLP 1001 B 1 
HETATM 14 O O2P PLP . . . E 2 30.788 5.706 15.709 1 56.72 ? O2P PLP 1001 B 1 
HETATM 15 O O3P PLP . . . E 2 28.55 5.793 16.927 1 56.57 ? O3P PLP 1001 B 1 
#
_model_server_stats.io_time_ms              33 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    35 
_model_server_stats.query_time_ms           335 
_model_server_stats.encode_time_ms          7 
_model_server_stats.element_count           15 
#