data_1O39 # _model_server_result.job_id bF43kM27WxWBUgBhPBYPmg _model_server_result.datetime_utc '2024-11-29 04:19:11' _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 1o39 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":246}' # _entry.id 1O39 # _exptl.entry_id 1O39 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 328.367 _entity.id 3 _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 1O39 _cell.length_a 63.86 _cell.length_b 62.42 _cell.length_c 69.66 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1O39 _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 _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 3 _struct_asym.id C _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf2 A SG CYS 25 A CYS 42 1_555 A SG CYS 41 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.977 ? disulf ? disulf3 A SG CYS 109 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 A SG CYS 116 A CYS 136 1_555 A SG CYS 183 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.992 ? disulf ? disulf5 A SG CYS 148 A CYS 168 1_555 A SG CYS 162 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2 ? disulf ? disulf6 A SG CYS 173 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? metalc ? metalc1 A OE2 GLU 52 A GLU 70 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.479 ? metalc ? metalc2 A O ASN 54 A ASN 72 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.225 ? metalc ? metalc3 A O VAL 57 A VAL 75 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.199 ? metalc ? metalc4 A OE2 GLU 62 A GLU 80 1_555 B CA CA . A CA 247 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.533 ? metalc ? metalc5 B CA CA . A CA 247 1_555 D O HOH . A HOH 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? metalc ? metalc6 B CA CA . A CA 247 1_555 D O HOH . A HOH 560 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.442 ? # _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 1O39 _atom_sites.fract_transf_matrix[1][1] 0.015659 _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] 0.016021 _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] 0.014355 _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 3 780 A 1 246 246 780 BZM . D 4 HOH A 1 248 248 HOH HOH . D 4 HOH A 2 249 249 HOH HOH . D 4 HOH A 3 250 250 HOH HOH . D 4 HOH A 4 252 252 HOH HOH . D 4 HOH A 5 253 253 HOH HOH . D 4 HOH A 6 254 254 HOH HOH . D 4 HOH A 7 255 255 HOH HOH . D 4 HOH A 8 256 256 HOH HOH . D 4 HOH A 9 258 258 HOH HOH . D 4 HOH A 10 259 259 HOH HOH . D 4 HOH A 11 261 261 HOH HOH . D 4 HOH A 12 262 262 HOH HOH . D 4 HOH A 13 263 263 HOH HOH . D 4 HOH A 14 264 264 HOH HOH . D 4 HOH A 15 266 266 HOH HOH . D 4 HOH A 16 267 267 HOH HOH . D 4 HOH A 17 268 268 HOH HOH . D 4 HOH A 18 270 270 HOH HOH . D 4 HOH A 19 272 272 HOH HOH . D 4 HOH A 20 273 273 HOH HOH . D 4 HOH A 21 274 274 HOH HOH . D 4 HOH A 22 275 275 HOH HOH . D 4 HOH A 23 277 277 HOH HOH . D 4 HOH A 24 278 278 HOH HOH . D 4 HOH A 25 280 280 HOH HOH . D 4 HOH A 26 281 281 HOH HOH . D 4 HOH A 27 282 282 HOH HOH . D 4 HOH A 28 283 283 HOH HOH . D 4 HOH A 29 284 284 HOH HOH . D 4 HOH A 30 285 285 HOH HOH . D 4 HOH A 31 286 286 HOH HOH . D 4 HOH A 32 287 287 HOH HOH . D 4 HOH A 33 288 288 HOH HOH . D 4 HOH A 34 289 289 HOH HOH . D 4 HOH A 35 290 290 HOH HOH . D 4 HOH A 36 291 291 HOH HOH . D 4 HOH A 37 292 292 HOH HOH . D 4 HOH A 38 293 293 HOH HOH . D 4 HOH A 39 294 294 HOH HOH . D 4 HOH A 40 295 295 HOH HOH . D 4 HOH A 41 296 296 HOH HOH . D 4 HOH A 42 297 297 HOH HOH . D 4 HOH A 43 299 299 HOH HOH . D 4 HOH A 44 300 300 HOH HOH . D 4 HOH A 45 302 302 HOH HOH . D 4 HOH A 46 303 303 HOH HOH . D 4 HOH A 47 308 308 HOH HOH . D 4 HOH A 48 309 309 HOH HOH . D 4 HOH A 49 312 312 HOH HOH . D 4 HOH A 50 315 315 HOH HOH . D 4 HOH A 51 317 317 HOH HOH . D 4 HOH A 52 318 318 HOH HOH . D 4 HOH A 53 321 321 HOH HOH . D 4 HOH A 54 322 322 HOH HOH . D 4 HOH A 55 323 323 HOH HOH . D 4 HOH A 56 326 326 HOH HOH . D 4 HOH A 57 327 327 HOH HOH . D 4 HOH A 58 328 328 HOH HOH . D 4 HOH A 59 331 331 HOH HOH . D 4 HOH A 60 333 333 HOH HOH . D 4 HOH A 61 336 336 HOH HOH . D 4 HOH A 62 338 338 HOH HOH . D 4 HOH A 63 339 339 HOH HOH . D 4 HOH A 64 342 342 HOH HOH . D 4 HOH A 65 346 346 HOH HOH . D 4 HOH A 66 348 348 HOH HOH . D 4 HOH A 67 349 349 HOH HOH . D 4 HOH A 68 352 352 HOH HOH . D 4 HOH A 69 354 354 HOH HOH . D 4 HOH A 70 356 356 HOH HOH . D 4 HOH A 71 358 358 HOH HOH . D 4 HOH A 72 360 360 HOH HOH . D 4 HOH A 73 361 361 HOH HOH . D 4 HOH A 74 363 363 HOH HOH . D 4 HOH A 75 369 369 HOH HOH . D 4 HOH A 76 371 371 HOH HOH . D 4 HOH A 77 372 372 HOH HOH . D 4 HOH A 78 374 374 HOH HOH . D 4 HOH A 79 375 375 HOH HOH . D 4 HOH A 80 377 377 HOH HOH . D 4 HOH A 81 378 378 HOH HOH . D 4 HOH A 82 380 380 HOH HOH . D 4 HOH A 83 381 381 HOH HOH . D 4 HOH A 84 382 382 HOH HOH . D 4 HOH A 85 383 383 HOH HOH . D 4 HOH A 86 384 384 HOH HOH . D 4 HOH A 87 385 385 HOH HOH . D 4 HOH A 88 389 389 HOH HOH . D 4 HOH A 89 390 390 HOH HOH . D 4 HOH A 90 391 391 HOH HOH . D 4 HOH A 91 392 392 HOH HOH . D 4 HOH A 92 393 393 HOH HOH . D 4 HOH A 93 395 395 HOH HOH . D 4 HOH A 94 402 402 HOH HOH . D 4 HOH A 95 403 403 HOH HOH . D 4 HOH A 96 404 404 HOH HOH . D 4 HOH A 97 406 406 HOH HOH . D 4 HOH A 98 410 410 HOH HOH . D 4 HOH A 99 412 412 HOH HOH . D 4 HOH A 100 421 421 HOH HOH . D 4 HOH A 101 430 430 HOH HOH . D 4 HOH A 102 431 431 HOH HOH . D 4 HOH A 103 432 432 HOH HOH . D 4 HOH A 104 434 434 HOH HOH . D 4 HOH A 105 439 439 HOH HOH . D 4 HOH A 106 448 448 HOH HOH . D 4 HOH A 107 450 450 HOH HOH . D 4 HOH A 108 480 480 HOH HOH . D 4 HOH A 109 489 489 HOH HOH . D 4 HOH A 110 502 502 HOH HOH . D 4 HOH A 111 504 504 HOH HOH . D 4 HOH A 112 505 505 HOH HOH . D 4 HOH A 113 508 508 HOH HOH . D 4 HOH A 114 537 537 HOH HOH . D 4 HOH A 115 539 539 HOH HOH . D 4 HOH A 116 542 542 HOH HOH . D 4 HOH A 117 547 547 HOH HOH . D 4 HOH A 118 557 557 HOH HOH . D 4 HOH A 119 560 560 HOH HOH . D 4 HOH A 120 561 561 HOH HOH . D 4 HOH A 121 567 567 HOH HOH . D 4 HOH A 122 588 588 HOH HOH . D 4 HOH A 123 650 650 HOH HOH . D 4 HOH A 124 664 664 HOH HOH . D 4 HOH A 125 678 678 HOH HOH . D 4 HOH A 126 683 683 HOH HOH . D 4 HOH A 127 703 703 HOH HOH . D 4 HOH A 128 706 706 HOH HOH . D 4 HOH A 129 714 714 HOH HOH . D 4 HOH A 130 724 724 HOH HOH . D 4 HOH A 131 727 727 HOH HOH . D 4 HOH A 132 728 728 HOH HOH . D 4 HOH A 133 750 750 HOH HOH . D 4 HOH A 134 773 773 HOH HOH . D 4 HOH A 135 803 803 HOH HOH . D 4 HOH A 136 857 857 HOH HOH . D 4 HOH A 137 866 866 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 . . . C 3 44.274 -3.025 25.901 1 19.08 ? C1 780 246 A 1 HETATM 2 C C2 780 . . . C 3 44.705 -1.671 25.998 1 19.12 ? C2 780 246 A 1 HETATM 3 C C3 780 . . . C 3 44.655 -0.929 27.186 1 23.74 ? C3 780 246 A 1 HETATM 4 C C4 780 . . . C 3 44.165 -1.568 28.282 1 23.41 ? C4 780 246 A 1 HETATM 5 C C5 780 . . . C 3 43.743 -2.833 28.254 1 24.5 ? C5 780 246 A 1 HETATM 6 C C6 780 . . . C 3 43.771 -3.616 27.095 1 21.09 ? C6 780 246 A 1 HETATM 7 C C7 780 . . . C 3 44.349 -3.73 24.664 1 21.01 ? C7 780 246 A 1 HETATM 8 N N1 780 . . . C 3 44.034 -5.009 24.582 1 20.48 ? N1 780 246 A 1 HETATM 9 N N2 780 . . . C 3 44.739 -3.074 23.599 1 20.4 ? N2 780 246 A 1 HETATM 10 N N3 780 . . . C 3 43.995 -1.136 29.488 1 25.69 ? N3 780 246 A 1 HETATM 11 N N4 780 . . . C 3 43.295 -3.238 29.433 1 26.56 ? N4 780 246 A 1 HETATM 12 C C8 780 . . . C 3 43.487 -2.131 30.134 1 27.44 ? C8 780 246 A 1 HETATM 13 C C1' 780 . . . C 3 43.251 -2.068 31.533 1 30.37 ? C1' 780 246 A 1 HETATM 14 C C2' 780 . . . C 3 42.899 -3.218 32.242 1 29.22 ? C2' 780 246 A 1 HETATM 15 C C3' 780 . . . C 3 42.665 -3.181 33.607 1 29.27 ? C3' 780 246 A 1 HETATM 16 C C4' 780 . . . C 3 42.771 -2.006 34.31 1 27.68 ? C4' 780 246 A 1 HETATM 17 C C5' 780 . . . C 3 43.118 -0.812 33.687 1 27.01 ? C5' 780 246 A 1 HETATM 18 C C6' 780 . . . C 3 43.356 -0.854 32.284 1 27.94 ? C6' 780 246 A 1 HETATM 19 O O6' 780 . . . C 3 43.696 0.317 31.622 1 28.08 ? O6' 780 246 A 1 HETATM 20 C C1B 780 . . . C 3 43.217 0.359 34.467 1 25.72 ? C1B 780 246 A 1 HETATM 21 C C2B 780 . . . C 3 44.394 1.126 34.549 1 24.67 ? C2B 780 246 A 1 HETATM 22 C C3B 780 . . . C 3 44.471 2.286 35.331 1 24.72 ? C3B 780 246 A 1 HETATM 23 C C4B 780 . . . C 3 43.365 2.709 36.056 1 26.37 ? C4B 780 246 A 1 HETATM 24 C C5B 780 . . . C 3 42.191 1.969 35.993 1 25.78 ? C5B 780 246 A 1 HETATM 25 C C6B 780 . . . C 3 42.123 0.819 35.214 1 26.24 ? C6B 780 246 A 1 HETATM 26 H HC2 780 . . . C 3 45.1 -1.172 25.134 1 20.7 ? HC2 780 246 A 1 HETATM 27 H HC3 780 . . . C 3 44.984 0.094 27.242 1 22.48 ? HC3 780 246 A 1 HETATM 28 H HC6 780 . . . C 3 43.421 -4.639 27.11 1 20.54 ? HC6 780 246 A 1 HETATM 29 H HH11 780 . . . C 3 43.769 -5.482 25.435 1 20.78 ? HH11 780 246 A 1 HETATM 30 H HH12 780 . . . C 3 44.051 -5.57 23.762 1 20.04 ? HH12 780 246 A 1 HETATM 31 H HH21 780 . . . C 3 44.963 -2.092 23.67 1 19.15 ? HH21 780 246 A 1 HETATM 32 H HH22 780 . . . C 3 44.846 -3.499 22.706 1 20.52 ? HH22 780 246 A 1 HETATM 33 H HN3 780 . . . C 3 44.175 -0.255 29.903 1 25.18 ? HN3 780 246 A 1 HETATM 34 H HC2' 780 . . . C 3 42.806 -4.162 31.724 1 29.22 ? HC2' 780 246 A 1 HETATM 35 H HC3' 780 . . . C 3 42.394 -4.087 34.128 1 29.41 ? HC3' 780 246 A 1 HETATM 36 H HC4' 780 . . . C 3 42.578 -2.02 35.374 1 27.39 ? HC4' 780 246 A 1 HETATM 37 H H2B 780 . . . C 3 45.265 0.811 33.993 1 25.3 ? H2B 780 246 A 1 HETATM 38 H H3B 780 . . . C 3 45.387 2.854 35.377 1 24.79 ? H3B 780 246 A 1 HETATM 39 H H4B 780 . . . C 3 43.415 3.602 36.662 1 25.6 ? H4B 780 246 A 1 HETATM 40 H H5B 780 . . . C 3 41.321 2.285 36.551 1 26.23 ? H5B 780 246 A 1 HETATM 41 H H6B 780 . . . C 3 41.195 0.264 35.189 1 26.39 ? H6B 780 246 A 1 # _model_server_stats.io_time_ms 53 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 41 #