data_5M7J
#
_model_server_result.job_id            eIOLy46cM_s_bgi1bOycNg 
_model_server_result.datetime_utc      '2024-11-27 08:06:52' 
_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          5m7j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"U","auth_seq_id":405}' 
#
_entry.id    5M7J 
#
_exptl.entry_id    5M7J 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              722.911 
_entity.id                          13 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE' 
_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            5M7J 
_cell.length_a            57.9 
_cell.length_b            84.8 
_cell.length_c            384.3 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5M7J 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        19 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 21 21 21' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    tetrameric 
_pdbx_struct_assembly.oligomeric_count      4 
_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,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 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      13 
_struct_asym.id                             U 
_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 D C FME 1 D FME 1 1_555 D N TYR 2 D TYR 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? 
metalc ? metalc1 A NE2 HIS 111 A HIS 91 1_555 E FE HEC . A HEC 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.522 ? 
metalc ? metalc2 A NE2 HIS 144 A HIS 124 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.415 ? 
metalc ? metalc3 A NE2 HIS 156 A HIS 136 1_555 F FE HEC . A HEC 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.543 ? 
metalc ? metalc4 A NE2 HIS 268 A HIS 248 1_555 G FE HEC . A HEC 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.461 ? 
metalc ? metalc5 A NE2 HIS 329 A HIS 309 1_555 H FE HEC . A HEC 404 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.327 ? 
metalc ? metalc6 B NE2 HIS 191 B HIS 190 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? 
metalc ? metalc7 B NE2 HIS 231 B HIS 230 1_555 P FE FE2 . B FE2 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.622 ? 
metalc ? metalc8 P FE FE2 . B FE2 307 1_555 C NE2 HIS 218 C HIS 217 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.459 ? 
metalc ? metalc9 P FE FE2 . B FE2 307 1_555 C OE1 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.602 ? 
metalc ? metalc10 P FE FE2 . B FE2 307 1_555 C OE2 GLU 233 C GLU 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? 
metalc ? metalc11 P FE FE2 . B FE2 307 1_555 C NE2 HIS 265 C HIS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
#
_chem_comp.formula           'C40 H68 O7 P2' 
_chem_comp.formula_weight    722.911 
_chem_comp.id                OTP 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2E,6E,10E,14E,18E,22E,26E)-3,7,11,15,19,23,27,31-OCTAMETHYLDOTRIACONTA-2,6,10,14,18,22,26,30-OCTAENYL TRIHYDROGEN DIPHOSPHATE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'OCTAPRENYL PYROPHOSPHATE' 
#
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
O7 P2 OTP sing 1027 n n 
O7 HO7 OTP sing 1028 n n 
P2 O5 OTP doub 1029 n n 
P2 O6 OTP sing 1030 n n 
P2 O4 OTP sing 1031 n n 
O6 HO6 OTP sing 1032 n n 
O4 P1 OTP sing 1033 n n 
P1 O2 OTP doub 1034 n n 
P1 O3 OTP sing 1035 n n 
P1 O1 OTP sing 1036 n n 
O3 HO3 OTP sing 1037 n n 
O1 C40 OTP sing 1038 n n 
C40 C39 OTP sing 1039 n n 
C40 H401 OTP sing 1040 n n 
C40 H402 OTP sing 1041 n n 
C39 C37 OTP doub 1042 e n 
C39 H39 OTP sing 1043 n n 
C37 C38 OTP sing 1044 n n 
C37 C36 OTP sing 1045 n n 
C38 H381 OTP sing 1046 n n 
C38 H382 OTP sing 1047 n n 
C38 H383 OTP sing 1048 n n 
C36 C35 OTP sing 1049 n n 
C36 H361 OTP sing 1050 n n 
C36 H362 OTP sing 1051 n n 
C35 C34 OTP sing 1052 n n 
C35 H351 OTP sing 1053 n n 
C35 H352 OTP sing 1054 n n 
C34 C32 OTP doub 1055 e n 
C34 H34 OTP sing 1056 n n 
C32 C33 OTP sing 1057 n n 
C32 C31 OTP sing 1058 n n 
C33 H331 OTP sing 1059 n n 
C33 H332 OTP sing 1060 n n 
C33 H333 OTP sing 1061 n n 
C31 C30 OTP sing 1062 n n 
C31 H311 OTP sing 1063 n n 
C31 H312 OTP sing 1064 n n 
C30 C29 OTP sing 1065 n n 
C30 H301 OTP sing 1066 n n 
C30 H302 OTP sing 1067 n n 
C29 C27 OTP doub 1068 e n 
C29 H29 OTP sing 1069 n n 
C27 C28 OTP sing 1070 n n 
C27 C26 OTP sing 1071 n n 
C28 H281 OTP sing 1072 n n 
C28 H282 OTP sing 1073 n n 
C28 H283 OTP sing 1074 n n 
C26 C25 OTP sing 1075 n n 
C26 H261 OTP sing 1076 n n 
C26 H262 OTP sing 1077 n n 
C25 C24 OTP sing 1078 n n 
C25 H251 OTP sing 1079 n n 
C25 H252 OTP sing 1080 n n 
C24 C22 OTP doub 1081 e n 
C24 H24 OTP sing 1082 n n 
C22 C23 OTP sing 1083 n n 
C22 C21 OTP sing 1084 n n 
C23 H231 OTP sing 1085 n n 
C23 H232 OTP sing 1086 n n 
C23 H233 OTP sing 1087 n n 
C21 C20 OTP sing 1088 n n 
C21 H211 OTP sing 1089 n n 
C21 H212 OTP sing 1090 n n 
C20 C19 OTP sing 1091 n n 
C20 H201 OTP sing 1092 n n 
C20 H202 OTP sing 1093 n n 
C19 C17 OTP doub 1094 e n 
C19 H19 OTP sing 1095 n n 
C17 C18 OTP sing 1096 n n 
C17 C16 OTP sing 1097 n n 
C18 H181 OTP sing 1098 n n 
C18 H182 OTP sing 1099 n n 
C18 H183 OTP sing 1100 n n 
C16 C15 OTP sing 1101 n n 
C16 H161 OTP sing 1102 n n 
C16 H162 OTP sing 1103 n n 
C15 C14 OTP sing 1104 n n 
C15 H151 OTP sing 1105 n n 
C15 H152 OTP sing 1106 n n 
C14 C12 OTP doub 1107 e n 
C14 H14 OTP sing 1108 n n 
C12 C13 OTP sing 1109 n n 
C12 C11 OTP sing 1110 n n 
C13 H131 OTP sing 1111 n n 
C13 H132 OTP sing 1112 n n 
C13 H133 OTP sing 1113 n n 
C11 C10 OTP sing 1114 n n 
C11 H111 OTP sing 1115 n n 
C11 H112 OTP sing 1116 n n 
C10 C9 OTP sing 1117 n n 
C10 H101 OTP sing 1118 n n 
C10 H102 OTP sing 1119 n n 
C9 C7 OTP doub 1120 e n 
C9 H9 OTP sing 1121 n n 
C7 C8 OTP sing 1122 n n 
C7 C6 OTP sing 1123 n n 
C8 H81 OTP sing 1124 n n 
C8 H82 OTP sing 1125 n n 
C8 H83 OTP sing 1126 n n 
C6 C5 OTP sing 1127 n n 
C6 H61 OTP sing 1128 n n 
C6 H62 OTP sing 1129 n n 
C5 C4 OTP sing 1130 n n 
C5 H51 OTP sing 1131 n n 
C5 H52 OTP sing 1132 n n 
C4 C2 OTP doub 1133 n n 
C4 H4 OTP sing 1134 n n 
C2 C3 OTP sing 1135 n n 
C2 C1 OTP sing 1136 n n 
C3 H31 OTP sing 1137 n n 
C3 H32 OTP sing 1138 n n 
C3 H33 OTP sing 1139 n n 
C1 H11 OTP sing 1140 n n 
C1 H12 OTP sing 1141 n n 
C1 H13 OTP sing 1142 n n 
#
_atom_sites.entry_id                     5M7J 
_atom_sites.fract_transf_matrix[1][1]    0.017271 
_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]    0.011792 
_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]    0.002602 
_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
E 5 HEC A 1 401 1333 HEC HEM . 
F 5 HEC A 1 402 1334 HEC HEM . 
G 5 HEC A 1 403 1335 HEC HEM . 
H 5 HEC A 1 404 1336 HEC HEM . 
I 6 DGA A 1 405 1278 DGA DGA . 
J 7 BCL B 1 301 1274 BCL BCL . 
K 7 BCL B 1 302 1275 BCL BCL . 
L 7 BCL B 1 303 1276 BCL BCL . 
M 8 BPB B 1 304 1277 BPB BPB . 
N 9 MPG B 1 305 1279 MPG MPG . 
O 9 MPG B 1 306 1280 MPG MPG . 
P 10 FE2 B 1 307 1326 FE2 FE2 . 
Q 7 BCL C 1 401 1324 BCL BCL . 
R 8 BPB C 1 402 1325 BPB BPB . 
S 11 MQ7 C 1 403 1327 MQ7 MQ7 . 
T 12 NS5 C 1 404 1328 NS5 NS5 . 
U 13 OTP C 1 405 1329 OTP OTP . 
V 9 MPG C 1 406 1330 MPG MPG . 
W 14 PO4 C 1 407 1331 PO4 PO4 . 
X 14 PO4 C 1 408 1332 PO4 PO4 . 
#
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 O O1 OTP . . . U 13 16.71 -0.502 59.875 1 58.66 ? O1 OTP 405 C 1 
HETATM 2 C C40 OTP . . . U 13 16.04 -1.658 59.43 1 60.17 ? C40 OTP 405 C 1 
HETATM 3 C C39 OTP . . . U 13 17.046 -2.679 58.941 1 53.22 ? C39 OTP 405 C 1 
HETATM 4 C C37 OTP . . . U 13 16.844 -4.003 59.112 1 52 ? C37 OTP 405 C 1 
HETATM 5 C C38 OTP . . . U 13 17.88 -4.982 58.606 1 46.04 ? C38 OTP 405 C 1 
HETATM 6 C C36 OTP . . . U 13 15.601 -4.523 59.81 1 52.09 ? C36 OTP 405 C 1 
HETATM 7 C C35 OTP . . . U 13 14.462 -4.692 58.821 1 60.16 ? C35 OTP 405 C 1 
HETATM 8 C C34 OTP . . . U 13 13.509 -5.773 59.285 1 60.82 ? C34 OTP 405 C 1 
HETATM 9 C C32 OTP . . . U 13 12.233 -5.785 58.849 1 59.53 ? C32 OTP 405 C 1 
HETATM 10 C C33 OTP . . . U 13 11.778 -4.688 57.907 1 60.98 ? C33 OTP 405 C 1 
HETATM 11 C C31 OTP . . . U 13 11.311 -6.891 59.342 1 46.85 ? C31 OTP 405 C 1 
HETATM 12 C C30 OTP . . . U 13 10.137 -7.219 58.439 1 41.14 ? C30 OTP 405 C 1 
HETATM 13 C C29 OTP . . . U 13 10.571 -7.603 57.039 1 39.31 ? C29 OTP 405 C 1 
HETATM 14 C C27 OTP . . . U 13 9.73 -8.256 56.216 1 40.89 ? C27 OTP 405 C 1 
HETATM 15 C C28 OTP . . . U 13 8.349 -8.643 56.695 1 37.09 ? C28 OTP 405 C 1 
HETATM 16 C C26 OTP . . . U 13 10.182 -8.613 54.818 1 44.31 ? C26 OTP 405 C 1 
HETATM 17 C C25 OTP . . . U 13 9.757 -7.546 53.83 1 44.09 ? C25 OTP 405 C 1 
HETATM 18 C C24 OTP . . . U 13 9.358 -8.245 52.549 1 45.32 ? C24 OTP 405 C 1 
HETATM 19 C C22 OTP . . . U 13 8.738 -7.619 51.525 1 51.3 ? C22 OTP 405 C 1 
HETATM 20 C C23 OTP . . . U 13 8.389 -6.147 51.594 1 52.71 ? C23 OTP 405 C 1 
HETATM 21 C C21 OTP . . . U 13 8.383 -8.446 50.308 1 45.68 ? C21 OTP 405 C 1 
HETATM 22 C C20 OTP . . . U 13 8.419 -7.677 49.006 1 46.05 ? C20 OTP 405 C 1 
HETATM 23 C C19 OTP . . . U 13 8.393 -8.742 47.932 1 45.48 ? C19 OTP 405 C 1 
HETATM 24 C C17 OTP . . . U 13 8.444 -8.494 46.608 1 62.7 ? C17 OTP 405 C 1 
HETATM 25 C C18 OTP . . . U 13 8.407 -9.678 45.667 1 59.64 ? C18 OTP 405 C 1 
HETATM 26 C C16 OTP . . . U 13 8.535 -7.083 46.06 1 73.41 ? C16 OTP 405 C 1 
HETATM 27 C C15 OTP . . . U 13 9.42 -7.049 44.828 1 76.86 ? C15 OTP 405 C 1 
HETATM 28 C C14 OTP . . . U 13 8.587 -7.024 43.559 1 73.91 ? C14 OTP 405 C 1 
HETATM 29 C C12 OTP . . . U 13 8.895 -6.177 42.555 1 62.36 ? C12 OTP 405 C 1 
HETATM 30 C C13 OTP . . . U 13 10.08 -5.248 42.705 1 75.05 ? C13 OTP 405 C 1 
HETATM 31 C C11 OTP . . . U 13 8.061 -6.164 41.289 1 62.7 ? C11 OTP 405 C 1 
HETATM 32 C C10 OTP . . . U 13 7.504 -4.781 41.021 1 72.67 ? C10 OTP 405 C 1 
HETATM 33 C C9 OTP . . . U 13 8.351 -4.08 39.979 1 73.52 ? C9 OTP 405 C 1 
HETATM 34 C C7 OTP . . . U 13 8.13 -2.788 39.659 1 79.32 ? C7 OTP 405 C 1 
HETATM 35 C C8 OTP . . . U 13 7.022 -2.009 40.336 1 63.42 ? C8 OTP 405 C 1 
HETATM 36 C C6 OTP . . . U 13 9.009 -2.13 38.615 1 90.45 ? C6 OTP 405 C 1 
HETATM 37 C C5 OTP . . . U 13 8.411 -0.826 38.133 1 90.48 ? C5 OTP 405 C 1 
HETATM 38 C C4 OTP . . . U 13 9.493 -0.023 37.443 1 85.48 ? C4 OTP 405 C 1 
HETATM 39 C C2 OTP . . . U 13 9.182 1.006 36.628 1 74.21 ? C2 OTP 405 C 1 
HETATM 40 C C3 OTP . . . U 13 10.285 1.79 35.952 1 69.3 ? C3 OTP 405 C 1 
HETATM 41 C C1 OTP . . . U 13 7.735 1.377 36.389 1 71.71 ? C1 OTP 405 C 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           19 
_model_server_stats.create_model_time_ms    42 
_model_server_stats.query_time_ms           351 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           41 
#