data_8DME
#
_model_server_result.job_id            enNhEjHRvKDxUu8hVr2oNQ 
_model_server_result.datetime_utc      '2024-10-18 19:26:02' 
_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          8dme 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"M","auth_seq_id":1102}' 
#
_entry.id    8DME 
#
_exptl.entry_id    8DME 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              329.417 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_pdbx_struct_assembly.details               author_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 
_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    ? 
_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 D N N 
? 3 M N 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 A SG CYS 398 A CYS 400 1_555 C FE HEM . A HEM 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? 
metalc ? metalc2 B SG CYS 398 B CYS 400 1_555 L FE HEM . B HEM 1101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.331 ? 
#
_chem_comp.formula           'C17 H19 N3 O2 S' 
_chem_comp.formula_weight    329.417 
_chem_comp.id                1C6 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              6-methoxy-2-{[(4-methoxy-3,5-dimethylpyridin-2-yl)methyl]sulfanyl}-1H-benzimidazole 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     omeprazole;prilosec 
#
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
C4 O3 1C6 sing 1 n n 
O3 CZ3 1C6 sing 2 n n 
CZ3 CE3 1C6 doub 3 n y 
CZ3 CH2 1C6 sing 4 n y 
CE3 CX2 1C6 sing 5 n y 
CH2 CZ2 1C6 doub 6 n y 
CX2 NV 1C6 sing 7 n y 
CX2 CS2 1C6 doub 8 n y 
NV CF1 1C6 sing 9 n y 
CZ2 CS2 1C6 sing 10 n y 
CS2 NE1 1C6 sing 11 n y 
CF1 NE1 1C6 doub 12 n y 
CF1 S 1C6 sing 13 n n 
S CB 1C6 sing 14 n n 
CB CG 1C6 sing 15 n n 
N1 CG 1C6 doub 16 n y 
N1 CE2 1C6 sing 17 n y 
CG CD1 1C6 sing 18 n y 
CE2 CZ 1C6 doub 19 n y 
CD1 C3 1C6 sing 20 n n 
CD1 CE1 1C6 doub 21 n y 
CZ C1 1C6 sing 22 n n 
CZ CE1 1C6 sing 23 n y 
CE1 O2 1C6 sing 24 n n 
O2 C2 1C6 sing 25 n n 
CB H1 1C6 sing 26 n n 
CB H2 1C6 sing 27 n n 
C3 H3 1C6 sing 28 n n 
C3 H4 1C6 sing 29 n n 
C3 H5 1C6 sing 30 n n 
C2 H6 1C6 sing 31 n n 
C2 H7 1C6 sing 32 n n 
C2 H8 1C6 sing 33 n n 
C1 H9 1C6 sing 34 n n 
C1 H10 1C6 sing 35 n n 
C1 H11 1C6 sing 36 n n 
CE2 H12 1C6 sing 37 n n 
NV H13 1C6 sing 38 n n 
CE3 H15 1C6 sing 39 n n 
C4 H16 1C6 sing 40 n n 
C4 H17 1C6 sing 41 n n 
C4 H18 1C6 sing 42 n n 
CH2 H19 1C6 sing 43 n n 
CZ2 H20 1C6 sing 44 n n 
#
_atom_sites.entry_id                     8DME 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 HEM A 1 1101 501 HEM HEM . 
D 3 1C6 A 1 1102 502 1C6 1C6 . 
E 4 FMN A 1 1103 1002 FMN FMN . 
F 5 FAD A 1 1104 1101 FAD FAD . 
G 6 SO4 A 1 1105 1102 SO4 SO4 . 
H 6 SO4 A 1 1106 1103 SO4 SO4 . 
I 6 SO4 A 1 1107 1104 SO4 SO4 . 
J 7 PG4 A 1 1108 1105 PG4 PG4 . 
K 7 PG4 A 1 1109 1106 PG4 PG4 . 
L 2 HEM B 1 1101 501 HEM HEM . 
M 3 1C6 B 1 1102 502 1C6 1C6 . 
N 4 FMN B 1 1103 1002 FMN FMN . 
O 5 FAD B 1 1104 1101 FAD FAD . 
P 6 SO4 B 1 1105 1102 SO4 SO4 . 
Q 6 SO4 B 1 1106 1103 SO4 SO4 . 
R 6 SO4 B 1 1107 1104 SO4 SO4 . 
S 7 PG4 B 1 1108 1105 PG4 PG4 . 
T 7 PG4 B 1 1109 1106 PG4 PG4 . 
#
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 S S 1C6 . . . M 3 180.875 142.839 205.081 1 29.85 ? S 1C6 1102 B 1 
HETATM 2 C CB 1C6 . . . M 3 182.565 142.647 204.881 1 31.05 ? CB 1C6 1102 B 1 
HETATM 3 C CG 1C6 . . . M 3 183.168 143.894 204.26 1 33.21 ? CG 1C6 1102 B 1 
HETATM 4 C CD1 1C6 . . . M 3 183.881 143.923 202.942 1 37.47 ? CD1 1C6 1102 B 1 
HETATM 5 C C3 1C6 . . . M 3 184.063 142.663 202.128 1 37.18 ? C3 1C6 1102 B 1 
HETATM 6 C CE1 1C6 . . . M 3 184.408 145.25 202.471 1 39.2 ? CE1 1C6 1102 B 1 
HETATM 7 O O2 1C6 . . . M 3 185.081 145.46 201.291 1 42.52 ? O2 1C6 1102 B 1 
HETATM 8 C C2 1C6 . . . M 3 184.606 144.831 200.082 1 43.81 ? C2 1C6 1102 B 1 
HETATM 9 C CZ 1C6 . . . M 3 184.196 146.43 203.351 1 43.68 ? CZ 1C6 1102 B 1 
HETATM 10 C C1 1C6 . . . M 3 184.73 147.802 202.938 1 41.28 ? C1 1C6 1102 B 1 
HETATM 11 C CE2 1C6 . . . M 3 183.522 146.257 204.576 1 42.5 ? CE2 1C6 1102 B 1 
HETATM 12 N N1 1C6 . . . M 3 183.07 145.041 204.982 1 40.4 ? N1 1C6 1102 B 1 
HETATM 13 C CF1 1C6 . . . M 3 180.46 141.222 205.447 1 26.86 ? CF1 1C6 1102 B 1 
HETATM 14 N NV 1C6 . . . M 3 181.082 140.396 206.344 1 25.71 ? NV 1C6 1102 B 1 
HETATM 15 C CX2 1C6 . . . M 3 180.433 139.202 206.338 1 26.73 ? CX2 1C6 1102 B 1 
HETATM 16 C CS2 1C6 . . . M 3 179.384 139.356 205.311 1 25.66 ? CS2 1C6 1102 B 1 
HETATM 17 N NE1 1C6 . . . M 3 179.471 140.632 204.801 1 24.93 ? NE1 1C6 1102 B 1 
HETATM 18 C CE3 1C6 . . . M 3 180.526 137.954 206.993 1 26.94 ? CE3 1C6 1102 B 1 
HETATM 19 C CZ3 1C6 . . . M 3 179.635 136.916 206.685 1 25.47 ? CZ3 1C6 1102 B 1 
HETATM 20 O O3 1C6 . . . M 3 179.719 135.662 207.315 1 37 ? O3 1C6 1102 B 1 
HETATM 21 C C4 1C6 . . . M 3 178.564 134.791 207.517 1 34.14 ? C4 1C6 1102 B 1 
HETATM 22 C CH2 1C6 . . . M 3 178.661 137.088 205.729 1 25.81 ? CH2 1C6 1102 B 1 
HETATM 23 C CZ2 1C6 . . . M 3 178.535 138.302 205.068 1 25.36 ? CZ2 1C6 1102 B 1 
#
_model_server_stats.io_time_ms              12 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    20 
_model_server_stats.query_time_ms           328 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           23 
#