data_5WXT # _model_server_result.job_id le9_UjDVKm-VHhBS_MsOXQ _model_server_result.datetime_utc '2024-11-22 23:50:16' _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 5wxt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5WXT # _exptl.entry_id 5WXT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 464.476 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-N-[2-[[(2S)-1-[[4-[bis(oxidanyl)amino]phenyl]amino]-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-pyrrolidine-2-carboxamide _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 120 _cell.entry_id 5WXT _cell.length_a 121.354 _cell.length_b 121.354 _cell.length_c 42.207 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WXT _symmetry.cell_setting ? _symmetry.Int_Tables_number 146 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'H 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _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 2 _struct_asym.id B _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 31 U CYS 42 1_555 A SG CYS 47 U CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.822 ? disulf ? disulf2 A SG CYS 39 U CYS 50 1_555 A SG CYS 110 U CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? disulf ? disulf3 A SG CYS 135 U CYS 136 1_555 A SG CYS 204 U CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf4 A SG CYS 167 U CYS 168 1_555 A SG CYS 183 U CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 194 U CYS 191 1_555 A SG CYS 222 U CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.982 ? # _chem_comp.formula 'C19 H28 N8 O6' _chem_comp.formula_weight 464.476 _chem_comp.id 7YR _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-N-[2-[[(2S)-1-[[4-[bis(oxidanyl)amino]phenyl]amino]-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-pyrrolidine-2-carboxamide _chem_comp.type peptide-like _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 O1 C1 7YR doub 1 n n C1 C2 7YR sing 2 n n C1 N1 7YR sing 3 n n C2 C3 7YR sing 4 n n N1 C4 7YR sing 5 n n C3 C4 7YR sing 6 n n C4 C5 7YR sing 7 n n C5 O2 7YR doub 8 n n C5 N2 7YR sing 9 n n N5 C13 7YR doub 10 n n N2 C6 7YR sing 11 n n C13 N4 7YR sing 12 n n C13 N6 7YR sing 13 n n N4 C12 7YR sing 14 n n N3 C8 7YR sing 15 n n N3 C7 7YR sing 16 n n C6 C7 7YR sing 17 n n C11 C12 7YR sing 18 n n C11 C10 7YR sing 19 n n C8 C10 7YR sing 20 n n C8 C9 7YR sing 21 n n C7 O3 7YR doub 22 n n C9 N7 7YR sing 23 n n C9 O4 7YR doub 24 n n N7 C14 7YR sing 25 n n C19 C14 7YR doub 26 n y C19 C18 7YR sing 27 n y C14 C15 7YR sing 28 n y C18 C17 7YR doub 29 n y C15 C16 7YR doub 30 n y C17 C16 7YR sing 31 n y C17 N8 7YR sing 32 n n N8 O5 7YR sing 33 n n N8 O6 7YR sing 34 n n C10 H1 7YR sing 35 n n C10 H2 7YR sing 36 n n C12 H3 7YR sing 37 n n C12 H4 7YR sing 38 n n N7 H5 7YR sing 39 n n C19 H6 7YR sing 40 n n C18 H7 7YR sing 41 n n C16 H8 7YR sing 42 n n C15 H9 7YR sing 43 n n O6 H10 7YR sing 44 n n O5 H11 7YR sing 45 n n C8 H12 7YR sing 46 n n C11 H13 7YR sing 47 n n C11 H14 7YR sing 48 n n N4 H15 7YR sing 49 n n N6 H16 7YR sing 50 n n N6 H17 7YR sing 51 n n N5 H18 7YR sing 52 n n N3 H19 7YR sing 53 n n C6 H20 7YR sing 54 n n C6 H21 7YR sing 55 n n N2 H22 7YR sing 56 n n C4 H23 7YR sing 57 n n N1 H24 7YR sing 58 n n C3 H25 7YR sing 59 n n C3 H26 7YR sing 60 n n C2 H27 7YR sing 61 n n C2 H28 7YR sing 62 n n # _atom_sites.entry_id 5WXT _atom_sites.fract_transf_matrix[1][1] 0.00824 _atom_sites.fract_transf_matrix[1][2] 0.004758 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009515 _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] 0.023693 _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 7YR U 1 301 1 7YR EGR . C 3 HOH U 1 401 25 HOH HOH . C 3 HOH U 2 402 27 HOH HOH . C 3 HOH U 3 403 37 HOH HOH . C 3 HOH U 4 404 24 HOH HOH . C 3 HOH U 5 405 26 HOH HOH . C 3 HOH U 6 406 7 HOH HOH . C 3 HOH U 7 407 36 HOH HOH . C 3 HOH U 8 408 14 HOH HOH . C 3 HOH U 9 409 29 HOH HOH . C 3 HOH U 10 410 49 HOH HOH . C 3 HOH U 11 411 45 HOH HOH . C 3 HOH U 12 412 13 HOH HOH . C 3 HOH U 13 413 20 HOH HOH . C 3 HOH U 14 414 51 HOH HOH . C 3 HOH U 15 415 17 HOH HOH . C 3 HOH U 16 416 10 HOH HOH . C 3 HOH U 17 417 32 HOH HOH . C 3 HOH U 18 418 9 HOH HOH . C 3 HOH U 19 419 23 HOH HOH . C 3 HOH U 20 420 28 HOH HOH . C 3 HOH U 21 421 34 HOH HOH . C 3 HOH U 22 422 16 HOH HOH . C 3 HOH U 23 423 11 HOH HOH . C 3 HOH U 24 424 30 HOH HOH . C 3 HOH U 25 425 4 HOH HOH . C 3 HOH U 26 426 50 HOH HOH . C 3 HOH U 27 427 15 HOH HOH . C 3 HOH U 28 428 38 HOH HOH . C 3 HOH U 29 429 35 HOH HOH . C 3 HOH U 30 430 47 HOH HOH . C 3 HOH U 31 431 21 HOH HOH . C 3 HOH U 32 432 39 HOH HOH . C 3 HOH U 33 433 2 HOH HOH . C 3 HOH U 34 434 52 HOH HOH . C 3 HOH U 35 435 22 HOH HOH . C 3 HOH U 36 436 31 HOH HOH . C 3 HOH U 37 437 12 HOH HOH . C 3 HOH U 38 438 1 HOH HOH . C 3 HOH U 39 439 44 HOH HOH . C 3 HOH U 40 440 46 HOH HOH . C 3 HOH U 41 441 33 HOH HOH . C 3 HOH U 42 442 43 HOH HOH . C 3 HOH U 43 443 6 HOH HOH . C 3 HOH U 44 444 5 HOH HOH . C 3 HOH U 45 445 19 HOH HOH . C 3 HOH U 46 446 3 HOH HOH . C 3 HOH U 47 447 8 HOH HOH . C 3 HOH U 48 448 40 HOH HOH . C 3 HOH U 49 449 48 HOH HOH . C 3 HOH U 50 450 41 HOH HOH . C 3 HOH U 51 451 42 HOH HOH . C 3 HOH U 52 452 18 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 C5 7YR . . . B 2 4.791 -31.971 -26.671 1 49.91 ? C5 7YR 301 U 1 HETATM 2 O O2 7YR . . . B 2 4.082 -32.901 -26.439 1 51.85 ? O2 7YR 301 U 1 HETATM 3 C C4 7YR . . . B 2 5.278 -31.781 -28.069 1 51.2 ? C4 7YR 301 U 1 HETATM 4 N N1 7YR . . . B 2 4.238 -31.574 -29.065 1 53.08 ? N1 7YR 301 U 1 HETATM 5 C C3 7YR . . . B 2 5.776 -33.127 -28.522 1 52.68 ? C3 7YR 301 U 1 HETATM 6 C C2 7YR . . . B 2 4.7 -33.78 -29.34 1 53 ? C2 7YR 301 U 1 HETATM 7 C C1 7YR . . . B 2 3.981 -32.607 -29.836 1 52.51 ? C1 7YR 301 U 1 HETATM 8 O O1 7YR . . . B 2 3.292 -32.676 -30.814 1 52.35 ? O1 7YR 301 U 1 HETATM 9 N N2 7YR . . . B 2 5.124 -31.147 -25.722 1 44.25 ? N2 7YR 301 U 1 HETATM 10 C C6 7YR . . . B 2 4.649 -31.276 -24.357 1 48.62 ? C6 7YR 301 U 1 HETATM 11 C C7 7YR . . . B 2 3.161 -31.172 -24.409 1 48.55 ? C7 7YR 301 U 1 HETATM 12 O O3 7YR . . . B 2 2.668 -30.525 -25.279 1 54.65 ? O3 7YR 301 U 1 HETATM 13 N N3 7YR . . . B 2 2.445 -31.791 -23.509 1 49.81 ? N3 7YR 301 U 1 HETATM 14 C C8 7YR . . . B 2 0.985 -31.711 -23.548 1 51.12 ? C8 7YR 301 U 1 HETATM 15 C C9 7YR . . . B 2 0.447 -30.494 -22.814 1 55.75 ? C9 7YR 301 U 1 HETATM 16 O O4 7YR . . . B 2 -0.641 -30.343 -22.323 1 54.36 ? O4 7YR 301 U 1 HETATM 17 C C10 7YR . . . B 2 0.512 -33.09 -23.122 1 48.15 ? C10 7YR 301 U 1 HETATM 18 C C11 7YR . . . B 2 0.336 -33.949 -24.357 1 44.68 ? C11 7YR 301 U 1 HETATM 19 C C12 7YR . . . B 2 0.563 -35.415 -24.091 1 42.22 ? C12 7YR 301 U 1 HETATM 20 N N4 7YR . . . B 2 0.41 -36.184 -25.289 1 42.01 ? N4 7YR 301 U 1 HETATM 21 C C13 7YR . . . B 2 0.012 -37.431 -25.299 1 39.9 ? C13 7YR 301 U 1 HETATM 22 N N6 7YR . . . B 2 -0.343 -38.024 -24.195 1 38.74 ? N6 7YR 301 U 1 HETATM 23 N N5 7YR . . . B 2 -0.039 -38.072 -26.35 1 39.76 ? N5 7YR 301 U 1 HETATM 24 N N7 7YR . . . B 2 1.323 -29.559 -22.829 1 63.71 ? N7 7YR 301 U 1 HETATM 25 C C14 7YR . . . B 2 1.342 -28.281 -22.361 1 73.24 ? C14 7YR 301 U 1 HETATM 26 C C19 7YR . . . B 2 2.525 -27.656 -22.649 1 77.12 ? C19 7YR 301 U 1 HETATM 27 C C18 7YR . . . B 2 2.733 -26.36 -22.289 1 78.97 ? C18 7YR 301 U 1 HETATM 28 C C17 7YR . . . B 2 1.739 -25.682 -21.641 1 79.19 ? C17 7YR 301 U 1 HETATM 29 N N8 7YR . . . B 2 1.932 -24.358 -21.273 1 83.65 ? N8 7YR 301 U 1 HETATM 30 O O6 7YR . . . B 2 1.464 -24.198 -19.951 1 88.62 ? O6 7YR 301 U 1 HETATM 31 O O5 7YR . . . B 2 3.311 -23.977 -21.199 1 84.11 ? O5 7YR 301 U 1 HETATM 32 C C16 7YR . . . B 2 0.532 -26.298 -21.376 1 76.55 ? C16 7YR 301 U 1 HETATM 33 C C15 7YR . . . B 2 0.313 -27.609 -21.737 1 74.92 ? C15 7YR 301 U 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 271 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 33 #