data_5WXS # _model_server_result.job_id wYF7-YXApX9xwfO0ZqLuuQ _model_server_result.datetime_utc '2024-10-22 03:28:33' _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 5wxs # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5WXS # _exptl.entry_id 5WXS _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.336 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2R)-N-[2-[[(2S)-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-1,2-dihydropyrrole-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 5WXS _cell.length_a 120.435 _cell.length_b 120.435 _cell.length_c 42.04 _cell.Z_PDB 9 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WXS _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf2 A SG CYS 39 U CYS 50 1_555 A SG CYS 110 U CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.934 ? disulf ? disulf3 A SG CYS 135 U CYS 136 1_555 A SG CYS 204 U CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.005 ? disulf ? disulf4 A SG CYS 167 U CYS 168 1_555 A SG CYS 183 U CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.868 ? disulf ? disulf5 A SG CYS 194 U CYS 191 1_555 A SG CYS 222 U CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.92 ? covale ? covale1 A OG SER 198 U SER 195 1_555 B C9 7YF . U 7YF 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.435 ? # _chem_comp.formula 'C13 H20 N6 O4' _chem_comp.formula_weight 324.336 _chem_comp.id 7YF _chem_comp.mon_nstd_flag . _chem_comp.name (2R)-N-[2-[[(2S)-5-carbamimidamido-1-oxidanylidene-pentan-2-yl]amino]-2-oxidanylidene-ethyl]-5-oxidanylidene-1,2-dihydropyrrole-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 7YF doub 1 n n C1 C2 7YF sing 2 n n C1 N1 7YF sing 3 n n C2 C3 7YF doub 4 n n N1 C4 7YF sing 5 n n C3 C4 7YF sing 6 n n C4 C5 7YF sing 7 n n C5 O2 7YF doub 8 n n C5 N2 7YF sing 9 n n N5 C13 7YF doub 10 n n N2 C6 7YF sing 11 n n O3 C7 7YF doub 12 n n C13 N4 7YF sing 13 n n C13 N6 7YF sing 14 n n N4 C12 7YF sing 15 n n C6 C7 7YF sing 16 n n C7 N3 7YF sing 17 n n C11 C12 7YF sing 18 n n C11 C10 7YF sing 19 n n N3 C8 7YF sing 20 n n C8 C10 7YF sing 21 n n C8 C9 7YF sing 22 n n O4 C9 7YF doub 23 n n C10 H1 7YF sing 24 n n C10 H2 7YF sing 25 n n C12 H3 7YF sing 26 n n C12 H4 7YF sing 27 n n C9 H5 7YF sing 28 n n C8 H6 7YF sing 29 n n C11 H7 7YF sing 30 n n C11 H8 7YF sing 31 n n N4 H9 7YF sing 32 n n N6 H10 7YF sing 33 n n N6 H11 7YF sing 34 n n N5 H12 7YF sing 35 n n N3 H13 7YF sing 36 n n C6 H14 7YF sing 37 n n C6 H15 7YF sing 38 n n N2 H16 7YF sing 39 n n C4 H17 7YF sing 40 n n N1 H18 7YF sing 41 n n C3 H19 7YF sing 42 n n C2 H20 7YF sing 43 n n # _atom_sites.entry_id 5WXS _atom_sites.fract_transf_matrix[1][1] 0.008303 _atom_sites.fract_transf_matrix[1][2] 0.004794 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009588 _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] 0.023787 _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 7YF U 1 301 301 7YF 7YF . C 3 HOH U 1 401 401 HOH HOH . C 3 HOH U 2 402 402 HOH HOH . C 3 HOH U 3 403 403 HOH HOH . C 3 HOH U 4 404 404 HOH HOH . C 3 HOH U 5 405 405 HOH HOH . C 3 HOH U 6 406 406 HOH HOH . C 3 HOH U 7 407 407 HOH HOH . C 3 HOH U 8 408 408 HOH HOH . C 3 HOH U 9 409 409 HOH HOH . C 3 HOH U 10 410 410 HOH HOH . C 3 HOH U 11 411 411 HOH HOH . C 3 HOH U 12 412 412 HOH HOH . C 3 HOH U 13 413 413 HOH HOH . C 3 HOH U 14 414 414 HOH HOH . C 3 HOH U 15 415 415 HOH HOH . C 3 HOH U 16 416 416 HOH HOH . C 3 HOH U 17 417 417 HOH HOH . C 3 HOH U 18 418 418 HOH HOH . C 3 HOH U 19 419 419 HOH HOH . C 3 HOH U 20 420 420 HOH HOH . C 3 HOH U 21 421 421 HOH HOH . C 3 HOH U 22 422 422 HOH HOH . C 3 HOH U 23 423 423 HOH HOH . C 3 HOH U 24 424 424 HOH HOH . C 3 HOH U 25 425 425 HOH HOH . C 3 HOH U 26 426 426 HOH HOH . C 3 HOH U 27 427 427 HOH HOH . C 3 HOH U 28 428 428 HOH HOH . C 3 HOH U 29 429 429 HOH HOH . C 3 HOH U 30 430 430 HOH HOH . C 3 HOH U 31 431 431 HOH HOH . C 3 HOH U 32 432 432 HOH HOH . C 3 HOH U 33 433 433 HOH HOH . C 3 HOH U 34 434 434 HOH HOH . C 3 HOH U 35 435 435 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 7YF . . . B 2 4.473 -31.833 -26.82 1 66.42 ? C5 7YF 301 U 1 HETATM 2 O O2 7YF . . . B 2 3.766 -32.767 -26.571 1 65.49 ? O2 7YF 301 U 1 HETATM 3 C C4 7YF . . . B 2 4.956 -31.651 -28.209 1 70.6 ? C4 7YF 301 U 1 HETATM 4 N N1 7YF . . . B 2 3.901 -31.278 -29.115 1 70.82 ? N1 7YF 301 U 1 HETATM 5 C C3 7YF . . . B 2 5.345 -33.01 -28.752 1 72.67 ? C3 7YF 301 U 1 HETATM 6 C C2 7YF . . . B 2 4.491 -33.337 -29.953 1 73.64 ? C2 7YF 301 U 1 HETATM 7 C C1 7YF . . . B 2 3.565 -32.194 -29.978 1 75.61 ? C1 7YF 301 U 1 HETATM 8 O O1 7YF . . . B 2 2.613 -32.172 -30.711 1 79.8 ? O1 7YF 301 U 1 HETATM 9 N N2 7YF . . . B 2 4.848 -30.96 -25.912 1 55.13 ? N2 7YF 301 U 1 HETATM 10 C C6 7YF . . . B 2 4.444 -30.992 -24.534 1 53.49 ? C6 7YF 301 U 1 HETATM 11 C C7 7YF . . . B 2 2.948 -30.878 -24.499 1 53.36 ? C7 7YF 301 U 1 HETATM 12 O O3 7YF . . . B 2 2.379 -30.27 -25.354 1 52.45 ? O3 7YF 301 U 1 HETATM 13 N N3 7YF . . . B 2 2.308 -31.463 -23.525 1 47.78 ? N3 7YF 301 U 1 HETATM 14 C C8 7YF . . . B 2 0.868 -31.404 -23.423 1 49.68 ? C8 7YF 301 U 1 HETATM 15 C C9 7YF . . . B 2 0.343 -30.447 -22.458 1 47.93 ? C9 7YF 301 U 1 HETATM 16 O O4 7YF . . . B 2 0.642 -29.283 -22.518 1 56.26 ? O4 7YF 301 U 1 HETATM 17 C C10 7YF . . . B 2 0.435 -32.815 -23.084 1 48.45 ? C10 7YF 301 U 1 HETATM 18 C C11 7YF . . . B 2 0.23 -33.643 -24.323 1 44.95 ? C11 7YF 301 U 1 HETATM 19 C C12 7YF . . . B 2 0.114 -35.11 -24.009 1 46.46 ? C12 7YF 301 U 1 HETATM 20 N N4 7YF . . . B 2 0.154 -35.858 -25.237 1 52.72 ? N4 7YF 301 U 1 HETATM 21 C C13 7YF . . . B 2 -0.152 -37.127 -25.337 1 51.62 ? C13 7YF 301 U 1 HETATM 22 N N6 7YF . . . B 2 -0.463 -37.806 -24.276 1 48.85 ? N6 7YF 301 U 1 HETATM 23 N N5 7YF . . . B 2 -0.159 -37.674 -26.446 1 48.15 ? N5 7YF 301 U 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 209 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 23 #