data_3W67
#
_model_server_result.job_id            IARybxrd4kfTG7YeIJyhBg 
_model_server_result.datetime_utc      '2025-03-06 00:11:09' 
_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          3w67 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"L","auth_seq_id":302}' 
#
_entry.id    3W67 
#
_exptl.entry_id    3W67 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              634.354 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            '(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate' 
_entity.pdbx_number_of_molecules    4 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         100.24 
_cell.angle_beta          109.72 
_cell.angle_gamma         100.46 
_cell.entry_id            3W67 
_cell.length_a            58.285 
_cell.length_b            69.665 
_cell.length_c            87.183 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3W67 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 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
? tetrameric 4 author_defined_assembly 1 
PISA monomeric 1 software_defined_assembly 2 
PISA monomeric 1 software_defined_assembly 3 
PISA monomeric 1 software_defined_assembly 4 
PISA monomeric 1 software_defined_assembly 5 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O 1 1 
A,E,F,M 2 1 
B,G,H,N 3 1 
C,I,J 4 1 
D,K,L,O 5 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 F N N 
? 3 H N N 
? 3 J N N 
? 3 L N N 
#
_chem_comp.formula           'C17 H33 O19 P3' 
_chem_comp.formula_weight    634.354 
_chem_comp.id                3PT 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              '(2R)-3-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6S)-2,3,6-trihydroxy-4,5-bis(phosphonooxy)cyclohexyl]oxy}phosphoryl]oxy}propane-1,2-diyl dibutanoate' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
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
O0M C0L 3PT doub 1 n n 
C0L C0N 3PT sing 2 n n 
C0L O0F 3PT sing 3 n n 
C0N C0P 3PT sing 4 n n 
O0F C0E 3PT sing 5 n n 
C0P C0Q 3PT sing 6 n n 
C0K C0J 3PT sing 7 n n 
C0E C0C 3PT sing 8 n n 
C0I C0J 3PT sing 9 n n 
C0I C0G 3PT sing 10 n n 
C0C O0D 3PT sing 11 n n 
C0C C0B 3PT sing 12 n n 
O0D C0G 3PT sing 13 n n 
C0G O0H 3PT doub 14 n n 
O6 C6 3PT sing 15 n n 
C0B OP1 3PT sing 16 n n 
O5 C5 3PT sing 17 n n 
OP5 P4 3PT doub 18 n n 
C5 C6 3PT sing 19 n n 
C5 C4 3PT sing 20 n n 
C6 C1 3PT sing 21 n n 
OP1 P1 3PT sing 22 n n 
OP4 P4 3PT sing 23 n n 
P4 O4 3PT sing 24 n n 
P4 OP6 3PT sing 25 n n 
O4 C4 3PT sing 26 n n 
C4 C3 3PT sing 27 n n 
C1 O1 3PT sing 28 n n 
C1 C2 3PT sing 29 n n 
OP2 P1 3PT doub 30 n n 
O1 P1 3PT sing 31 n n 
P1 OP3 3PT sing 32 n n 
C3 C2 3PT sing 33 n n 
C3 O3 3PT sing 34 n n 
C2 O2 3PT sing 35 n n 
O3 P3 3PT sing 36 n n 
O10 P3 3PT doub 37 n n 
P3 O12 3PT sing 38 n n 
P3 O11 3PT sing 39 n n 
C0I H1 3PT sing 40 n n 
C0I H2 3PT sing 41 n n 
C0J H3 3PT sing 42 n n 
C0J H4 3PT sing 43 n n 
C0K H5 3PT sing 44 n n 
C0K H6 3PT sing 45 n n 
C0K H7 3PT sing 46 n n 
C0C H8 3PT sing 47 n n 
C0E H9 3PT sing 48 n n 
C0E H10 3PT sing 49 n n 
C0N H11 3PT sing 50 n n 
C0N H12 3PT sing 51 n n 
C0P H13 3PT sing 52 n n 
C0P H14 3PT sing 53 n n 
C0Q H15 3PT sing 54 n n 
C0Q H16 3PT sing 55 n n 
C0Q H17 3PT sing 56 n n 
C0B H18 3PT sing 57 n n 
C0B H19 3PT sing 58 n n 
OP3 H20 3PT sing 59 n n 
C1 H21 3PT sing 60 n n 
C2 H22 3PT sing 61 n n 
O2 H23 3PT sing 62 n n 
C3 H24 3PT sing 63 n n 
O12 H25 3PT sing 64 n n 
O11 H26 3PT sing 65 n n 
C4 H27 3PT sing 66 n n 
OP4 H28 3PT sing 67 n n 
OP6 H29 3PT sing 68 n n 
C5 H30 3PT sing 69 n n 
O5 H31 3PT sing 70 n n 
C6 H32 3PT sing 71 n n 
O6 H33 3PT sing 72 n n 
#
_atom_sites.entry_id                     3W67 
_atom_sites.fract_transf_matrix[1][1]    0.017157 
_atom_sites.fract_transf_matrix[1][2]    0.003169 
_atom_sites.fract_transf_matrix[1][3]    0.007214 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.014597 
_atom_sites.fract_transf_matrix[2][3]    0.003903 
_atom_sites.fract_transf_matrix[3][1]    0 
_atom_sites.fract_transf_matrix[3][2]    0 
_atom_sites.fract_transf_matrix[3][3]    0.012613 
_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 2 VIV A 1 301 1278 VIV VIV . 
F 3 3PT A 1 302 870 3PT 4PT . 
G 2 VIV B 1 301 1278 VIV VIV . 
H 3 3PT B 1 302 870 3PT 4PT . 
I 2 VIV C 1 301 1278 VIV VIV . 
J 3 3PT C 1 302 870 3PT 4PT . 
K 2 VIV D 1 301 1278 VIV VIV . 
L 3 3PT D 1 302 870 3PT 4PT . 
M 4 HOH A 1 401 2 HOH HOH . 
M 4 HOH A 2 402 3 HOH HOH . 
M 4 HOH A 3 403 4 HOH HOH . 
M 4 HOH A 4 404 6 HOH HOH . 
M 4 HOH A 5 405 7 HOH HOH . 
M 4 HOH A 6 406 11 HOH HOH . 
M 4 HOH A 7 407 12 HOH HOH . 
M 4 HOH A 8 408 13 HOH HOH . 
M 4 HOH A 9 409 17 HOH HOH . 
M 4 HOH A 10 410 18 HOH HOH . 
M 4 HOH A 11 411 21 HOH HOH . 
M 4 HOH A 12 412 22 HOH HOH . 
M 4 HOH A 13 413 23 HOH HOH . 
M 4 HOH A 14 414 27 HOH HOH . 
M 4 HOH A 15 415 28 HOH HOH . 
M 4 HOH A 16 416 33 HOH HOH . 
M 4 HOH A 17 417 34 HOH HOH . 
M 4 HOH A 18 418 35 HOH HOH . 
M 4 HOH A 19 419 36 HOH HOH . 
M 4 HOH A 20 420 37 HOH HOH . 
M 4 HOH A 21 421 38 HOH HOH . 
M 4 HOH A 22 422 39 HOH HOH . 
M 4 HOH A 23 423 40 HOH HOH . 
M 4 HOH A 24 424 41 HOH HOH . 
M 4 HOH A 25 425 42 HOH HOH . 
M 4 HOH A 26 426 43 HOH HOH . 
M 4 HOH A 27 427 44 HOH HOH . 
M 4 HOH A 28 428 45 HOH HOH . 
M 4 HOH A 29 429 46 HOH HOH . 
M 4 HOH A 30 430 71 HOH HOH . 
M 4 HOH A 31 431 72 HOH HOH . 
M 4 HOH A 32 432 73 HOH HOH . 
M 4 HOH A 33 433 74 HOH HOH . 
M 4 HOH A 34 434 75 HOH HOH . 
M 4 HOH A 35 435 76 HOH HOH . 
M 4 HOH A 36 436 77 HOH HOH . 
M 4 HOH A 37 437 78 HOH HOH . 
M 4 HOH A 38 438 79 HOH HOH . 
M 4 HOH A 39 439 80 HOH HOH . 
M 4 HOH A 40 440 81 HOH HOH . 
M 4 HOH A 41 441 82 HOH HOH . 
M 4 HOH A 42 442 83 HOH HOH . 
N 4 HOH B 1 401 1 HOH HOH . 
N 4 HOH B 2 402 9 HOH HOH . 
N 4 HOH B 3 403 10 HOH HOH . 
N 4 HOH B 4 404 14 HOH HOH . 
N 4 HOH B 5 405 16 HOH HOH . 
N 4 HOH B 6 406 24 HOH HOH . 
N 4 HOH B 7 407 25 HOH HOH . 
N 4 HOH B 8 408 26 HOH HOH . 
N 4 HOH B 9 409 29 HOH HOH . 
N 4 HOH B 10 410 30 HOH HOH . 
N 4 HOH B 11 411 47 HOH HOH . 
N 4 HOH B 12 412 48 HOH HOH . 
N 4 HOH B 13 413 49 HOH HOH . 
N 4 HOH B 14 414 50 HOH HOH . 
N 4 HOH B 15 415 51 HOH HOH . 
N 4 HOH B 16 416 52 HOH HOH . 
N 4 HOH B 17 417 53 HOH HOH . 
N 4 HOH B 18 418 54 HOH HOH . 
N 4 HOH B 19 419 55 HOH HOH . 
N 4 HOH B 20 420 56 HOH HOH . 
N 4 HOH B 21 421 57 HOH HOH . 
N 4 HOH B 22 422 58 HOH HOH . 
N 4 HOH B 23 423 59 HOH HOH . 
N 4 HOH B 24 424 84 HOH HOH . 
N 4 HOH B 25 425 85 HOH HOH . 
N 4 HOH B 26 426 86 HOH HOH . 
N 4 HOH B 27 427 87 HOH HOH . 
N 4 HOH B 28 428 88 HOH HOH . 
N 4 HOH B 29 429 89 HOH HOH . 
N 4 HOH B 30 430 90 HOH HOH . 
N 4 HOH B 31 431 91 HOH HOH . 
N 4 HOH B 32 432 92 HOH HOH . 
N 4 HOH B 33 433 93 HOH HOH . 
N 4 HOH B 34 434 94 HOH HOH . 
N 4 HOH B 35 435 95 HOH HOH . 
N 4 HOH B 36 436 96 HOH HOH . 
N 4 HOH B 37 437 97 HOH HOH . 
N 4 HOH B 38 438 98 HOH HOH . 
N 4 HOH B 39 439 99 HOH HOH . 
N 4 HOH B 40 440 100 HOH HOH . 
N 4 HOH B 41 441 101 HOH HOH . 
N 4 HOH B 42 442 102 HOH HOH . 
O 4 HOH D 1 401 20 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 O O0H 3PT . . . L 3 27.373 -22.511 -34.94 1 169.18 ? O0H 3PT 302 D 1 
HETATM 2 C C0G 3PT . . . L 3 26.229 -22.982 -34.22 1 169.51 ? C0G 3PT 302 D 1 
HETATM 3 C C0I 3PT . . . L 3 26.441 -22.759 -32.707 1 168.93 ? C0I 3PT 302 D 1 
HETATM 4 C C0J 3PT . . . L 3 25.965 -21.373 -32.255 1 168.43 ? C0J 3PT 302 D 1 
HETATM 5 C C0K 3PT . . . L 3 25.115 -21.454 -30.984 1 167.91 ? C0K 3PT 302 D 1 
HETATM 6 O O0D 3PT . . . L 3 26.039 -24.401 -34.498 1 170.46 ? O0D 3PT 302 D 1 
HETATM 7 C C0C 3PT . . . L 3 24.712 -24.777 -35.007 1 171.15 ? C0C 3PT 302 D 1 
HETATM 8 C C0E 3PT . . . L 3 23.615 -24.734 -33.922 1 171.86 ? C0E 3PT 302 D 1 
HETATM 9 O O0F 3PT . . . L 3 22.301 -24.509 -34.494 1 172.55 ? O0F 3PT 302 D 1 
HETATM 10 C C0L 3PT . . . L 3 21.289 -25.078 -33.771 1 172.87 ? C0L 3PT 302 D 1 
HETATM 11 C C0N 3PT . . . L 3 20.122 -24.201 -33.279 1 173.04 ? C0N 3PT 302 D 1 
HETATM 12 C C0P 3PT . . . L 3 18.776 -24.644 -33.878 1 172.99 ? C0P 3PT 302 D 1 
HETATM 13 C C0Q 3PT . . . L 3 17.629 -23.721 -33.449 1 172.66 ? C0Q 3PT 302 D 1 
HETATM 14 O O0M 3PT . . . L 3 21.301 -26.289 -33.543 1 172.87 ? O0M 3PT 302 D 1 
HETATM 15 C C0B 3PT . . . L 3 24.673 -26.213 -35.609 1 170.72 ? C0B 3PT 302 D 1 
HETATM 16 O OP1 3PT . . . L 3 25.883 -26.576 -36.3 1 170.27 ? OP1 3PT 302 D 1 
HETATM 17 P P1 3PT . . . L 3 25.987 -26.484 -37.93 1 170.33 ? P1 3PT 302 D 1 
HETATM 18 O OP3 3PT . . . L 3 25.884 -24.897 -38.259 1 170.46 ? OP3 3PT 302 D 1 
HETATM 19 O OP2 3PT . . . L 3 24.913 -27.252 -38.609 1 170.61 ? OP2 3PT 302 D 1 
HETATM 20 O O1 3PT . . . L 3 27.494 -26.923 -38.37 1 169.39 ? O1 3PT 302 D 1 
HETATM 21 C C1 3PT . . . L 3 27.977 -26.9 -39.735 1 167.74 ? C1 3PT 302 D 1 
HETATM 22 C C2 3PT . . . L 3 28.61 -28.296 -40.055 1 167.06 ? C2 3PT 302 D 1 
HETATM 23 O O2 3PT . . . L 3 29.089 -28.917 -38.849 1 167.47 ? O2 3PT 302 D 1 
HETATM 24 C C3 3PT . . . L 3 29.742 -28.331 -41.119 1 166.08 ? C3 3PT 302 D 1 
HETATM 25 O O3 3PT . . . L 3 30.51 -29.547 -40.976 1 165.28 ? O3 3PT 302 D 1 
HETATM 26 P P3 3PT . . . L 3 30.031 -31.034 -41.489 1 164.52 ? P3 3PT 302 D 1 
HETATM 27 O O12 3PT . . . L 3 29.387 -30.828 -42.965 1 164.53 ? O12 3PT 302 D 1 
HETATM 28 O O10 3PT . . . L 3 28.8 -31.497 -40.532 1 164.31 ? O10 3PT 302 D 1 
HETATM 29 O O11 3PT . . . L 3 31.143 -32.01 -41.482 1 164.24 ? O11 3PT 302 D 1 
HETATM 30 C C4 3PT . . . L 3 30.695 -27.125 -40.999 1 165.71 ? C4 3PT 302 D 1 
HETATM 31 O O4 3PT . . . L 3 31.711 -27.186 -42.022 1 164.6 ? O4 3PT 302 D 1 
HETATM 32 P P4 3PT . . . L 3 33.307 -27.333 -41.661 1 163.58 ? P4 3PT 302 D 1 
HETATM 33 O OP4 3PT . . . L 3 33.422 -28.584 -40.649 1 163.55 ? OP4 3PT 302 D 1 
HETATM 34 O OP6 3PT . . . L 3 33.649 -26.044 -40.772 1 163.21 ? OP6 3PT 302 D 1 
HETATM 35 O OP5 3PT . . . L 3 34.199 -27.471 -42.837 1 163.34 ? OP5 3PT 302 D 1 
HETATM 36 C C5 3PT . . . L 3 29.906 -25.808 -41.086 1 166.34 ? C5 3PT 302 D 1 
HETATM 37 O O5 3PT . . . L 3 30.797 -24.694 -41.051 1 166.43 ? O5 3PT 302 D 1 
HETATM 38 C C6 3PT . . . L 3 28.915 -25.671 -39.921 1 167.07 ? C6 3PT 302 D 1 
HETATM 39 O O6 3PT . . . L 3 28.138 -24.482 -40.128 1 166.91 ? O6 3PT 302 D 1 
#
_model_server_stats.io_time_ms              16 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           226 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           39 
#