data_1O3C # _model_server_result.job_id jHO6hdE6mzVEkpLe5Oiipw _model_server_result.datetime_utc '2024-11-25 13:49:56' _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 1o3c # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":246}' # _entry.id 1O3C # _exptl.entry_id 1O3C _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 328.367 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "3-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-1,1'-BIPHENYL-2-OLATE" _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 1O3C _cell.length_a 63.73 _cell.length_b 63.45 _cell.length_c 69.23 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O3C _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _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 7 A CYS 22 1_555 A SG CYS 137 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.007 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.99 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? metalc ? metalc1 A OE2 GLU 52 A GLU 70 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.387 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.145 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc5 B CA CA . A CA 247 1_555 E O HOH . A HOH 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc6 B CA CA . A CA 247 1_555 E O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.3 ? # _chem_comp.formula 'C20 H16 N4 O' _chem_comp.formula_weight 328.367 _chem_comp.id 780 _chem_comp.mon_nstd_flag . _chem_comp.name "3-{5-[AMINO(IMINIO)METHYL]-1H-BENZIMIDAZOL-2-YL}-1,1'-BIPHENYL-2-OLATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms CRA_7806 # 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 780 doub 1 n y C1 C6 780 sing 2 n y C1 C7 780 sing 3 n n C2 C3 780 sing 4 n y C2 HC2 780 sing 5 n n C3 C4 780 doub 6 n y C3 HC3 780 sing 7 n n C4 C5 780 sing 8 n y C4 N3 780 sing 9 n y C5 C6 780 doub 10 n y C5 N4 780 sing 11 n y C6 HC6 780 sing 12 n n C7 N1 780 sing 13 n n C7 N2 780 doub 14 n n N1 HH11 780 sing 15 n n N1 HH12 780 sing 16 n n N2 HH21 780 sing 17 n n N2 HH22 780 sing 18 n n N3 C8 780 sing 19 n y N3 HN3 780 sing 20 n n N4 C8 780 doub 21 n y C8 C1' 780 sing 22 n y C1' C2' 780 doub 23 n y C1' C6' 780 sing 24 n y C2' C3' 780 sing 25 n y C2' HC2' 780 sing 26 n n C3' C4' 780 doub 27 n y C3' HC3' 780 sing 28 n n C4' C5' 780 sing 29 n y C4' HC4' 780 sing 30 n n C5' C6' 780 doub 31 n y C5' C1B 780 sing 32 n y C6' O6' 780 sing 33 n n C1B C2B 780 doub 34 n y C1B C6B 780 sing 35 n y C2B C3B 780 sing 36 n y C2B H2B 780 sing 37 n n C3B C4B 780 doub 38 n y C3B H3B 780 sing 39 n n C4B C5B 780 sing 40 n y C4B H4B 780 sing 41 n n C5B C6B 780 doub 42 n y C5B H5B 780 sing 43 n n C6B H6B 780 sing 44 n n # _atom_sites.entry_id 1O3C _atom_sites.fract_transf_matrix[1][1] 0.015691 _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] 0.01576 _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] 0.014445 _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 B 2 CA A 1 247 247 CA CA . C 3 CL A 1 260 260 CL CL . D 4 780 A 1 246 246 780 BZM . E 5 HOH A 1 248 248 HOH HOH . E 5 HOH A 2 249 249 HOH HOH . E 5 HOH A 3 250 250 HOH HOH . E 5 HOH A 4 251 251 HOH HOH . E 5 HOH A 5 252 252 HOH HOH . E 5 HOH A 6 253 253 HOH HOH . E 5 HOH A 7 254 254 HOH HOH . E 5 HOH A 8 255 255 HOH HOH . E 5 HOH A 9 256 256 HOH HOH . E 5 HOH A 10 258 258 HOH HOH . E 5 HOH A 11 259 259 HOH HOH . E 5 HOH A 12 261 261 HOH HOH . E 5 HOH A 13 262 262 HOH HOH . E 5 HOH A 14 263 263 HOH HOH . E 5 HOH A 15 264 264 HOH HOH . E 5 HOH A 16 266 266 HOH HOH . E 5 HOH A 17 267 267 HOH HOH . E 5 HOH A 18 268 268 HOH HOH . E 5 HOH A 19 269 269 HOH HOH . E 5 HOH A 20 270 270 HOH HOH . E 5 HOH A 21 272 272 HOH HOH . E 5 HOH A 22 273 273 HOH HOH . E 5 HOH A 23 274 274 HOH HOH . E 5 HOH A 24 275 275 HOH HOH . E 5 HOH A 25 277 277 HOH HOH . E 5 HOH A 26 278 278 HOH HOH . E 5 HOH A 27 280 280 HOH HOH . E 5 HOH A 28 281 281 HOH HOH . E 5 HOH A 29 282 282 HOH HOH . E 5 HOH A 30 283 283 HOH HOH . E 5 HOH A 31 284 284 HOH HOH . E 5 HOH A 32 285 285 HOH HOH . E 5 HOH A 33 286 286 HOH HOH . E 5 HOH A 34 287 287 HOH HOH . E 5 HOH A 35 289 289 HOH HOH . E 5 HOH A 36 290 290 HOH HOH . E 5 HOH A 37 291 291 HOH HOH . E 5 HOH A 38 292 292 HOH HOH . E 5 HOH A 39 293 293 HOH HOH . E 5 HOH A 40 294 294 HOH HOH . E 5 HOH A 41 295 295 HOH HOH . E 5 HOH A 42 296 296 HOH HOH . E 5 HOH A 43 297 297 HOH HOH . E 5 HOH A 44 299 299 HOH HOH . E 5 HOH A 45 300 300 HOH HOH . E 5 HOH A 46 302 302 HOH HOH . E 5 HOH A 47 308 308 HOH HOH . E 5 HOH A 48 309 309 HOH HOH . E 5 HOH A 49 312 312 HOH HOH . E 5 HOH A 50 315 315 HOH HOH . E 5 HOH A 51 317 317 HOH HOH . E 5 HOH A 52 318 318 HOH HOH . E 5 HOH A 53 321 321 HOH HOH . E 5 HOH A 54 322 322 HOH HOH . E 5 HOH A 55 323 323 HOH HOH . E 5 HOH A 56 324 324 HOH HOH . E 5 HOH A 57 326 326 HOH HOH . E 5 HOH A 58 327 327 HOH HOH . E 5 HOH A 59 328 328 HOH HOH . E 5 HOH A 60 331 331 HOH HOH . E 5 HOH A 61 333 333 HOH HOH . E 5 HOH A 62 336 336 HOH HOH . E 5 HOH A 63 338 338 HOH HOH . E 5 HOH A 64 339 339 HOH HOH . E 5 HOH A 65 342 342 HOH HOH . E 5 HOH A 66 346 346 HOH HOH . E 5 HOH A 67 348 348 HOH HOH . E 5 HOH A 68 349 349 HOH HOH . E 5 HOH A 69 351 351 HOH HOH . E 5 HOH A 70 352 352 HOH HOH . E 5 HOH A 71 353 353 HOH HOH . E 5 HOH A 72 354 354 HOH HOH . E 5 HOH A 73 356 356 HOH HOH . E 5 HOH A 74 358 358 HOH HOH . E 5 HOH A 75 360 360 HOH HOH . E 5 HOH A 76 361 361 HOH HOH . E 5 HOH A 77 363 363 HOH HOH . E 5 HOH A 78 364 364 HOH HOH . E 5 HOH A 79 369 369 HOH HOH . E 5 HOH A 80 370 370 HOH HOH . E 5 HOH A 81 372 372 HOH HOH . E 5 HOH A 82 374 374 HOH HOH . E 5 HOH A 83 375 375 HOH HOH . E 5 HOH A 84 376 376 HOH HOH . E 5 HOH A 85 377 377 HOH HOH . E 5 HOH A 86 378 378 HOH HOH . E 5 HOH A 87 380 380 HOH HOH . E 5 HOH A 88 381 381 HOH HOH . E 5 HOH A 89 382 382 HOH HOH . E 5 HOH A 90 383 383 HOH HOH . E 5 HOH A 91 384 384 HOH HOH . E 5 HOH A 92 385 385 HOH HOH . E 5 HOH A 93 389 389 HOH HOH . E 5 HOH A 94 390 390 HOH HOH . E 5 HOH A 95 391 391 HOH HOH . E 5 HOH A 96 392 392 HOH HOH . E 5 HOH A 97 393 393 HOH HOH . E 5 HOH A 98 395 395 HOH HOH . E 5 HOH A 99 397 397 HOH HOH . E 5 HOH A 100 402 402 HOH HOH . E 5 HOH A 101 403 403 HOH HOH . E 5 HOH A 102 404 404 HOH HOH . E 5 HOH A 103 406 406 HOH HOH . E 5 HOH A 104 410 410 HOH HOH . E 5 HOH A 105 412 412 HOH HOH . E 5 HOH A 106 421 421 HOH HOH . E 5 HOH A 107 430 430 HOH HOH . E 5 HOH A 108 431 431 HOH HOH . E 5 HOH A 109 432 432 HOH HOH . E 5 HOH A 110 434 434 HOH HOH . E 5 HOH A 111 439 439 HOH HOH . E 5 HOH A 112 442 442 HOH HOH . E 5 HOH A 113 452 452 HOH HOH . E 5 HOH A 114 480 480 HOH HOH . E 5 HOH A 115 489 489 HOH HOH . E 5 HOH A 116 497 497 HOH HOH . E 5 HOH A 117 502 502 HOH HOH . E 5 HOH A 118 504 504 HOH HOH . E 5 HOH A 119 505 505 HOH HOH . E 5 HOH A 120 508 508 HOH HOH . E 5 HOH A 121 537 537 HOH HOH . E 5 HOH A 122 540 540 HOH HOH . E 5 HOH A 123 542 542 HOH HOH . E 5 HOH A 124 543 543 HOH HOH . E 5 HOH A 125 547 547 HOH HOH . E 5 HOH A 126 548 548 HOH HOH . E 5 HOH A 127 552 552 HOH HOH . E 5 HOH A 128 559 559 HOH HOH . E 5 HOH A 129 560 560 HOH HOH . E 5 HOH A 130 561 561 HOH HOH . E 5 HOH A 131 567 567 HOH HOH . E 5 HOH A 132 636 636 HOH HOH . E 5 HOH A 133 650 650 HOH HOH . E 5 HOH A 134 664 664 HOH HOH . E 5 HOH A 135 683 683 HOH HOH . E 5 HOH A 136 691 691 HOH HOH . E 5 HOH A 137 706 706 HOH HOH . E 5 HOH A 138 709 709 HOH HOH . E 5 HOH A 139 714 714 HOH HOH . E 5 HOH A 140 716 716 HOH HOH . E 5 HOH A 141 727 727 HOH HOH . E 5 HOH A 142 728 728 HOH HOH . E 5 HOH A 143 746 746 HOH HOH . E 5 HOH A 144 750 750 HOH HOH . E 5 HOH A 145 773 773 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 780 . . . D 4 44.331 -2.889 26.523 1 21.31 ? C1 780 246 A 1 HETATM 2 C C2 780 . . . D 4 44.766 -1.53 26.536 1 19.33 ? C2 780 246 A 1 HETATM 3 C C3 780 . . . D 4 44.759 -0.732 27.689 1 19.77 ? C3 780 246 A 1 HETATM 4 C C4 780 . . . D 4 44.309 -1.321 28.82 1 20.37 ? C4 780 246 A 1 HETATM 5 C C5 780 . . . D 4 43.895 -2.593 28.868 1 22.33 ? C5 780 246 A 1 HETATM 6 C C6 780 . . . D 4 43.882 -3.423 27.75 1 22.25 ? C6 780 246 A 1 HETATM 7 C C7 780 . . . D 4 44.359 -3.657 25.344 1 22.6 ? C7 780 246 A 1 HETATM 8 N N1 780 . . . D 4 44.13 -4.95 25.384 1 24.85 ? N1 780 246 A 1 HETATM 9 N N2 780 . . . D 4 44.611 -3.068 24.195 1 24.09 ? N2 780 246 A 1 HETATM 10 N N3 780 . . . D 4 44.209 -0.835 30.014 1 22.11 ? N3 780 246 A 1 HETATM 11 N N4 780 . . . D 4 43.517 -2.962 30.084 1 22.29 ? N4 780 246 A 1 HETATM 12 C C8 780 . . . D 4 43.744 -1.826 30.721 1 23.05 ? C8 780 246 A 1 HETATM 13 C C1' 780 . . . D 4 43.414 -1.711 32.069 1 22.05 ? C1' 780 246 A 1 HETATM 14 C C2' 780 . . . D 4 43.088 -2.83 32.83 1 23.43 ? C2' 780 246 A 1 HETATM 15 C C3' 780 . . . D 4 42.756 -2.715 34.161 1 21.61 ? C3' 780 246 A 1 HETATM 16 C C4' 780 . . . D 4 42.742 -1.477 34.762 1 22.96 ? C4' 780 246 A 1 HETATM 17 C C5' 780 . . . D 4 43.061 -0.296 34.058 1 21.87 ? C5' 780 246 A 1 HETATM 18 C C6' 780 . . . D 4 43.394 -0.463 32.699 1 20.26 ? C6' 780 246 A 1 HETATM 19 O O6' 780 . . . D 4 43.735 0.598 31.896 1 15.15 ? O6' 780 246 A 1 HETATM 20 C C1B 780 . . . D 4 43.014 0.936 34.745 1 21.28 ? C1B 780 246 A 1 HETATM 21 C C2B 780 . . . D 4 44.081 1.825 34.77 1 20.54 ? C2B 780 246 A 1 HETATM 22 C C3B 780 . . . D 4 44.031 3.016 35.477 1 22.34 ? C3B 780 246 A 1 HETATM 23 C C4B 780 . . . D 4 42.89 3.358 36.188 1 23.13 ? C4B 780 246 A 1 HETATM 24 C C5B 780 . . . D 4 41.807 2.503 36.19 1 22.26 ? C5B 780 246 A 1 HETATM 25 C C6B 780 . . . D 4 41.871 1.312 35.477 1 23.38 ? C6B 780 246 A 1 HETATM 26 H HC2 780 . . . D 4 45.123 -1.078 25.626 1 21.1 ? HC2 780 246 A 1 HETATM 27 H HC3 780 . . . D 4 45.087 0.292 27.699 1 20 ? HC3 780 246 A 1 HETATM 28 H HC6 780 . . . D 4 43.536 -4.444 27.824 1 22.42 ? HC6 780 246 A 1 HETATM 29 H HH11 780 . . . D 4 43.961 -5.387 26.28 1 25.26 ? HH11 780 246 A 1 HETATM 30 H HH12 780 . . . D 4 44.124 -5.563 24.598 1 23.91 ? HH12 780 246 A 1 HETATM 31 H HH21 780 . . . D 4 44.74 -2.07 24.166 1 23.22 ? HH21 780 246 A 1 HETATM 32 H HH22 780 . . . D 4 44.703 -3.558 23.331 1 23.49 ? HH22 780 246 A 1 HETATM 33 H HN3 780 . . . D 4 44.419 0.074 30.316 1 20.86 ? HN3 780 246 A 1 HETATM 34 H HC2' 780 . . . D 4 43.095 -3.809 32.369 1 22.49 ? HC2' 780 246 A 1 HETATM 35 H HC3' 780 . . . D 4 42.505 -3.595 34.732 1 22.72 ? HC3' 780 246 A 1 HETATM 36 H HC4' 780 . . . D 4 42.479 -1.421 35.808 1 22.24 ? HC4' 780 246 A 1 HETATM 37 H H2B 780 . . . D 4 44.972 1.584 34.22 1 21.91 ? H2B 780 246 A 1 HETATM 38 H H3B 780 . . . D 4 44.883 3.68 35.472 1 22.09 ? H3B 780 246 A 1 HETATM 39 H H4B 780 . . . D 4 42.839 4.283 36.736 1 23.05 ? H4B 780 246 A 1 HETATM 40 H H5B 780 . . . D 4 40.915 2.759 36.741 1 23 ? H5B 780 246 A 1 HETATM 41 H H6B 780 . . . D 4 41.01 0.658 35.489 1 23.29 ? H6B 780 246 A 1 # _model_server_stats.io_time_ms 71 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 300 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 41 #