data_3MDB
#
_model_server_result.job_id            NpJ4Zq-GI4KSYvA0k3wVyA 
_model_server_result.datetime_utc      '2024-10-20 05:30:32' 
_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          3mdb 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"I","auth_seq_id":375}' 
#
_entry.id    3MDB 
#
_exptl.entry_id    3MDB 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              826.546 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate' 
_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            3MDB 
_cell.length_a            115.797 
_cell.length_b            115.797 
_cell.length_c            189.269 
_cell.Z_PDB               16 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3MDB 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_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,E,F,H,I,J,K,L 1 1 
B,D,G,M,N,O,P,Q,R 2 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                             I 
_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
metalc ? metalc1 C SG CYS 39 C CYS 21 1_555 H ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? 
metalc ? metalc2 C SG CYS 42 C CYS 24 1_555 H ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? 
metalc ? metalc3 C SG CYS 59 C CYS 41 1_555 H ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.24 ? 
metalc ? metalc4 C SG CYS 62 C CYS 44 1_555 H ZN ZN . C ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.134 ? 
metalc ? metalc5 D SG CYS 39 D CYS 21 1_555 M ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.184 ? 
metalc ? metalc6 D SG CYS 42 D CYS 24 1_555 M ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.963 ? 
metalc ? metalc7 D SG CYS 59 D CYS 41 1_555 M ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? 
metalc ? metalc8 D SG CYS 62 D CYS 44 1_555 M ZN ZN . D ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? 
#
_chem_comp.formula           'C25 H50 O22 P4' 
_chem_comp.formula_weight    826.546 
_chem_comp.id                IP9 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-3-{[(R)-{[(1S,2S,3R,4S,5S,6S)-2,6-dihydroxy-3,4,5-tris(phosphonooxy)cyclohexyl]oxy}(hydroxy)phosphoryl]oxy}propane -1,2-diyl dioctanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     'L-a-Phosphatidyl-D-myo-inositol 3,4,5-triphosphate, dioctanoyl;[(2R)-3-[[(2S,3S,5R,6S)-2,6-dihydroxy-3,4,5-triphosphonooxy-cyclohexyl]oxy-hydroxy-phosphoryl]oxy-2-octanoyloxy-propyl] octanoate' 
#
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
C1 O1 IP9 sing 171 n n 
C1 C2 IP9 sing 172 n n 
C1 C6 IP9 sing 173 n n 
C1 H1 IP9 sing 174 n n 
O1 P1 IP9 sing 175 n n 
C2 O2 IP9 sing 176 n n 
C2 C3 IP9 sing 177 n n 
C2 H2 IP9 sing 178 n n 
O2 HO2 IP9 sing 179 n n 
C3 O3 IP9 sing 180 n n 
C3 C4 IP9 sing 181 n n 
C3 H3 IP9 sing 182 n n 
O3 P3 IP9 sing 183 n n 
C4 O4 IP9 sing 184 n n 
C4 C5 IP9 sing 185 n n 
C4 H4 IP9 sing 186 n n 
O4 P4 IP9 sing 187 n n 
C5 O5 IP9 sing 188 n n 
C5 C6 IP9 sing 189 n n 
C5 H5 IP9 sing 190 n n 
O5 P5 IP9 sing 191 n n 
C6 O6 IP9 sing 192 n n 
C6 H6 IP9 sing 193 n n 
O6 HO6 IP9 sing 194 n n 
P1 O1P IP9 doub 195 n n 
P1 O2P IP9 sing 196 n n 
P1 O3P IP9 sing 197 n n 
O2P HO2P IP9 sing 198 n n 
O3P C7 IP9 sing 199 n n 
P3 O4P IP9 doub 200 n n 
P3 O5P IP9 sing 201 n n 
P3 O6P IP9 sing 202 n n 
O5P HO5P IP9 sing 203 n n 
O6P HO6P IP9 sing 204 n n 
P4 O7P IP9 sing 205 n n 
P4 O8P IP9 sing 206 n n 
P4 O9P IP9 doub 207 n n 
O7P HO7P IP9 sing 208 n n 
O8P HO8P IP9 sing 209 n n 
P5 OPF IP9 sing 210 n n 
P5 OPG IP9 doub 211 n n 
P5 OPH IP9 sing 212 n n 
OPF HOP1 IP9 sing 213 n n 
OPH HOP3 IP9 sing 214 n n 
C7 C8 IP9 sing 215 n n 
C7 H16 IP9 sing 216 n n 
C7 H17 IP9 sing 217 n n 
C8 C9 IP9 sing 218 n n 
C8 O19 IP9 sing 219 n n 
C9 O20 IP9 sing 220 n n 
C9 H18 IP9 sing 221 n n 
C9 H19 IP9 sing 222 n n 
O19 C10 IP9 sing 223 n n 
O20 C11 IP9 sing 224 n n 
C10 O21 IP9 doub 225 n n 
C10 C12 IP9 sing 226 n n 
C11 C13 IP9 sing 227 n n 
C11 O22 IP9 doub 228 n n 
C8 H20 IP9 sing 229 n n 
C12 C14 IP9 sing 230 n n 
C12 H21 IP9 sing 231 n n 
C12 H22 IP9 sing 232 n n 
C13 C15 IP9 sing 233 n n 
C13 H23 IP9 sing 234 n n 
C13 H24 IP9 sing 235 n n 
C14 H25 IP9 sing 236 n n 
C14 H26 IP9 sing 237 n n 
C14 C16 IP9 sing 238 n n 
C15 H27 IP9 sing 239 n n 
C15 H28 IP9 sing 240 n n 
C15 C17 IP9 sing 241 n n 
C16 H29 IP9 sing 242 n n 
C16 C18 IP9 sing 243 n n 
C16 H30 IP9 sing 244 n n 
C17 H31 IP9 sing 245 n n 
C17 H32 IP9 sing 246 n n 
C17 C19 IP9 sing 247 n n 
C18 C20 IP9 sing 248 n n 
C18 H33 IP9 sing 249 n n 
C18 H34 IP9 sing 250 n n 
C19 H35 IP9 sing 251 n n 
C19 C21 IP9 sing 252 n n 
C19 H36 IP9 sing 253 n n 
C20 C22 IP9 sing 254 n n 
C20 H37 IP9 sing 255 n n 
C20 H38 IP9 sing 256 n n 
C21 H39 IP9 sing 257 n n 
C21 H40 IP9 sing 258 n n 
C21 C23 IP9 sing 259 n n 
C22 H41 IP9 sing 260 n n 
C22 H42 IP9 sing 261 n n 
C22 C24 IP9 sing 262 n n 
C23 C25 IP9 sing 263 n n 
C23 H43 IP9 sing 264 n n 
C23 H44 IP9 sing 265 n n 
C24 H45 IP9 sing 266 n n 
C24 H46 IP9 sing 267 n n 
C24 H47 IP9 sing 268 n n 
C25 H48 IP9 sing 269 n n 
C25 H49 IP9 sing 270 n n 
C25 H50 IP9 sing 271 n n 
#
_atom_sites.entry_id                     3MDB 
_atom_sites.fract_transf_matrix[1][1]    0.008636 
_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]    0.008636 
_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]    0.005283 
_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 3 UNX A 1 1 1 UNX UNX . 
F 3 UNX A 1 5 5 UNX UNX . 
G 3 UNX B 1 11 11 UNX UNX . 
H 4 ZN C 1 401 401 ZN ZN . 
I 5 IP9 C 1 375 1 IP9 IP9 . 
J 3 UNX C 1 376 2 UNX UNX . 
K 3 UNX C 1 377 3 UNX UNX . 
L 3 UNX C 1 378 4 UNX UNX . 
M 4 ZN D 1 401 401 ZN ZN . 
N 3 UNX D 1 375 6 UNX UNX . 
O 3 UNX D 1 376 7 UNX UNX . 
P 3 UNX D 1 377 12 UNX UNX . 
Q 3 UNX D 1 378 13 UNX UNX . 
R 3 UNX D 1 379 14 UNX UNX . 
#
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 C C1 IP9 . . . I 5 -22.239 -18.016 -11.763 1 67.95 ? C1 IP9 375 C 1 
HETATM 2 O O1 IP9 . . . I 5 -21.759 -18.273 -10.43 1 69.36 ? O1 IP9 375 C 1 
HETATM 3 C C2 IP9 . . . I 5 -22.979 -16.655 -11.817 1 67.48 ? C2 IP9 375 C 1 
HETATM 4 O O2 IP9 . . . I 5 -23.991 -16.591 -10.8 1 67.28 ? O2 IP9 375 C 1 
HETATM 5 C C3 IP9 . . . I 5 -23.599 -16.427 -13.206 1 66.3 ? C3 IP9 375 C 1 
HETATM 6 O O3 IP9 . . . I 5 -24.323 -15.225 -13.227 1 65.89 ? O3 IP9 375 C 1 
HETATM 7 C C4 IP9 . . . I 5 -24.541 -17.538 -13.598 1 65.87 ? C4 IP9 375 C 1 
HETATM 8 O O4 IP9 . . . I 5 -24.977 -17.267 -14.936 1 64.51 ? O4 IP9 375 C 1 
HETATM 9 C C5 IP9 . . . I 5 -23.815 -18.906 -13.568 1 66.74 ? C5 IP9 375 C 1 
HETATM 10 O O5 IP9 . . . I 5 -24.74 -19.956 -13.9 1 67.97 ? O5 IP9 375 C 1 
HETATM 11 C C6 IP9 . . . I 5 -23.133 -19.187 -12.209 1 67.23 ? C6 IP9 375 C 1 
HETATM 12 O O6 IP9 . . . I 5 -22.324 -20.374 -12.271 1 66.02 ? O6 IP9 375 C 1 
HETATM 13 P P1 IP9 . . . I 5 -20.245 -18.821 -10.153 1 69.95 ? P1 IP9 375 C 1 
HETATM 14 O O1P IP9 . . . I 5 -19.65 -19.439 -11.367 1 69.85 ? O1P IP9 375 C 1 
HETATM 15 O O2P IP9 . . . I 5 -20.396 -19.86 -8.874 1 70.6 ? O2P IP9 375 C 1 
HETATM 16 O O3P IP9 . . . I 5 -19.378 -17.584 -9.572 1 67.97 ? O3P IP9 375 C 1 
HETATM 17 P P3 IP9 . . . I 5 -23.679 -13.975 -13.99 1 66.74 ? P3 IP9 375 C 1 
HETATM 18 O O4P IP9 . . . I 5 -23.857 -14.089 -15.44 1 66.22 ? O4P IP9 375 C 1 
HETATM 19 O O5P IP9 . . . I 5 -24.365 -12.675 -13.289 1 66.01 ? O5P IP9 375 C 1 
HETATM 20 O O6P IP9 . . . I 5 -22.107 -13.87 -13.584 1 65.7 ? O6P IP9 375 C 1 
HETATM 21 P P4 IP9 . . . I 5 -26.314 -16.512 -15.365 1 62.32 ? P4 IP9 375 C 1 
HETATM 22 O O7P IP9 . . . I 5 -27.111 -17.131 -16.448 1 60.66 ? O7P IP9 375 C 1 
HETATM 23 O O8P IP9 . . . I 5 -27.185 -16.232 -14.038 1 63.01 ? O8P IP9 375 C 1 
HETATM 24 O O9P IP9 . . . I 5 -25.797 -15.087 -15.831 1 61.58 ? O9P IP9 375 C 1 
HETATM 25 P P5 IP9 . . . I 5 -25.068 -20.367 -15.482 1 69.4 ? P5 IP9 375 C 1 
HETATM 26 O OPF IP9 . . . I 5 -25.174 -21.834 -15.668 1 69.45 ? OPF IP9 375 C 1 
HETATM 27 O OPG IP9 . . . I 5 -23.893 -19.71 -16.392 1 68.53 ? OPG IP9 375 C 1 
HETATM 28 O OPH IP9 . . . I 5 -26.442 -19.604 -15.906 1 67.86 ? OPH IP9 375 C 1 
#
_model_server_stats.io_time_ms              50 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    8 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           28 
#