data_3PGL
#
_model_server_result.job_id            3Y-IXGreVcFCNrciB6U8tg 
_model_server_result.datetime_utc      '2024-11-14 17:04:12' 
_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          3pgl 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":257}' 
#
_entry.id    3PGL 
#
_exptl.entry_id    3PGL 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              359.443 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole 
_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          111.93 
_cell.angle_gamma         90 
_cell.entry_id            3PGL 
_cell.length_a            125.525 
_cell.length_b            78.26 
_cell.length_c            62.682 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3PGL 
_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 monomeric 1 author_and_software_defined_assembly 1 
PISA monomeric 1 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 
B,E,G 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                      3 
_struct_asym.id                             D 
_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 MG MG . A MG 1 1_555 F O HOH . A HOH 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.876 ? 
metalc ? metalc2 C MG MG . A MG 1 1_555 F O HOH . A HOH 32 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.273 ? 
metalc ? metalc3 C MG MG . A MG 1 1_555 A OD2 ASP 20 A ASP 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? 
metalc ? metalc4 C MG MG . A MG 1 1_555 A O ASP 22 A ASP 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? 
metalc ? metalc5 C MG MG . A MG 1 1_555 A OD1 ASN 131 A ASN 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? 
metalc ? metalc6 C MG MG . A MG 1 1_555 F O HOH . A HOH 258 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.887 ? 
metalc ? metalc7 E MG MG . B MG 1 1_555 G O HOH . B HOH 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.266 ? 
metalc ? metalc8 E MG MG . B MG 1 1_555 G O HOH . B HOH 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.924 ? 
metalc ? metalc9 E MG MG . B MG 1 1_555 B OD2 ASP 20 B ASP 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? 
metalc ? metalc10 E MG MG . B MG 1 1_555 B O ASP 22 B ASP 98 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? 
metalc ? metalc11 E MG MG . B MG 1 1_555 B OD1 ASN 131 B ASN 207 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? 
#
_chem_comp.formula           'C18 H21 N3 O3 S' 
_chem_comp.formula_weight    359.443 
_chem_comp.id                RZX 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              2-[(R)-{[4-(3-methoxypropoxy)-3-methylpyridin-2-yl]methyl}sulfinyl]-1H-benzimidazole 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     Rabeprazole 
#
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 C2 RZX doub 277 n y 
C1 C6 RZX sing 278 n y 
C2 C3 RZX sing 279 n y 
C2 N9 RZX sing 280 n y 
C3 C4 RZX doub 281 n y 
C3 N7 RZX sing 282 n y 
C4 C5 RZX sing 283 n y 
C5 C6 RZX doub 284 n y 
N7 C8 RZX sing 285 n y 
C8 N9 RZX doub 286 n y 
C8 S10 RZX sing 287 n n 
S10 C11 RZX sing 288 n n 
S10 O18 RZX doub 289 n n 
C11 C12 RZX sing 290 n n 
C12 N13 RZX doub 291 n y 
C12 C17 RZX sing 292 n y 
N13 C14 RZX sing 293 n y 
C14 C15 RZX doub 294 n y 
C15 C16 RZX sing 295 n y 
C16 C17 RZX doub 296 n y 
C16 O19 RZX sing 297 n n 
C17 C25 RZX sing 298 n n 
O19 C20 RZX sing 299 n n 
C20 C21 RZX sing 300 n n 
C21 C22 RZX sing 301 n n 
C22 O23 RZX sing 302 n n 
O23 C24 RZX sing 303 n n 
C1 H1 RZX sing 304 n n 
C4 H4 RZX sing 305 n n 
C5 H5 RZX sing 306 n n 
C6 H6 RZX sing 307 n n 
N7 HN7 RZX sing 308 n n 
C11 H11 RZX sing 309 n n 
C11 H11A RZX sing 310 n n 
C14 H14 RZX sing 311 n n 
C15 H15 RZX sing 312 n n 
C20 H20 RZX sing 313 n n 
C20 H20A RZX sing 314 n n 
C21 H21 RZX sing 315 n n 
C21 H21A RZX sing 316 n n 
C22 H22 RZX sing 317 n n 
C22 H22A RZX sing 318 n n 
C24 H24 RZX sing 319 n n 
C24 H24A RZX sing 320 n n 
C24 H24B RZX sing 321 n n 
C25 H25 RZX sing 322 n n 
C25 H25A RZX sing 323 n n 
C25 H25B RZX sing 324 n n 
#
_atom_sites.entry_id                     3PGL 
_atom_sites.fract_transf_matrix[1][1]    0.007967 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.003207 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012778 
_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]    0.017198 
_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 MG A 1 1 1 MG MG . 
D 3 RZX A 1 257 1 RZX RZX . 
E 2 MG B 1 1 1 MG MG . 
F 4 HOH A 1 2 2 HOH HOH . 
F 4 HOH A 2 3 3 HOH HOH . 
F 4 HOH A 3 7 7 HOH HOH . 
F 4 HOH A 4 8 8 HOH HOH . 
F 4 HOH A 5 9 9 HOH HOH . 
F 4 HOH A 6 12 12 HOH HOH . 
F 4 HOH A 7 13 13 HOH HOH . 
F 4 HOH A 8 14 14 HOH HOH . 
F 4 HOH A 9 16 16 HOH HOH . 
F 4 HOH A 10 17 17 HOH HOH . 
F 4 HOH A 11 19 19 HOH HOH . 
F 4 HOH A 12 20 20 HOH HOH . 
F 4 HOH A 13 21 21 HOH HOH . 
F 4 HOH A 14 22 22 HOH HOH . 
F 4 HOH A 15 23 23 HOH HOH . 
F 4 HOH A 16 24 24 HOH HOH . 
F 4 HOH A 17 26 26 HOH HOH . 
F 4 HOH A 18 29 29 HOH HOH . 
F 4 HOH A 19 30 30 HOH HOH . 
F 4 HOH A 20 31 31 HOH HOH . 
F 4 HOH A 21 32 32 HOH HOH . 
F 4 HOH A 22 34 34 HOH HOH . 
F 4 HOH A 23 35 35 HOH HOH . 
F 4 HOH A 24 36 36 HOH HOH . 
F 4 HOH A 25 37 37 HOH HOH . 
F 4 HOH A 26 39 39 HOH HOH . 
F 4 HOH A 27 40 40 HOH HOH . 
F 4 HOH A 28 41 41 HOH HOH . 
F 4 HOH A 29 43 43 HOH HOH . 
F 4 HOH A 30 44 44 HOH HOH . 
F 4 HOH A 31 45 45 HOH HOH . 
F 4 HOH A 32 46 46 HOH HOH . 
F 4 HOH A 33 47 47 HOH HOH . 
F 4 HOH A 34 48 48 HOH HOH . 
F 4 HOH A 35 51 51 HOH HOH . 
F 4 HOH A 36 52 52 HOH HOH . 
F 4 HOH A 37 53 53 HOH HOH . 
F 4 HOH A 38 55 55 HOH HOH . 
F 4 HOH A 39 60 60 HOH HOH . 
F 4 HOH A 40 61 61 HOH HOH . 
F 4 HOH A 41 63 63 HOH HOH . 
F 4 HOH A 42 64 64 HOH HOH . 
F 4 HOH A 43 65 65 HOH HOH . 
F 4 HOH A 44 74 74 HOH HOH . 
F 4 HOH A 45 258 1 HOH HOH . 
F 4 HOH A 46 259 1 HOH HOH . 
F 4 HOH A 47 260 2 HOH HOH . 
F 4 HOH A 48 261 77 HOH HOH . 
F 4 HOH A 49 262 78 HOH HOH . 
F 4 HOH A 50 263 80 HOH HOH . 
F 4 HOH A 51 264 85 HOH HOH . 
F 4 HOH A 52 265 88 HOH HOH . 
F 4 HOH A 53 266 90 HOH HOH . 
F 4 HOH A 54 267 91 HOH HOH . 
F 4 HOH A 55 268 92 HOH HOH . 
F 4 HOH A 56 269 93 HOH HOH . 
F 4 HOH A 57 270 94 HOH HOH . 
F 4 HOH A 58 271 95 HOH HOH . 
F 4 HOH A 59 272 96 HOH HOH . 
F 4 HOH A 60 273 97 HOH HOH . 
F 4 HOH A 61 274 98 HOH HOH . 
F 4 HOH A 62 275 100 HOH HOH . 
F 4 HOH A 63 276 101 HOH HOH . 
F 4 HOH A 64 277 104 HOH HOH . 
F 4 HOH A 65 278 107 HOH HOH . 
F 4 HOH A 66 279 109 HOH HOH . 
G 4 HOH B 1 2 2 HOH HOH . 
G 4 HOH B 2 4 4 HOH HOH . 
G 4 HOH B 3 5 5 HOH HOH . 
G 4 HOH B 4 6 6 HOH HOH . 
G 4 HOH B 5 10 10 HOH HOH . 
G 4 HOH B 6 11 11 HOH HOH . 
G 4 HOH B 7 15 15 HOH HOH . 
G 4 HOH B 8 18 18 HOH HOH . 
G 4 HOH B 9 25 25 HOH HOH . 
G 4 HOH B 10 27 27 HOH HOH . 
G 4 HOH B 11 28 28 HOH HOH . 
G 4 HOH B 12 33 33 HOH HOH . 
G 4 HOH B 13 38 38 HOH HOH . 
G 4 HOH B 14 42 42 HOH HOH . 
G 4 HOH B 15 49 49 HOH HOH . 
G 4 HOH B 16 50 50 HOH HOH . 
G 4 HOH B 17 54 54 HOH HOH . 
G 4 HOH B 18 56 56 HOH HOH . 
G 4 HOH B 19 57 57 HOH HOH . 
G 4 HOH B 20 58 58 HOH HOH . 
G 4 HOH B 21 59 59 HOH HOH . 
G 4 HOH B 22 62 62 HOH HOH . 
G 4 HOH B 23 66 66 HOH HOH . 
G 4 HOH B 24 67 67 HOH HOH . 
G 4 HOH B 25 68 68 HOH HOH . 
G 4 HOH B 26 69 69 HOH HOH . 
G 4 HOH B 27 71 71 HOH HOH . 
G 4 HOH B 28 72 72 HOH HOH . 
G 4 HOH B 29 73 73 HOH HOH . 
G 4 HOH B 30 75 75 HOH HOH . 
G 4 HOH B 31 76 76 HOH HOH . 
G 4 HOH B 32 257 1 HOH HOH . 
G 4 HOH B 33 258 79 HOH HOH . 
G 4 HOH B 34 259 81 HOH HOH . 
G 4 HOH B 35 260 82 HOH HOH . 
G 4 HOH B 36 261 83 HOH HOH . 
G 4 HOH B 37 262 84 HOH HOH . 
G 4 HOH B 38 263 86 HOH HOH . 
G 4 HOH B 39 264 87 HOH HOH . 
G 4 HOH B 40 265 89 HOH HOH . 
G 4 HOH B 41 266 99 HOH HOH . 
G 4 HOH B 42 267 102 HOH HOH . 
G 4 HOH B 43 268 103 HOH HOH . 
G 4 HOH B 44 269 105 HOH HOH . 
G 4 HOH B 45 270 106 HOH HOH . 
G 4 HOH B 46 271 108 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 C C1 RZX . . . D 3 3.451 11.372 -3.179 0.5 58.81 ? C1 RZX 257 A 1 
HETATM 2 C C2 RZX . . . D 3 3.165 11.725 -4.486 0.5 58.86 ? C2 RZX 257 A 1 
HETATM 3 C C3 RZX . . . D 3 3.877 12.874 -5.101 0.5 58.42 ? C3 RZX 257 A 1 
HETATM 4 C C4 RZX . . . D 3 4.82 13.561 -4.351 0.5 59.23 ? C4 RZX 257 A 1 
HETATM 5 C C5 RZX . . . D 3 5.084 13.173 -3.041 0.5 58.75 ? C5 RZX 257 A 1 
HETATM 6 C C6 RZX . . . D 3 4.404 12.103 -2.475 0.5 58.96 ? C6 RZX 257 A 1 
HETATM 7 N N7 RZX . . . D 3 3.415 13.005 -6.362 0.5 58.17 ? N7 RZX 257 A 1 
HETATM 8 C C8 RZX . . . D 3 2.51 12.009 -6.499 0.5 58.69 ? C8 RZX 257 A 1 
HETATM 9 N N9 RZX . . . D 3 2.316 11.231 -5.417 0.5 59.06 ? N9 RZX 257 A 1 
HETATM 10 S S10 RZX . . . D 3 1.652 11.846 -7.961 1 60.8 ? S10 RZX 257 A 1 
HETATM 11 C C11 RZX . . . D 3 0.72 10.44 -8.327 1 55.1 ? C11 RZX 257 A 1 
HETATM 12 C C12 RZX . . . D 3 0.52 9.266 -7.391 1 52.59 ? C12 RZX 257 A 1 
HETATM 13 N N13 RZX . . . D 3 0.58 8.095 -8.041 1 51.1 ? N13 RZX 257 A 1 
HETATM 14 C C14 RZX . . . D 3 0.432 6.923 -7.413 1 52.04 ? C14 RZX 257 A 1 
HETATM 15 C C15 RZX . . . D 3 0.171 6.85 -6.049 1 50.89 ? C15 RZX 257 A 1 
HETATM 16 C C16 RZX . . . D 3 0.073 8.037 -5.33 1 52.62 ? C16 RZX 257 A 1 
HETATM 17 C C17 RZX . . . D 3 0.243 9.271 -5.999 1 53.1 ? C17 RZX 257 A 1 
HETATM 18 O O18 RZX . . . D 3 0.601 12.933 -7.994 1 59.49 ? O18 RZX 257 A 1 
HETATM 19 O O19 RZX . . . D 3 -0.185 7.965 -3.969 0.5 50.81 ? O19 RZX 257 A 1 
HETATM 20 C C20 RZX . . . D 3 -1.422 7.443 -3.469 0.5 47.36 ? C20 RZX 257 A 1 
HETATM 21 C C21 RZX . . . D 3 -2.426 8.589 -3.436 0.5 43.94 ? C21 RZX 257 A 1 
HETATM 22 C C22 RZX . . . D 3 -3.795 8.142 -2.957 1 40.61 ? C22 RZX 257 A 1 
HETATM 23 O O23 RZX . . . D 3 -4.743 8.92 -3.698 1 37.55 ? O23 RZX 257 A 1 
HETATM 24 C C24 RZX . . . D 3 -5.849 8.142 -4.163 1 36.93 ? C24 RZX 257 A 1 
HETATM 25 C C25 RZX . . . D 3 0.134 10.544 -5.178 0.5 51.82 ? C25 RZX 257 A 1 
#
_model_server_stats.io_time_ms              7 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           215 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           25 
#