data_3APV
#
_model_server_result.job_id            Y6tALMYGLs6iRAUf3IUbxw 
_model_server_result.datetime_utc      '2025-01-23 16:54:59' 
_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          3apv 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":190}' 
#
_entry.id    3APV 
#
_exptl.entry_id    3APV 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              277.403 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            Amitriptyline 
_entity.pdbx_number_of_molecules    2 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          92.14 
_cell.angle_gamma         90 
_cell.entry_id            3APV 
_cell.length_a            66.65 
_cell.length_b            45.948 
_cell.length_c            120.732 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3APV 
_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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 2 C N N 
? 2 E 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
disulf ? disulf1 A SG CYS 6 A CYS 5 1_555 A SG CYS 148 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? 
disulf ? disulf2 A SG CYS 73 A CYS 72 1_555 A SG CYS 166 A CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? 
disulf ? disulf3 B SG CYS 6 B CYS 5 1_555 B SG CYS 148 B CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? 
disulf ? disulf4 B SG CYS 73 B CYS 72 1_555 B SG CYS 166 B CYS 165 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? 
#
_chem_comp.formula           'C20 H23 N' 
_chem_comp.formula_weight    277.403 
_chem_comp.id                TP0 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              Amitriptyline 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     3-(10,11-dihydro-5H-dibenzo[a,d][7]annulen-5-ylidene)-N,N-dimethylpropan-1-amine 
#
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
N1 C14 TP0 sing 313 n n 
N1 C19 TP0 sing 314 n n 
N1 C20 TP0 sing 315 n n 
C3 C6 TP0 sing 316 n n 
C3 C7 TP0 sing 317 n n 
C3 C8 TP0 doub 318 n n 
C4 C6 TP0 doub 319 n y 
C4 C10 TP0 sing 320 n y 
C4 C21 TP0 sing 321 n n 
C5 C7 TP0 doub 322 n y 
C5 C11 TP0 sing 323 n y 
C5 C22 TP0 sing 324 n n 
C6 C12 TP0 sing 325 n y 
C7 C13 TP0 sing 326 n y 
C8 C29 TP0 sing 327 n n 
C10 C15 TP0 doub 328 n y 
C11 C16 TP0 doub 329 n y 
C12 C17 TP0 doub 330 n y 
C13 C18 TP0 doub 331 n y 
C14 C29 TP0 sing 332 n n 
C15 C17 TP0 sing 333 n y 
C16 C18 TP0 sing 334 n y 
C21 C22 TP0 sing 335 n n 
C8 H8 TP0 sing 336 n n 
C10 H10 TP0 sing 337 n n 
C11 H11 TP0 sing 338 n n 
C12 H12 TP0 sing 339 n n 
C13 H13 TP0 sing 340 n n 
C14 H14 TP0 sing 341 n n 
C14 H14A TP0 sing 342 n n 
C15 H15 TP0 sing 343 n n 
C16 H16 TP0 sing 344 n n 
C17 H17 TP0 sing 345 n n 
C18 H18 TP0 sing 346 n n 
C19 H19 TP0 sing 347 n n 
C19 H19A TP0 sing 348 n n 
C19 H19B TP0 sing 349 n n 
C20 H20 TP0 sing 350 n n 
C20 H20A TP0 sing 351 n n 
C20 H20B TP0 sing 352 n n 
C21 H21 TP0 sing 353 n n 
C21 H21A TP0 sing 354 n n 
C22 H22 TP0 sing 355 n n 
C22 H22A TP0 sing 356 n n 
C29 H29 TP0 sing 357 n n 
C29 H29A TP0 sing 358 n n 
#
_atom_sites.entry_id                     3APV 
_atom_sites.fract_transf_matrix[1][1]    0.015004 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.000561 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.021764 
_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]    0.008289 
_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 TP0 A 1 190 1 TP0 TP0 . 
D 3 ACY A 1 191 1 ACY ACY . 
E 2 TP0 B 1 190 2 TP0 TP0 . 
F 4 HOH A 1 192 1 HOH HOH . 
F 4 HOH A 2 193 2 HOH HOH . 
F 4 HOH A 3 194 3 HOH HOH . 
F 4 HOH A 4 195 4 HOH HOH . 
F 4 HOH A 5 196 5 HOH HOH . 
F 4 HOH A 6 197 6 HOH HOH . 
F 4 HOH A 7 198 7 HOH HOH . 
F 4 HOH A 8 199 9 HOH HOH . 
F 4 HOH A 9 200 10 HOH HOH . 
F 4 HOH A 10 201 11 HOH HOH . 
F 4 HOH A 11 202 12 HOH HOH . 
F 4 HOH A 12 203 13 HOH HOH . 
F 4 HOH A 13 204 14 HOH HOH . 
F 4 HOH A 14 205 15 HOH HOH . 
F 4 HOH A 15 206 16 HOH HOH . 
F 4 HOH A 16 207 17 HOH HOH . 
F 4 HOH A 17 208 18 HOH HOH . 
F 4 HOH A 18 209 19 HOH HOH . 
F 4 HOH A 19 210 20 HOH HOH . 
F 4 HOH A 20 211 22 HOH HOH . 
F 4 HOH A 21 212 23 HOH HOH . 
F 4 HOH A 22 213 25 HOH HOH . 
F 4 HOH A 23 214 26 HOH HOH . 
F 4 HOH A 24 215 27 HOH HOH . 
F 4 HOH A 25 216 28 HOH HOH . 
F 4 HOH A 26 217 31 HOH HOH . 
F 4 HOH A 27 218 32 HOH HOH . 
F 4 HOH A 28 219 33 HOH HOH . 
F 4 HOH A 29 220 34 HOH HOH . 
F 4 HOH A 30 221 35 HOH HOH . 
F 4 HOH A 31 222 36 HOH HOH . 
F 4 HOH A 32 223 37 HOH HOH . 
F 4 HOH A 33 224 38 HOH HOH . 
F 4 HOH A 34 225 40 HOH HOH . 
F 4 HOH A 35 226 42 HOH HOH . 
F 4 HOH A 36 227 43 HOH HOH . 
F 4 HOH A 37 228 44 HOH HOH . 
F 4 HOH A 38 229 45 HOH HOH . 
F 4 HOH A 39 230 47 HOH HOH . 
F 4 HOH A 40 231 48 HOH HOH . 
F 4 HOH A 41 232 49 HOH HOH . 
F 4 HOH A 42 233 50 HOH HOH . 
F 4 HOH A 43 234 51 HOH HOH . 
F 4 HOH A 44 235 61 HOH HOH . 
F 4 HOH A 45 236 63 HOH HOH . 
F 4 HOH A 46 237 64 HOH HOH . 
F 4 HOH A 47 238 65 HOH HOH . 
F 4 HOH A 48 239 66 HOH HOH . 
F 4 HOH A 49 240 68 HOH HOH . 
F 4 HOH A 50 241 69 HOH HOH . 
F 4 HOH A 51 242 70 HOH HOH . 
F 4 HOH A 52 243 73 HOH HOH . 
F 4 HOH A 53 244 74 HOH HOH . 
F 4 HOH A 54 245 75 HOH HOH . 
F 4 HOH A 55 246 81 HOH HOH . 
F 4 HOH A 56 247 82 HOH HOH . 
F 4 HOH A 57 248 83 HOH HOH . 
F 4 HOH A 58 249 84 HOH HOH . 
F 4 HOH A 59 250 85 HOH HOH . 
F 4 HOH A 60 251 86 HOH HOH . 
F 4 HOH A 61 252 87 HOH HOH . 
F 4 HOH A 62 253 88 HOH HOH . 
F 4 HOH A 63 254 91 HOH HOH . 
F 4 HOH A 64 255 92 HOH HOH . 
F 4 HOH A 65 256 93 HOH HOH . 
F 4 HOH A 66 257 121 HOH HOH . 
F 4 HOH A 67 258 122 HOH HOH . 
F 4 HOH A 68 259 131 HOH HOH . 
F 4 HOH A 69 260 132 HOH HOH . 
F 4 HOH A 70 261 133 HOH HOH . 
F 4 HOH A 71 262 134 HOH HOH . 
F 4 HOH A 72 263 136 HOH HOH . 
F 4 HOH A 73 264 137 HOH HOH . 
G 4 HOH B 1 191 21 HOH HOH . 
G 4 HOH B 2 192 29 HOH HOH . 
G 4 HOH B 3 193 30 HOH HOH . 
G 4 HOH B 4 194 52 HOH HOH . 
G 4 HOH B 5 195 53 HOH HOH . 
G 4 HOH B 6 196 77 HOH HOH . 
G 4 HOH B 7 197 78 HOH HOH . 
G 4 HOH B 8 198 89 HOH HOH . 
G 4 HOH B 9 199 95 HOH HOH . 
G 4 HOH B 10 200 96 HOH HOH . 
G 4 HOH B 11 201 97 HOH HOH . 
G 4 HOH B 12 202 98 HOH HOH . 
G 4 HOH B 13 203 99 HOH HOH . 
G 4 HOH B 14 204 110 HOH HOH . 
G 4 HOH B 15 205 111 HOH HOH . 
G 4 HOH B 16 206 112 HOH HOH . 
G 4 HOH B 17 207 113 HOH HOH . 
G 4 HOH B 18 208 123 HOH HOH . 
G 4 HOH B 19 209 124 HOH HOH . 
G 4 HOH B 20 210 135 HOH HOH . 
G 4 HOH B 21 211 138 HOH HOH . 
G 4 HOH B 22 212 139 HOH HOH . 
G 4 HOH B 23 213 140 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 N N1 TP0 . . . C 2 16.345 0.88 18.393 1 35.33 ? N1 TP0 190 A 1 
HETATM 2 C C3 TP0 . . . C 2 12.801 2.422 17.647 1 39.08 ? C3 TP0 190 A 1 
HETATM 3 C C4 TP0 . . . C 2 13.079 3.652 19.751 1 39.75 ? C4 TP0 190 A 1 
HETATM 4 C C5 TP0 . . . C 2 10.932 1.416 19.068 1 36.84 ? C5 TP0 190 A 1 
HETATM 5 C C6 TP0 . . . C 2 13.012 3.714 18.372 1 38.84 ? C6 TP0 190 A 1 
HETATM 6 C C7 TP0 . . . C 2 11.454 1.762 17.812 1 37.83 ? C7 TP0 190 A 1 
HETATM 7 C C8 TP0 . . . C 2 13.749 1.81 16.894 1 38.51 ? C8 TP0 190 A 1 
HETATM 8 C C10 TP0 . . . C 2 13.262 4.827 20.494 1 39.86 ? C10 TP0 190 A 1 
HETATM 9 C C11 TP0 . . . C 2 9.688 0.793 19.134 1 36.36 ? C11 TP0 190 A 1 
HETATM 10 C C12 TP0 . . . C 2 13.075 4.932 17.692 1 38.74 ? C12 TP0 190 A 1 
HETATM 11 C C13 TP0 . . . C 2 10.743 1.458 16.661 1 35.79 ? C13 TP0 190 A 1 
HETATM 12 C C14 TP0 . . . C 2 16.238 1.304 16.967 1 36.21 ? C14 TP0 190 A 1 
HETATM 13 C C15 TP0 . . . C 2 13.34 6.045 19.809 1 39.46 ? C15 TP0 190 A 1 
HETATM 14 C C16 TP0 . . . C 2 8.989 0.501 17.992 1 33.74 ? C16 TP0 190 A 1 
HETATM 15 C C17 TP0 . . . C 2 13.261 6.107 18.422 1 36.85 ? C17 TP0 190 A 1 
HETATM 16 C C18 TP0 . . . C 2 9.502 0.839 16.749 1 36.34 ? C18 TP0 190 A 1 
HETATM 17 C C19 TP0 . . . C 2 17.59 0.09 18.576 1 36.7 ? C19 TP0 190 A 1 
HETATM 18 C C20 TP0 . . . C 2 16.321 1.92 19.44 1 29.86 ? C20 TP0 190 A 1 
HETATM 19 C C21 TP0 . . . C 2 12.972 2.298 20.437 1 40.07 ? C21 TP0 190 A 1 
HETATM 20 C C22 TP0 . . . C 2 11.56 1.686 20.417 1 36.15 ? C22 TP0 190 A 1 
HETATM 21 C C29 TP0 . . . C 2 15.146 2.348 16.668 1 38.81 ? C29 TP0 190 A 1 
#
_model_server_stats.io_time_ms              54 
_model_server_stats.parse_time_ms           9 
_model_server_stats.create_model_time_ms    4 
_model_server_stats.query_time_ms           283 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           21 
#