data_6SKD # _model_server_result.job_id ABqI3E_J6ih1YFzPJsXPbA _model_server_result.datetime_utc '2024-11-23 07:20:29' _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 6skd # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":304}' # _entry.id 6SKD # _exptl.entry_id 6SKD _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 295.144 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]methylamino]benzenecarboximidamide _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 98.58 _cell.angle_gamma 90 _cell.entry_id 6SKD _cell.length_a 58.03 _cell.length_b 46.24 _cell.length_c 80.44 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6SKD _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,I 1 1 B,E,F,G,H,J 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 ? 3 D N N ? 3 H 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 7 A CYS 22 1_555 A SG CYS 136 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf2 A SG CYS 26 A CYS 42 1_555 A SG CYS 42 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf3 A SG CYS 110 A CYS 128 1_555 A SG CYS 210 A CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 A SG CYS 117 A CYS 136 1_555 A SG CYS 182 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 A SG CYS 147 A CYS 168 1_555 A SG CYS 161 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf6 A SG CYS 172 A CYS 191 1_555 A SG CYS 197 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf7 B SG CYS 7 B CYS 22 1_555 B SG CYS 136 B CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf8 B SG CYS 26 B CYS 42 1_555 B SG CYS 42 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf9 B SG CYS 110 B CYS 128 1_555 B SG CYS 210 B CYS 232 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf10 B SG CYS 117 B CYS 136 1_555 B SG CYS 182 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 B SG CYS 147 B CYS 168 1_555 B SG CYS 161 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 B SG CYS 172 B CYS 191 1_555 B SG CYS 197 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? covale ? covale1 A OG SER 176 A SER 195 1_555 D B33 LH2 . A LH2 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.599 ? # _chem_comp.formula 'C16 H18 B N3 O2' _chem_comp.formula_weight 295.144 _chem_comp.id LH2 _chem_comp.mon_nstd_flag . _chem_comp.name 4-[[(3~{S})-1-oxidanyl-3,4-dihydro-2,1-benzoxaborinin-3-yl]methylamino]benzenecarboximidamide _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 N05 C04 LH2 doub 207 n n C04 N01 LH2 sing 208 n n C04 C07 LH2 sing 209 n n C08 C07 LH2 doub 210 n y C08 C10 LH2 sing 211 n y C07 C39 LH2 sing 212 n y C10 C12 LH2 doub 213 n y C39 C37 LH2 doub 214 n y O34 B33 LH2 sing 215 n n C12 C37 LH2 sing 216 n y C12 N13 LH2 sing 217 n n B33 O36 LH2 sing 218 n n B33 C32 LH2 sing 219 n n N13 C15 LH2 sing 220 n n O36 C18 LH2 sing 221 n n C15 C18 LH2 sing 222 n n C32 C30 LH2 doub 223 n y C32 C23 LH2 sing 224 n y C30 C28 LH2 sing 225 n y C18 C20 LH2 sing 226 n n C28 C26 LH2 doub 227 n y C23 C20 LH2 sing 228 n n C23 C24 LH2 doub 229 n y C26 C24 LH2 sing 230 n y C10 H1 LH2 sing 231 n n C15 H2 LH2 sing 232 n n C15 H3 LH2 sing 233 n n C20 H4 LH2 sing 234 n n C20 H5 LH2 sing 235 n n C24 H6 LH2 sing 236 n n C26 H7 LH2 sing 237 n n C28 H8 LH2 sing 238 n n N01 H9 LH2 sing 239 n n N01 H10 LH2 sing 240 n n N05 H11 LH2 sing 241 n n C08 H12 LH2 sing 242 n n N13 H13 LH2 sing 243 n n C18 H14 LH2 sing 244 n n C30 H15 LH2 sing 245 n n C37 H16 LH2 sing 246 n n C39 H17 LH2 sing 247 n n O34 H18 LH2 sing 248 n n # _atom_sites.entry_id 6SKD _atom_sites.fract_transf_matrix[1][1] 0.017232 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.0026 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021626 _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] 0.012572 _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 UNX A 1 301 2 UNX UNX . D 3 LH2 A 1 302 1 LH2 LIG . E 4 GOL B 1 301 1 GOL GOL . F 4 GOL B 1 302 2 GOL GOL . G 2 UNX B 1 303 1 UNX UNX . H 3 LH2 B 1 304 2 LH2 LIG . I 5 HOH A 1 401 10 HOH HOH . I 5 HOH A 2 402 99 HOH HOH . I 5 HOH A 3 403 112 HOH HOH . I 5 HOH A 4 404 17 HOH HOH . I 5 HOH A 5 405 69 HOH HOH . I 5 HOH A 6 406 98 HOH HOH . I 5 HOH A 7 407 97 HOH HOH . I 5 HOH A 8 408 110 HOH HOH . I 5 HOH A 9 409 101 HOH HOH . I 5 HOH A 10 410 18 HOH HOH . I 5 HOH A 11 411 89 HOH HOH . I 5 HOH A 12 412 28 HOH HOH . I 5 HOH A 13 413 37 HOH HOH . I 5 HOH A 14 414 20 HOH HOH . I 5 HOH A 15 415 36 HOH HOH . I 5 HOH A 16 416 108 HOH HOH . I 5 HOH A 17 417 41 HOH HOH . I 5 HOH A 18 418 88 HOH HOH . I 5 HOH A 19 419 95 HOH HOH . I 5 HOH A 20 420 49 HOH HOH . I 5 HOH A 21 421 47 HOH HOH . I 5 HOH A 22 422 45 HOH HOH . I 5 HOH A 23 423 34 HOH HOH . I 5 HOH A 24 424 102 HOH HOH . I 5 HOH A 25 425 93 HOH HOH . I 5 HOH A 26 426 114 HOH HOH . I 5 HOH A 27 427 96 HOH HOH . I 5 HOH A 28 428 91 HOH HOH . I 5 HOH A 29 429 103 HOH HOH . I 5 HOH A 30 430 44 HOH HOH . I 5 HOH A 31 431 92 HOH HOH . I 5 HOH A 32 432 107 HOH HOH . I 5 HOH A 33 433 94 HOH HOH . I 5 HOH A 34 434 43 HOH HOH . I 5 HOH A 35 435 39 HOH HOH . I 5 HOH A 36 436 100 HOH HOH . I 5 HOH A 37 437 30 HOH HOH . I 5 HOH A 38 438 90 HOH HOH . I 5 HOH A 39 439 54 HOH HOH . J 5 HOH B 1 401 24 HOH HOH . J 5 HOH B 2 402 74 HOH HOH . J 5 HOH B 3 403 84 HOH HOH . J 5 HOH B 4 404 13 HOH HOH . J 5 HOH B 5 405 35 HOH HOH . J 5 HOH B 6 406 9 HOH HOH . J 5 HOH B 7 407 6 HOH HOH . J 5 HOH B 8 408 85 HOH HOH . J 5 HOH B 9 409 61 HOH HOH . J 5 HOH B 10 410 63 HOH HOH . J 5 HOH B 11 411 105 HOH HOH . J 5 HOH B 12 412 15 HOH HOH . J 5 HOH B 13 413 4 HOH HOH . J 5 HOH B 14 414 71 HOH HOH . J 5 HOH B 15 415 21 HOH HOH . J 5 HOH B 16 416 64 HOH HOH . J 5 HOH B 17 417 19 HOH HOH . J 5 HOH B 18 418 80 HOH HOH . J 5 HOH B 19 419 86 HOH HOH . J 5 HOH B 20 420 23 HOH HOH . J 5 HOH B 21 421 7 HOH HOH . J 5 HOH B 22 422 115 HOH HOH . J 5 HOH B 23 423 16 HOH HOH . J 5 HOH B 24 424 72 HOH HOH . J 5 HOH B 25 425 48 HOH HOH . J 5 HOH B 26 426 32 HOH HOH . J 5 HOH B 27 427 57 HOH HOH . J 5 HOH B 28 428 68 HOH HOH . J 5 HOH B 29 429 81 HOH HOH . J 5 HOH B 30 430 14 HOH HOH . J 5 HOH B 31 431 60 HOH HOH . J 5 HOH B 32 432 42 HOH HOH . J 5 HOH B 33 433 79 HOH HOH . J 5 HOH B 34 434 5 HOH HOH . J 5 HOH B 35 435 70 HOH HOH . J 5 HOH B 36 436 22 HOH HOH . J 5 HOH B 37 437 53 HOH HOH . J 5 HOH B 38 438 12 HOH HOH . J 5 HOH B 39 439 51 HOH HOH . J 5 HOH B 40 440 2 HOH HOH . J 5 HOH B 41 441 25 HOH HOH . J 5 HOH B 42 442 87 HOH HOH . J 5 HOH B 43 443 67 HOH HOH . J 5 HOH B 44 444 58 HOH HOH . J 5 HOH B 45 445 11 HOH HOH . J 5 HOH B 46 446 31 HOH HOH . J 5 HOH B 47 447 82 HOH HOH . J 5 HOH B 48 448 73 HOH HOH . J 5 HOH B 49 449 66 HOH HOH . J 5 HOH B 50 450 113 HOH HOH . J 5 HOH B 51 451 50 HOH HOH . J 5 HOH B 52 452 3 HOH HOH . J 5 HOH B 53 453 111 HOH HOH . J 5 HOH B 54 454 46 HOH HOH . J 5 HOH B 55 455 8 HOH HOH . J 5 HOH B 56 456 78 HOH HOH . J 5 HOH B 57 457 59 HOH HOH . J 5 HOH B 58 458 40 HOH HOH . J 5 HOH B 59 459 62 HOH HOH . J 5 HOH B 60 460 26 HOH HOH . J 5 HOH B 61 461 27 HOH HOH . J 5 HOH B 62 462 52 HOH HOH . J 5 HOH B 63 463 1 HOH HOH . J 5 HOH B 64 464 55 HOH HOH . J 5 HOH B 65 465 83 HOH HOH . J 5 HOH B 66 466 104 HOH HOH . J 5 HOH B 67 467 75 HOH HOH . J 5 HOH B 68 468 38 HOH HOH . J 5 HOH B 69 469 65 HOH HOH . J 5 HOH B 70 470 29 HOH HOH . J 5 HOH B 71 471 76 HOH HOH . J 5 HOH B 72 472 106 HOH HOH . J 5 HOH B 73 473 109 HOH HOH . J 5 HOH B 74 474 33 HOH HOH . J 5 HOH B 75 475 56 HOH HOH . J 5 HOH B 76 476 77 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 C10 LH2 . . . H 3 -21.49 -5.209 -17.393 1 42.02 ? C10 LH2 304 B 1 HETATM 2 C C15 LH2 . . . H 3 -20.137 -7.908 -17.184 1 44.69 ? C15 LH2 304 B 1 HETATM 3 C C20 LH2 . . . H 3 -20.242 -9.984 -15.863 1 44.04 ? C20 LH2 304 B 1 HETATM 4 C C24 LH2 . . . H 3 -20.052 -12.331 -14.956 1 45.76 ? C24 LH2 304 B 1 HETATM 5 C C26 LH2 . . . H 3 -19.338 -13.359 -14.359 1 45.56 ? C26 LH2 304 B 1 HETATM 6 C C28 LH2 . . . H 3 -18.007 -13.178 -14.039 1 46.27 ? C28 LH2 304 B 1 HETATM 7 N N01 LH2 . . . H 3 -20.904 -0.529 -16.268 1 39.14 ? N01 LH2 304 B 1 HETATM 8 C C04 LH2 . . . H 3 -21.441 -1.434 -17.108 1 40.71 ? C04 LH2 304 B 1 HETATM 9 N N05 LH2 . . . H 3 -22.149 -1.03 -18.115 1 39.45 ? N05 LH2 304 B 1 HETATM 10 C C07 LH2 . . . H 3 -21.168 -2.877 -16.839 1 40.53 ? C07 LH2 304 B 1 HETATM 11 C C08 LH2 . . . H 3 -21.752 -3.87 -17.628 1 40.87 ? C08 LH2 304 B 1 HETATM 12 C C12 LH2 . . . H 3 -20.612 -5.587 -16.379 1 43.72 ? C12 LH2 304 B 1 HETATM 13 N N13 LH2 . . . H 3 -20.357 -6.922 -16.129 1 45.52 ? N13 LH2 304 B 1 HETATM 14 C C18 LH2 . . . H 3 -19.341 -9.095 -16.687 1 44.73 ? C18 LH2 304 B 1 HETATM 15 C C23 LH2 . . . H 3 -19.443 -11.109 -15.244 1 46.01 ? C23 LH2 304 B 1 HETATM 16 C C30 LH2 . . . H 3 -17.384 -11.97 -14.324 1 46.92 ? C30 LH2 304 B 1 HETATM 17 C C32 LH2 . . . H 3 -18.084 -10.897 -14.903 1 46.73 ? C32 LH2 304 B 1 HETATM 18 B B33 LH2 . . . H 3 -17.444 -9.542 -15.257 1 46.22 ? B33 LH2 304 B 1 HETATM 19 O O34 LH2 . . . H 3 -16.107 -9.36 -15.339 1 47.11 ? O34 LH2 304 B 1 HETATM 20 O O36 LH2 . . . H 3 -18.218 -8.628 -15.931 1 46.8 ? O36 LH2 304 B 1 HETATM 21 C C37 LH2 . . . H 3 -20.053 -4.605 -15.566 1 41.6 ? C37 LH2 304 B 1 HETATM 22 C C39 LH2 . . . H 3 -20.328 -3.264 -15.795 1 39.55 ? C39 LH2 304 B 1 # _model_server_stats.io_time_ms 44 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 302 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #