data_6GPV
#
_model_server_result.job_id            ttTxbgAVmrXyeJvq7uG20g 
_model_server_result.datetime_utc      '2024-11-27 17:58:25' 
_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          6gpv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"E","auth_seq_id":1004}' 
#
_entry.id    6GPV 
#
_exptl.entry_id    6GPV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              242.233 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            LUMICHROME 
_entity.pdbx_number_of_molecules    1 
_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            6GPV 
_cell.length_a            40.5 
_cell.length_b            40.5 
_cell.length_c            133.76 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 6GPV 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        96 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 43 21 2' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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 
_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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      5 
_struct_asym.id                             E 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    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 C ASN 72 A ASN 72 1_555 A N F7Q 73 A F7Q 73 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.328 ? 
covale ? covale2 A C F7Q 73 A F7Q 73 1_555 A N THR 74 A THR 74 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.319 ? 
covale ? covale3 A C PHE 80 A PHE 80 1_555 A N NFK 81 A NFK 81 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.316 ? 
covale ? covale4 A C NFK 81 A NFK 81 1_555 A N ASN 82 A ASN 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? 
covale ? covale5 A C LEU 84 A LEU 84 1_555 A N HOO 85 A HOO 85 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.341 ? 
covale ? covale6 A C LEU 84 A LEU 84 1_555 A N OHI 85 A OHI 85 1_555 ? ? ? ? B ? ? ? ? ? ? ? 1.341 ? 
covale ? covale7 A C HOO 85 A HOO 85 1_555 A N LEU 86 A LEU 86 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.349 ? 
covale ? covale8 A C OHI 85 A OHI 85 1_555 A N LEU 86 A LEU 86 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.349 ? 
metalc ? metalc1 C MG MG . A MG 1002 1_555 F O HOH . A HOH 1104 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.07 ? 
metalc ? metalc2 C MG MG . A MG 1002 1_555 F O HOH . A HOH 1114 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.366 ? 
metalc ? metalc3 C MG MG . A MG 1002 1_555 F O HOH . A HOH 1116 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.074 ? 
metalc ? metalc4 C MG MG . A MG 1002 1_555 F O HOH . A HOH 1212 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.007 ? 
metalc ? metalc5 C MG MG . A MG 1002 1_555 F O HOH . A HOH 1216 1_555 ? A ? ? A ? ? ? ? ? ? ? 2.048 ? 
#
_chem_comp.formula           'C12 H10 N4 O2' 
_chem_comp.formula_weight    242.233 
_chem_comp.id                LUM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              LUMICHROME 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     7,8-DIMETHYLALLOXAZINE;6,7-DIMETHYLALLOXAZINE 
#
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 LUM sing 294 n y 
N1 C10 LUM sing 295 n y 
N1 HN1 LUM sing 296 n n 
C2 O2 LUM doub 297 n n 
C2 N3 LUM sing 298 n y 
C10 C4A LUM doub 299 n y 
C10 N10 LUM sing 300 n y 
N3 C4 LUM sing 301 n y 
N3 HN3 LUM sing 302 n n 
C4 O4 LUM doub 303 n n 
C4 C4A LUM sing 304 n y 
C4A N5 LUM sing 305 n y 
N5 C5A LUM doub 306 n y 
C5A C6 LUM sing 307 n y 
C5A C9A LUM sing 308 n y 
C6 C7 LUM doub 309 n y 
C6 HC6 LUM sing 310 n n 
C9A C9 LUM sing 311 n y 
C9A N10 LUM doub 312 n y 
C7 C7M LUM sing 313 n n 
C7 C8 LUM sing 314 n y 
C7M H7M1 LUM sing 315 n n 
C7M H7M2 LUM sing 316 n n 
C7M H7M3 LUM sing 317 n n 
C8 C8M LUM sing 318 n n 
C8 C9 LUM doub 319 n y 
C8M H8M1 LUM sing 320 n n 
C8M H8M2 LUM sing 321 n n 
C8M H8M3 LUM sing 322 n n 
C9 HC9 LUM sing 323 n n 
#
_atom_sites.entry_id                     6GPV 
_atom_sites.fract_transf_matrix[1][1]    0.024691 
_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]    0.024691 
_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]    0.007476 
_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
B 2 FMN A 1 1001 1001 FMN FMN . 
C 3 MG A 1 1002 1 MG MG . 
D 4 CL A 1 1003 1002 CL CL . 
E 5 LUM A 1 1004 1 LUM LUM . 
F 6 HOH A 1 1101 123 HOH HOH . 
F 6 HOH A 2 1102 55 HOH HOH . 
F 6 HOH A 3 1103 120 HOH HOH . 
F 6 HOH A 4 1104 25 HOH HOH . 
F 6 HOH A 5 1105 38 HOH HOH . 
F 6 HOH A 6 1106 40 HOH HOH . 
F 6 HOH A 7 1107 78 HOH HOH . 
F 6 HOH A 8 1108 61 HOH HOH . 
F 6 HOH A 9 1109 107 HOH HOH . 
F 6 HOH A 10 1110 98 HOH HOH . 
F 6 HOH A 11 1111 114 HOH HOH . 
F 6 HOH A 12 1112 125 HOH HOH . 
F 6 HOH A 13 1113 124 HOH HOH . 
F 6 HOH A 14 1114 17 HOH HOH . 
F 6 HOH A 15 1115 70 HOH HOH . 
F 6 HOH A 16 1116 6 HOH HOH . 
F 6 HOH A 17 1117 100 HOH HOH . 
F 6 HOH A 18 1118 69 HOH HOH . 
F 6 HOH A 19 1119 33 HOH HOH . 
F 6 HOH A 20 1120 44 HOH HOH . 
F 6 HOH A 21 1121 109 HOH HOH . 
F 6 HOH A 22 1122 116 HOH HOH . 
F 6 HOH A 23 1123 64 HOH HOH . 
F 6 HOH A 24 1124 46 HOH HOH . 
F 6 HOH A 25 1125 14 HOH HOH . 
F 6 HOH A 26 1126 26 HOH HOH . 
F 6 HOH A 27 1127 22 HOH HOH . 
F 6 HOH A 28 1128 126 HOH HOH . 
F 6 HOH A 29 1129 21 HOH HOH . 
F 6 HOH A 30 1130 54 HOH HOH . 
F 6 HOH A 31 1131 73 HOH HOH . 
F 6 HOH A 32 1132 92 HOH HOH . 
F 6 HOH A 33 1133 8 HOH HOH . 
F 6 HOH A 34 1134 5 HOH HOH . 
F 6 HOH A 35 1135 18 HOH HOH . 
F 6 HOH A 36 1136 30 HOH HOH . 
F 6 HOH A 37 1137 67 HOH HOH . 
F 6 HOH A 38 1138 96 HOH HOH . 
F 6 HOH A 39 1139 19 HOH HOH . 
F 6 HOH A 40 1140 20 HOH HOH . 
F 6 HOH A 41 1141 117 HOH HOH . 
F 6 HOH A 42 1142 52 HOH HOH . 
F 6 HOH A 43 1143 122 HOH HOH . 
F 6 HOH A 44 1144 62 HOH HOH . 
F 6 HOH A 45 1145 4 HOH HOH . 
F 6 HOH A 46 1146 71 HOH HOH . 
F 6 HOH A 47 1147 59 HOH HOH . 
F 6 HOH A 48 1148 95 HOH HOH . 
F 6 HOH A 49 1149 84 HOH HOH . 
F 6 HOH A 50 1150 9 HOH HOH . 
F 6 HOH A 51 1151 29 HOH HOH . 
F 6 HOH A 52 1152 90 HOH HOH . 
F 6 HOH A 53 1153 103 HOH HOH . 
F 6 HOH A 54 1154 10 HOH HOH . 
F 6 HOH A 55 1155 51 HOH HOH . 
F 6 HOH A 56 1156 93 HOH HOH . 
F 6 HOH A 57 1157 45 HOH HOH . 
F 6 HOH A 58 1158 68 HOH HOH . 
F 6 HOH A 59 1159 1 HOH HOH . 
F 6 HOH A 60 1160 108 HOH HOH . 
F 6 HOH A 61 1161 57 HOH HOH . 
F 6 HOH A 62 1162 104 HOH HOH . 
F 6 HOH A 63 1163 43 HOH HOH . 
F 6 HOH A 64 1164 24 HOH HOH . 
F 6 HOH A 65 1165 36 HOH HOH . 
F 6 HOH A 66 1166 41 HOH HOH . 
F 6 HOH A 67 1167 15 HOH HOH . 
F 6 HOH A 68 1168 49 HOH HOH . 
F 6 HOH A 69 1169 3 HOH HOH . 
F 6 HOH A 70 1170 106 HOH HOH . 
F 6 HOH A 71 1171 7 HOH HOH . 
F 6 HOH A 72 1172 53 HOH HOH . 
F 6 HOH A 73 1173 11 HOH HOH . 
F 6 HOH A 74 1174 85 HOH HOH . 
F 6 HOH A 75 1175 115 HOH HOH . 
F 6 HOH A 76 1176 60 HOH HOH . 
F 6 HOH A 77 1177 12 HOH HOH . 
F 6 HOH A 78 1178 37 HOH HOH . 
F 6 HOH A 79 1179 112 HOH HOH . 
F 6 HOH A 80 1180 47 HOH HOH . 
F 6 HOH A 81 1181 119 HOH HOH . 
F 6 HOH A 82 1182 58 HOH HOH . 
F 6 HOH A 83 1183 74 HOH HOH . 
F 6 HOH A 84 1184 48 HOH HOH . 
F 6 HOH A 85 1185 65 HOH HOH . 
F 6 HOH A 86 1186 31 HOH HOH . 
F 6 HOH A 87 1187 2 HOH HOH . 
F 6 HOH A 88 1188 13 HOH HOH . 
F 6 HOH A 89 1189 102 HOH HOH . 
F 6 HOH A 90 1190 34 HOH HOH . 
F 6 HOH A 91 1191 99 HOH HOH . 
F 6 HOH A 92 1192 28 HOH HOH . 
F 6 HOH A 93 1193 77 HOH HOH . 
F 6 HOH A 94 1194 42 HOH HOH . 
F 6 HOH A 95 1195 66 HOH HOH . 
F 6 HOH A 96 1196 39 HOH HOH . 
F 6 HOH A 97 1197 88 HOH HOH . 
F 6 HOH A 98 1198 97 HOH HOH . 
F 6 HOH A 99 1199 105 HOH HOH . 
F 6 HOH A 100 1200 23 HOH HOH . 
F 6 HOH A 101 1201 16 HOH HOH . 
F 6 HOH A 102 1202 89 HOH HOH . 
F 6 HOH A 103 1203 82 HOH HOH . 
F 6 HOH A 104 1204 63 HOH HOH . 
F 6 HOH A 105 1205 111 HOH HOH . 
F 6 HOH A 106 1206 72 HOH HOH . 
F 6 HOH A 107 1207 50 HOH HOH . 
F 6 HOH A 108 1208 35 HOH HOH . 
F 6 HOH A 109 1209 87 HOH HOH . 
F 6 HOH A 110 1210 80 HOH HOH . 
F 6 HOH A 111 1211 56 HOH HOH . 
F 6 HOH A 112 1212 27 HOH HOH . 
F 6 HOH A 113 1213 81 HOH HOH . 
F 6 HOH A 114 1214 110 HOH HOH . 
F 6 HOH A 115 1215 118 HOH HOH . 
F 6 HOH A 116 1216 32 HOH HOH . 
F 6 HOH A 117 1217 86 HOH HOH . 
F 6 HOH A 118 1218 79 HOH HOH . 
F 6 HOH A 119 1219 113 HOH HOH . 
F 6 HOH A 120 1220 101 HOH HOH . 
F 6 HOH A 121 1221 83 HOH HOH . 
F 6 HOH A 122 1222 121 HOH HOH . 
F 6 HOH A 123 1223 75 HOH HOH . 
F 6 HOH A 124 1224 76 HOH HOH . 
F 6 HOH A 125 1225 91 HOH HOH . 
F 6 HOH A 126 1226 94 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 LUM . B . E 5 -1.76 -7.433 -12.899 0.25 23.91 ? N1 LUM 1004 A 1 
HETATM 2 C C2 LUM . B . E 5 -1.969 -8.115 -14.037 0.25 24.28 ? C2 LUM 1004 A 1 
HETATM 3 C C10 LUM . B . E 5 -0.658 -6.708 -12.718 0.25 23.83 ? C10 LUM 1004 A 1 
HETATM 4 O O2 LUM . B . E 5 -3.022 -8.775 -14.125 0.25 24.66 ? O2 LUM 1004 A 1 
HETATM 5 N N3 LUM . B . E 5 -1.106 -8.116 -15.076 0.25 24.22 ? N3 LUM 1004 A 1 
HETATM 6 C C4 LUM . B . E 5 0.046 -7.431 -15.031 0.25 24.49 ? C4 LUM 1004 A 1 
HETATM 7 O O4 LUM . B . E 5 0.858 -7.434 -15.985 0.25 24.28 ? O4 LUM 1004 A 1 
HETATM 8 C C4A LUM . B . E 5 0.337 -6.659 -13.806 0.25 24.23 ? C4A LUM 1004 A 1 
HETATM 9 N N5 LUM . B . E 5 1.463 -5.943 -13.677 0.25 24.64 ? N5 LUM 1004 A 1 
HETATM 10 C C5A LUM . B . E 5 1.684 -5.257 -12.538 0.25 24.18 ? C5A LUM 1004 A 1 
HETATM 11 C C6 LUM . B . E 5 2.85 -4.524 -12.403 0.25 23.73 ? C6 LUM 1004 A 1 
HETATM 12 C C9A LUM . B . E 5 0.686 -5.297 -11.433 0.25 24.28 ? C9A LUM 1004 A 1 
HETATM 13 C C7 LUM . B . E 5 3.088 -3.819 -11.236 0.25 23.67 ? C7 LUM 1004 A 1 
HETATM 14 C C7M LUM . B . E 5 4.351 -3.018 -11.09 0.25 23.79 ? C7M LUM 1004 A 1 
HETATM 15 C C8 LUM . B . E 5 2.096 -3.852 -10.133 0.25 23.81 ? C8 LUM 1004 A 1 
HETATM 16 C C8M LUM . B . E 5 2.374 -3.088 -8.867 0.25 24.63 ? C8M LUM 1004 A 1 
HETATM 17 C C9 LUM . B . E 5 0.93 -4.592 -10.261 0.25 23.67 ? C9 LUM 1004 A 1 
HETATM 18 N N10 LUM . B . E 5 -0.446 -6.027 -11.576 0.25 24.4 ? N10 LUM 1004 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    11 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           18 
#