data_1TMU # _model_server_result.job_id 0Jd27C3v_bfoysTHj_lJhw _model_server_result.datetime_utc '2024-11-21 23:46:22' _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 1tmu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1}' # _entry.id 1TMU # _exptl.entry_id 1TMU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.986 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide _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 1TMU _cell.length_a 80.9 _cell.length_b 107.5 _cell.length_c 45.9 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1TMU _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G _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 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 4 _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 disulf ? disulf1 A SG CYS 4 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.01 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? covale ? covale1 D C3 0G6 . H 0G6 1 1_555 B NE2 HIS 43 H HIS 57 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.368 ? covale ? covale2 D C2 0G6 . H 0G6 1 1_555 B OG SER 205 H SER 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.375 ? covale ? covale3 B ND2 ASN 53 H ASN 60 1_555 E C1 NAG . H NAG 250 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.317 ? covale ? covale4 C C GLU 8 J GLU 62 1_555 C N TYS 9 J TYS 63 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.297 ? covale ? covale5 C C TYS 9 J TYS 63 1_555 C N LEU 10 J LEU 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C21 H34 Cl N6 O3 1' _chem_comp.formula_weight 453.986 _chem_comp.id 0G6 _chem_comp.mon_nstd_flag . _chem_comp.name D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms PPACK # 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 N CA 0G6 sing 1 n n N H 0G6 sing 2 n n N H2 0G6 sing 3 n n CA C 0G6 sing 4 n n CA CB 0G6 sing 5 n n CA HA 0G6 sing 6 n n C O 0G6 doub 7 n n C N1 0G6 sing 8 n n CB CG 0G6 sing 9 n n CB HB2 0G6 sing 10 n n CB HB3 0G6 sing 11 n n CG CD1 0G6 doub 12 n y CG CD2 0G6 sing 13 n y CD1 CE1 0G6 sing 14 n y CD1 HD1 0G6 sing 15 n n CD2 CE2 0G6 doub 16 n y CD2 HD2 0G6 sing 17 n n CE1 CZ 0G6 doub 18 n y CE1 HE1 0G6 sing 19 n n CE2 CZ 0G6 sing 20 n y CE2 HE2 0G6 sing 21 n n CZ HZ 0G6 sing 22 n n N1 CA1 0G6 sing 23 n n N1 CD 0G6 sing 24 n n CA1 C1 0G6 sing 25 n n CA1 CB1 0G6 sing 26 n n CA1 HA1 0G6 sing 27 n n C1 O1 0G6 doub 28 n n C1 N2 0G6 sing 29 n n CB1 CG1 0G6 sing 30 n n CB1 HB21 0G6 sing 31 n n CB1 HB31 0G6 sing 32 n n CG1 CD 0G6 sing 33 n n CG1 HG2 0G6 sing 34 n n CG1 HG3 0G6 sing 35 n n CD HD21 0G6 sing 36 n n CD HD3 0G6 sing 37 n n N2 CA2 0G6 sing 38 n n N2 H1 0G6 sing 39 n n CA2 C2 0G6 sing 40 n n CA2 CB2 0G6 sing 41 n n CA2 HA2 0G6 sing 42 n n C2 O2 0G6 sing 43 n n C2 C3 0G6 sing 44 n n CB2 CG2 0G6 sing 45 n n CB2 HB22 0G6 sing 46 n n CB2 HB32 0G6 sing 47 n n CG2 CD3 0G6 sing 48 n n CG2 HG21 0G6 sing 49 n n CG2 HG31 0G6 sing 50 n n CD3 NE 0G6 sing 51 n n CD3 HD22 0G6 sing 52 n n CD3 HD31 0G6 sing 53 n n NE CZ1 0G6 sing 54 n n NE HE 0G6 sing 55 n n CZ1 NH1 0G6 sing 56 n n CZ1 NH2 0G6 doub 57 n n NH1 HH11 0G6 sing 58 n n NH1 HH12 0G6 sing 59 n n NH2 HH21 0G6 sing 60 n n NH2 HH22 0G6 sing 61 n n C3 H11 0G6 sing 62 n n C3 H21 0G6 sing 63 n n CL C3 0G6 sing 64 n n C2 H33 0G6 sing 65 n n O2 H34 0G6 sing 66 n n # _atom_sites.entry_id 1TMU _atom_sites.fract_transf_matrix[1][1] 0.012361 _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] 0.009302 _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] 0.021786 _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 D 4 0G6 H 1 1 1 0G6 DPN . E 5 NAG H 1 250 250 NAG NAG . F 6 HOH L 1 15 15 HOH HOH . F 6 HOH L 2 34 34 HOH HOH . F 6 HOH L 3 55 55 HOH HOH . G 6 HOH H 1 251 251 HOH HOH . G 6 HOH H 2 252 252 HOH HOH . G 6 HOH H 3 253 253 HOH HOH . G 6 HOH H 4 254 254 HOH HOH . G 6 HOH H 5 255 255 HOH HOH . G 6 HOH H 6 256 256 HOH HOH . G 6 HOH H 7 257 257 HOH HOH . G 6 HOH H 8 258 258 HOH HOH . G 6 HOH H 9 259 259 HOH HOH . G 6 HOH H 10 260 260 HOH HOH . G 6 HOH H 11 261 261 HOH HOH . G 6 HOH H 12 262 262 HOH HOH . G 6 HOH H 13 263 263 HOH HOH . G 6 HOH H 14 264 264 HOH HOH . G 6 HOH H 15 265 265 HOH HOH . G 6 HOH H 16 266 266 HOH HOH . G 6 HOH H 17 267 267 HOH HOH . G 6 HOH H 18 268 268 HOH HOH . G 6 HOH H 19 269 269 HOH HOH . G 6 HOH H 20 270 270 HOH HOH . G 6 HOH H 21 271 271 HOH HOH . G 6 HOH H 22 272 272 HOH HOH . G 6 HOH H 23 273 273 HOH HOH . G 6 HOH H 24 274 274 HOH HOH . G 6 HOH H 25 275 275 HOH HOH . G 6 HOH H 26 276 276 HOH HOH . G 6 HOH H 27 277 277 HOH HOH . G 6 HOH H 28 278 278 HOH HOH . G 6 HOH H 29 279 279 HOH HOH . G 6 HOH H 30 280 280 HOH HOH . G 6 HOH H 31 281 281 HOH HOH . G 6 HOH H 32 282 282 HOH HOH . G 6 HOH H 33 283 283 HOH HOH . G 6 HOH H 34 284 284 HOH HOH . G 6 HOH H 35 285 285 HOH HOH . G 6 HOH H 36 286 286 HOH HOH . G 6 HOH H 37 287 287 HOH HOH . G 6 HOH H 38 288 288 HOH HOH . G 6 HOH H 39 289 289 HOH HOH . G 6 HOH H 40 290 290 HOH HOH . G 6 HOH H 41 291 291 HOH HOH . G 6 HOH H 42 292 292 HOH HOH . G 6 HOH H 43 293 293 HOH HOH . G 6 HOH H 44 294 294 HOH HOH . G 6 HOH H 45 295 295 HOH HOH . G 6 HOH H 46 296 296 HOH HOH . G 6 HOH H 47 297 297 HOH HOH . G 6 HOH H 48 298 298 HOH HOH . G 6 HOH H 49 299 299 HOH HOH . G 6 HOH H 50 300 300 HOH HOH . G 6 HOH H 51 301 301 HOH HOH . G 6 HOH H 52 302 302 HOH HOH . G 6 HOH H 53 303 303 HOH HOH . G 6 HOH H 54 304 304 HOH HOH . G 6 HOH H 55 305 305 HOH HOH . G 6 HOH H 56 306 306 HOH HOH . G 6 HOH H 57 307 307 HOH HOH . G 6 HOH H 58 308 308 HOH HOH . G 6 HOH H 59 309 309 HOH HOH . G 6 HOH H 60 310 310 HOH HOH . G 6 HOH H 61 311 311 HOH HOH . G 6 HOH H 62 312 312 HOH HOH . G 6 HOH H 63 313 313 HOH HOH . G 6 HOH H 64 314 314 HOH HOH . G 6 HOH H 65 315 315 HOH HOH . G 6 HOH H 66 316 316 HOH HOH . G 6 HOH H 67 317 317 HOH HOH . G 6 HOH H 68 318 318 HOH HOH . G 6 HOH H 69 319 319 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 N 0G6 . . . D 4 86.187 43.343 43.723 1 8.08 ? N 0G6 1 H 1 HETATM 2 C CA 0G6 . . . D 4 86.938 42.274 44.351 1 8.08 ? CA 0G6 1 H 1 HETATM 3 C C 0G6 . . . D 4 86.637 40.992 43.626 1 8.08 ? C 0G6 1 H 1 HETATM 4 O O 0G6 . . . D 4 86.574 41.027 42.415 1 8.08 ? O 0G6 1 H 1 HETATM 5 C CB 0G6 . . . D 4 88.394 42.632 44.027 1 8.08 ? CB 0G6 1 H 1 HETATM 6 C CG 0G6 . . . D 4 89.442 41.677 44.594 1 8.08 ? CG 0G6 1 H 1 HETATM 7 C CD1 0G6 . . . D 4 89.508 41.441 45.974 1 8.08 ? CD1 0G6 1 H 1 HETATM 8 C CD2 0G6 . . . D 4 90.397 41.077 43.737 1 8.08 ? CD2 0G6 1 H 1 HETATM 9 C CE1 0G6 . . . D 4 90.487 40.58 46.473 1 8.08 ? CE1 0G6 1 H 1 HETATM 10 C CE2 0G6 . . . D 4 91.375 40.225 44.238 1 8.08 ? CE2 0G6 1 H 1 HETATM 11 C CZ 0G6 . . . D 4 91.415 39.975 45.608 1 8.08 ? CZ 0G6 1 H 1 HETATM 12 N N1 0G6 . . . D 4 86.454 39.858 44.256 1 8.08 ? N1 0G6 1 H 1 HETATM 13 C CA1 0G6 . . . D 4 86.204 38.697 43.476 1 8.08 ? CA1 0G6 1 H 1 HETATM 14 C C1 0G6 . . . D 4 84.861 38.747 42.808 1 8.08 ? C1 0G6 1 H 1 HETATM 15 O O1 0G6 . . . D 4 83.904 39.219 43.394 1 8.08 ? O1 0G6 1 H 1 HETATM 16 C CB1 0G6 . . . D 4 86.149 37.574 44.495 1 8.08 ? CB1 0G6 1 H 1 HETATM 17 C CG1 0G6 . . . D 4 86.146 38.223 45.884 1 8.08 ? CG1 0G6 1 H 1 HETATM 18 C CD 0G6 . . . D 4 86.47 39.69 45.718 1 8.08 ? CD 0G6 1 H 1 HETATM 19 N N2 0G6 . . . D 4 84.796 38.219 41.576 1 8.08 ? N2 0G6 1 H 1 HETATM 20 C CA2 0G6 . . . D 4 83.55 38.141 40.84 1 8.08 ? CA2 0G6 1 H 1 HETATM 21 C C2 0G6 . . . D 4 83.151 36.649 40.818 1 8.08 ? C2 0G6 1 H 1 HETATM 22 O O2 0G6 . . . D 4 81.746 36.646 40.584 1 8.08 ? O2 0G6 1 H 1 HETATM 23 C CB2 0G6 . . . D 4 83.633 38.73 39.413 1 8.08 ? CB2 0G6 1 H 1 HETATM 24 C CG2 0G6 . . . D 4 84.592 39.919 39.418 1 8.08 ? CG2 0G6 1 H 1 HETATM 25 C CD3 0G6 . . . D 4 83.927 41.197 38.913 1 8.08 ? CD3 0G6 1 H 1 HETATM 26 N NE 0G6 . . . D 4 84.341 41.616 37.59 1 8.08 ? NE 0G6 1 H 1 HETATM 27 C CZ1 0G6 . . . D 4 84.529 42.656 36.765 1 8.08 ? CZ1 0G6 1 H 1 HETATM 28 N NH1 0G6 . . . D 4 84.314 43.893 37.19 1 8.08 ? NH1 0G6 1 H 1 HETATM 29 N NH2 0G6 . . . D 4 84.949 42.378 35.523 1 8.08 ? NH2 0G6 1 H 1 HETATM 30 C C3 0G6 . . . D 4 83.436 36.011 42.214 1 8.08 ? C3 0G6 1 H 1 # _model_server_stats.io_time_ms 41 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 16 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 30 #