data_1BDA # _model_server_result.job_id ZNrCPu7L-yBWzpdAi_d6Hw _model_server_result.datetime_utc '2024-11-21 22:46:54' _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 1bda # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":245}' # _entry.id 1BDA # _exptl.entry_id 1BDA _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 627.133 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide' _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 90 _cell.angle_gamma 90 _cell.entry_id 1BDA _cell.length_a 43.99 _cell.length_b 80.78 _cell.length_c 159.16 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1BDA _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_software_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,E 1 1 B,D,F 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 ? 2 C N N ? 2 D 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 2 A CYS 1 1_555 A SG CYS 133 A CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? disulf ? disulf2 A SG CYS 45 A CYS 42 1_555 A SG CYS 61 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? disulf ? disulf3 A SG CYS 53 A CYS 50 1_555 A SG CYS 122 A CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 A SG CYS 147 A CYS 136 1_555 A SG CYS 222 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf5 A SG CYS 179 A CYS 168 1_555 A SG CYS 195 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf6 A SG CYS 212 A CYS 191 1_555 A SG CYS 240 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf7 B SG CYS 2 B CYS 1 1_555 B SG CYS 133 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.015 ? disulf ? disulf8 B SG CYS 45 B CYS 42 1_555 B SG CYS 61 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf9 B SG CYS 53 B CYS 50 1_555 B SG CYS 122 B CYS 111 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf10 B SG CYS 147 B CYS 136 1_555 B SG CYS 222 B CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf11 B SG CYS 179 B CYS 168 1_555 B SG CYS 195 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf12 B SG CYS 212 B CYS 191 1_555 B SG CYS 240 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? covale ? covale1 A NE2 HIS 60 A HIS 57 1_555 C CE 2Z0 . A 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.516 ? covale ? covale2 A OG SER 216 A SER 195 1_555 C CC 2Z0 . A 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.397 ? covale ? covale3 B NE2 HIS 60 B HIS 57 1_555 D CE 2Z0 . B 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.527 ? covale ? covale4 B OG SER 216 B SER 195 1_555 D CC 2Z0 . B 2Z0 245 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.415 ? # _chem_comp.formula 'C26 H37 Cl N7 O7 S 1' _chem_comp.formula_weight 627.133 _chem_comp.id 2Z0 _chem_comp.mon_nstd_flag . _chem_comp.name 'N-{[5-(dimethylamino)naphthalen-2-yl]sulfonyl}-L-alpha-glutamyl-N-[(1S)-4-{[amino(iminio)methyl]amino}-1-(chloroacetyl) butyl]glycinamide' _chem_comp.type peptide-like _chem_comp.pdbx_synonyms dansyl-Glu-Gly-Arg-chloromethyl-ketone # 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 2Z0 doub 1 n y C1 C8A 2Z0 sing 2 n y C1 H1 2Z0 sing 3 n n C2 C3 2Z0 sing 4 n y C2 S 2Z0 sing 5 n n C3 C4 2Z0 doub 6 n y C3 H3 2Z0 sing 7 n n C4 C4A 2Z0 sing 8 n y C4 H4 2Z0 sing 9 n n C4A C5 2Z0 doub 10 n y C4A C8A 2Z0 sing 11 n y C5 C6 2Z0 sing 12 n y C5 N 2Z0 sing 13 n n C6 C7 2Z0 doub 14 n y C6 H6 2Z0 sing 15 n n C7 C8 2Z0 sing 16 n y C7 H7 2Z0 sing 17 n n C8 C8A 2Z0 doub 18 n y C8 H8 2Z0 sing 19 n n N CM1 2Z0 sing 20 n n N CM2 2Z0 sing 21 n n CM1 HM11 2Z0 sing 22 n n CM1 HM12 2Z0 sing 23 n n CM1 HM13 2Z0 sing 24 n n CM2 HM21 2Z0 sing 25 n n CM2 HM22 2Z0 sing 26 n n CM2 HM23 2Z0 sing 27 n n S O1S 2Z0 doub 28 n n S N1 2Z0 sing 29 n n S O2S 2Z0 doub 30 n n N1 CA 2Z0 sing 31 n n N1 H 2Z0 sing 32 n n CA C 2Z0 sing 33 n n CA CB 2Z0 sing 34 n n CA HA 2Z0 sing 35 n n C O 2Z0 doub 36 n n C N2 2Z0 sing 37 n n CB CG 2Z0 sing 38 n n CB HB2 2Z0 sing 39 n n CB HB3 2Z0 sing 40 n n CG CD 2Z0 sing 41 n n CG HG2 2Z0 sing 42 n n CG HG3 2Z0 sing 43 n n CD OE1 2Z0 doub 44 n n CD OE2 2Z0 sing 45 n n OE2 HE2 2Z0 sing 46 n n N2 CA1 2Z0 sing 47 n n N2 H2 2Z0 sing 48 n n CA1 C9 2Z0 sing 49 n n CA1 HA2 2Z0 sing 50 n n CA1 HA3 2Z0 sing 51 n n C9 O1 2Z0 doub 52 n n C9 N3 2Z0 sing 53 n n N3 CA2 2Z0 sing 54 n n N3 H5 2Z0 sing 55 n n CA2 CC 2Z0 sing 56 n n CA2 CB1 2Z0 sing 57 n n CA2 HA1 2Z0 sing 58 n n CC O2 2Z0 doub 59 n n CC CE 2Z0 sing 60 n n CB1 CG1 2Z0 sing 61 n n CB1 HB21 2Z0 sing 62 n n CB1 HB31 2Z0 sing 63 n n CG1 CD1 2Z0 sing 64 n n CG1 HG21 2Z0 sing 65 n n CG1 HG31 2Z0 sing 66 n n CD1 NE 2Z0 sing 67 n n CD1 HD2 2Z0 sing 68 n n CD1 HD3 2Z0 sing 69 n n NE CZ 2Z0 sing 70 n n NE HE 2Z0 sing 71 n n CZ NH1 2Z0 sing 72 n n CZ NH2 2Z0 doub 73 n n NH1 HH11 2Z0 sing 74 n n NH1 HH12 2Z0 sing 75 n n NH2 HH21 2Z0 sing 76 n n NH2 HH22 2Z0 sing 77 n n CE H11 2Z0 sing 78 n n CE H21 2Z0 sing 79 n n CL1 CE 2Z0 sing 80 n n # _atom_sites.entry_id 1BDA _atom_sites.fract_transf_matrix[1][1] 0.022732 _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] 0.012379 _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] 0.006283 _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 2Z0 A 1 245 1 2Z0 DSY . D 2 2Z0 B 1 245 1 2Z0 DSY . E 3 HOH A 1 246 3 HOH HOH . E 3 HOH A 2 247 4 HOH HOH . E 3 HOH A 3 248 5 HOH HOH . E 3 HOH A 4 249 6 HOH HOH . E 3 HOH A 5 250 7 HOH HOH . E 3 HOH A 6 251 11 HOH HOH . E 3 HOH A 7 252 12 HOH HOH . E 3 HOH A 8 253 14 HOH HOH . E 3 HOH A 9 254 16 HOH HOH . E 3 HOH A 10 255 17 HOH HOH . E 3 HOH A 11 256 2 HOH HOH . F 3 HOH B 1 246 11 HOH HOH . F 3 HOH B 2 247 15 HOH HOH . F 3 HOH B 3 248 20 HOH HOH . F 3 HOH B 4 249 21 HOH HOH . F 3 HOH B 5 250 22 HOH HOH . F 3 HOH B 6 251 23 HOH HOH . F 3 HOH B 7 252 24 HOH HOH . F 3 HOH B 8 253 15 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 2Z0 . . . C 2 8.589 11.583 36.893 1 22.97 ? C1 2Z0 245 A 1 HETATM 2 C C2 2Z0 . . . C 2 8.084 10.963 35.823 1 23.38 ? C2 2Z0 245 A 1 HETATM 3 C C3 2Z0 . . . C 2 6.749 10.506 35.811 1 22.62 ? C3 2Z0 245 A 1 HETATM 4 C C4 2Z0 . . . C 2 5.939 10.697 36.933 1 22.96 ? C4 2Z0 245 A 1 HETATM 5 C C4A 2Z0 . . . C 2 6.471 11.351 38.057 1 26.3 ? C4A 2Z0 245 A 1 HETATM 6 C C5 2Z0 . . . C 2 5.701 11.573 39.237 1 28.55 ? C5 2Z0 245 A 1 HETATM 7 C C6 2Z0 . . . C 2 6.272 12.214 40.304 1 28.28 ? C6 2Z0 245 A 1 HETATM 8 C C7 2Z0 . . . C 2 7.578 12.643 40.251 1 29.56 ? C7 2Z0 245 A 1 HETATM 9 C C8 2Z0 . . . C 2 8.362 12.444 39.136 1 27.86 ? C8 2Z0 245 A 1 HETATM 10 C C8A 2Z0 . . . C 2 7.821 11.794 38.027 1 24.69 ? C8A 2Z0 245 A 1 HETATM 11 N N 2Z0 . . . C 2 4.29 11.169 39.444 1 31.19 ? N 2Z0 245 A 1 HETATM 12 C CM1 2Z0 . . . C 2 3.231 11.867 38.775 1 32.37 ? CM1 2Z0 245 A 1 HETATM 13 C CM2 2Z0 . . . C 2 3.993 10.037 40.363 1 34.18 ? CM2 2Z0 245 A 1 HETATM 14 S S 2Z0 . . . C 2 9.27 10.874 34.621 1 25.54 ? S 2Z0 245 A 1 HETATM 15 O O1S 2Z0 . . . C 2 10.641 10.514 35.274 1 24.71 ? O1S 2Z0 245 A 1 HETATM 16 O O2S 2Z0 . . . C 2 8.845 9.855 33.505 1 29.04 ? O2S 2Z0 245 A 1 HETATM 17 N N1 2Z0 . . . C 2 9.561 12.489 34.353 1 20.73 ? N1 2Z0 245 A 1 HETATM 18 C CA 2Z0 . . . C 2 8.697 12.948 33.284 1 19.06 ? CA 2Z0 245 A 1 HETATM 19 C C 2Z0 . . . C 2 9.348 12.559 31.977 1 18.03 ? C 2Z0 245 A 1 HETATM 20 O O 2Z0 . . . C 2 10.57 12.498 31.883 1 20.77 ? O 2Z0 245 A 1 HETATM 21 C CB 2Z0 . . . C 2 8.514 14.468 33.336 1 19.32 ? CB 2Z0 245 A 1 HETATM 22 C CG 2Z0 . . . C 2 7.685 14.969 34.5 1 19.39 ? CG 2Z0 245 A 1 HETATM 23 C CD 2Z0 . . . C 2 8.504 15.756 35.507 1 21.33 ? CD 2Z0 245 A 1 HETATM 24 O OE1 2Z0 . . . C 2 9.041 15.139 36.454 1 19.52 ? OE1 2Z0 245 A 1 HETATM 25 O OE2 2Z0 . . . C 2 8.599 17 35.359 1 24.44 ? OE2 2Z0 245 A 1 HETATM 26 N N2 2Z0 . . . C 2 8.537 12.219 30.992 1 15.79 ? N2 2Z0 245 A 1 HETATM 27 C CA1 2Z0 . . . C 2 9.094 11.875 29.705 1 13.54 ? CA1 2Z0 245 A 1 HETATM 28 C C9 2Z0 . . . C 2 9.663 13.134 29.089 1 12.08 ? C9 2Z0 245 A 1 HETATM 29 O O1 2Z0 . . . C 2 9.469 14.241 29.619 1 10.02 ? O1 2Z0 245 A 1 HETATM 30 O O2 2Z0 . . . C 2 10.874 15.32 25.303 1 14.31 ? O2 2Z0 245 A 1 HETATM 31 N N3 2Z0 . . . C 2 10.362 12.963 27.973 1 9.8 ? N3 2Z0 245 A 1 HETATM 32 C CA2 2Z0 . . . C 2 10.963 14.082 27.269 1 11.95 ? CA2 2Z0 245 A 1 HETATM 33 C CC 2Z0 . . . C 2 10.792 13.959 25.782 1 13.99 ? CC 2Z0 245 A 1 HETATM 34 C CB1 2Z0 . . . C 2 12.434 14.223 27.665 1 8.56 ? CB1 2Z0 245 A 1 HETATM 35 C CG1 2Z0 . . . C 2 12.667 14.549 29.145 1 8.86 ? CG1 2Z0 245 A 1 HETATM 36 C CD1 2Z0 . . . C 2 14.137 14.77 29.375 1 8.18 ? CD1 2Z0 245 A 1 HETATM 37 N NE 2Z0 . . . C 2 14.475 15.062 30.758 1 10.27 ? NE 2Z0 245 A 1 HETATM 38 C CZ 2Z0 . . . C 2 15.726 15.13 31.213 1 12.36 ? CZ 2Z0 245 A 1 HETATM 39 N NH2 2Z0 . . . C 2 15.943 15.476 32.476 1 16.49 ? NH2 2Z0 245 A 1 HETATM 40 N NH1 2Z0 . . . C 2 16.758 14.921 30.394 1 5 ? NH1 2Z0 245 A 1 HETATM 41 C CE 2Z0 . . . C 2 9.45 13.204 25.42 1 17.66 ? CE 2Z0 245 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 41 #