data_6Z8X # _model_server_result.job_id jJCtigPnNXTtoU5SERMyjw _model_server_result.datetime_utc '2024-11-20 01:11:18' _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 6z8x # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 6Z8X # _exptl.entry_id 6Z8X _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.986 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide _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 6Z8X _cell.length_a 94.671 _cell.length_b 94.671 _cell.length_c 124.693 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Z8X _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H _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 4 _struct_asym.id D _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 9 L CYS 1 1_555 B SG CYS 119 H CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf2 B SG CYS 28 H CYS 42 1_555 B SG CYS 44 H CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.021 ? disulf ? disulf3 B SG CYS 173 H CYS 168 1_555 B SG CYS 187 H CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf4 B SG CYS 201 H CYS 191 1_555 B SG CYS 231 H CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? covale ? covale1 B NE2 HIS 43 H HIS 57 1_555 D C3 0G6 . H 0G6 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.47 ? covale ? covale2 B OG SER 205 H SER 195 1_555 D C2 0G6 . H 0G6 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.432 ? covale ? covale3 C O3' DG 2 B DG 2 1_555 C P QCE 3 B QCE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.476 ? covale ? covale4 C O3' QCE 3 B QCE 3 1_555 C P DT 4 B DT 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.48 ? metalc ? metalc1 B O ARG 233 H ARG 221 1_555 E NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.095 ? metalc ? metalc2 B O LYS 236 H LYS 224 1_555 E NA NA . H NA 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.527 ? metalc ? metalc3 C O6 DG 1 B DG 1 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.704 ? metalc ? metalc4 C O6 DG 2 B DG 2 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.656 ? metalc ? metalc5 C O6 DG 5 B DG 5 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? metalc ? metalc6 C O6 DG 6 B DG 6 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.823 ? metalc ? metalc7 C O6 DG 10 B DG 10 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc8 C O6 DG 11 B DG 11 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.734 ? metalc ? metalc9 C O6 DG 14 B DG 14 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.669 ? metalc ? metalc10 C O6 DG 15 B DG 15 1_555 F K K . B K 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.593 ? hydrog TYPE_6_PAIR hydrog1 C N1 DG 1 B DG 1 1_555 C O6 DG 6 B DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog2 C N2 DG 1 B DG 1 1_555 C N7 DG 6 B DG 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog3 C N7 DG 1 B DG 1 1_555 C N2 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog4 C O6 DG 1 B DG 1 1_555 C N1 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog5 C N7 DG 2 B DG 2 1_555 C N2 DG 5 B DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog6 C O6 DG 2 B DG 2 1_555 C N1 DG 5 B DG 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog7 C N1 DG 2 B DG 2 1_555 C O6 DG 14 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog8 C N2 DG 2 B DG 2 1_555 C N7 DG 14 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog9 C N7 DG 5 B DG 5 1_555 C N2 DG 11 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog10 C O6 DG 5 B DG 5 1_555 C N1 DG 11 B DG 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog11 C N1 DG 6 B DG 6 1_555 C O6 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog12 C N2 DG 6 B DG 6 1_555 C N7 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog13 C N1 DG 10 B DG 10 1_555 C O6 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog14 C N2 DG 10 B DG 10 1_555 C N7 DG 15 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog15 C N7 DG 11 B DG 11 1_555 C N2 DG 14 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog TYPE_6_PAIR hydrog16 C O6 DG 11 B DG 11 1_555 C N1 DG 14 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C21 H34 Cl N6 O3 1' _chem_comp.formula_weight 453.986 _chem_comp.id 0G6 _chem_comp.mon_nstd_flag . _chem_comp.name D-phenylalanyl-N-[(2S,3S)-6-{[amino(iminio)methyl]amino}-1-chloro-2-hydroxyhexan-3-yl]-L-prolinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms PPACK # 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 N CA 0G6 sing 1 n n N H 0G6 sing 2 n n N H2 0G6 sing 3 n n CA C 0G6 sing 4 n n CA CB 0G6 sing 5 n n CA HA 0G6 sing 6 n n C O 0G6 doub 7 n n C N1 0G6 sing 8 n n CB CG 0G6 sing 9 n n CB HB2 0G6 sing 10 n n CB HB3 0G6 sing 11 n n CG CD1 0G6 doub 12 n y CG CD2 0G6 sing 13 n y CD1 CE1 0G6 sing 14 n y CD1 HD1 0G6 sing 15 n n CD2 CE2 0G6 doub 16 n y CD2 HD2 0G6 sing 17 n n CE1 CZ 0G6 doub 18 n y CE1 HE1 0G6 sing 19 n n CE2 CZ 0G6 sing 20 n y CE2 HE2 0G6 sing 21 n n CZ HZ 0G6 sing 22 n n N1 CA1 0G6 sing 23 n n N1 CD 0G6 sing 24 n n CA1 C1 0G6 sing 25 n n CA1 CB1 0G6 sing 26 n n CA1 HA1 0G6 sing 27 n n C1 O1 0G6 doub 28 n n C1 N2 0G6 sing 29 n n CB1 CG1 0G6 sing 30 n n CB1 HB21 0G6 sing 31 n n CB1 HB31 0G6 sing 32 n n CG1 CD 0G6 sing 33 n n CG1 HG2 0G6 sing 34 n n CG1 HG3 0G6 sing 35 n n CD HD21 0G6 sing 36 n n CD HD3 0G6 sing 37 n n N2 CA2 0G6 sing 38 n n N2 H1 0G6 sing 39 n n CA2 C2 0G6 sing 40 n n CA2 CB2 0G6 sing 41 n n CA2 HA2 0G6 sing 42 n n C2 O2 0G6 sing 43 n n C2 C3 0G6 sing 44 n n CB2 CG2 0G6 sing 45 n n CB2 HB22 0G6 sing 46 n n CB2 HB32 0G6 sing 47 n n CG2 CD3 0G6 sing 48 n n CG2 HG21 0G6 sing 49 n n CG2 HG31 0G6 sing 50 n n CD3 NE 0G6 sing 51 n n CD3 HD22 0G6 sing 52 n n CD3 HD31 0G6 sing 53 n n NE CZ1 0G6 sing 54 n n NE HE 0G6 sing 55 n n CZ1 NH1 0G6 sing 56 n n CZ1 NH2 0G6 doub 57 n n NH1 HH11 0G6 sing 58 n n NH1 HH12 0G6 sing 59 n n NH2 HH21 0G6 sing 60 n n NH2 HH22 0G6 sing 61 n n C3 H11 0G6 sing 62 n n C3 H21 0G6 sing 63 n n CL C3 0G6 sing 64 n n C2 H33 0G6 sing 65 n n O2 H34 0G6 sing 66 n n # _atom_sites.entry_id 6Z8X _atom_sites.fract_transf_matrix[1][1] 0.010563 _atom_sites.fract_transf_matrix[1][2] 0.006098 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012197 _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] 0.00802 _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 D 4 0G6 H 1 301 301 0G6 0G6 . E 5 NA H 1 302 302 NA NA . F 6 K B 1 201 101 K K . G 7 HOH H 1 401 401 HOH HOH . G 7 HOH H 2 402 402 HOH HOH . H 7 HOH B 1 301 201 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 N N 0G6 . . . D 4 -44.998 17.789 -14.494 1 57.7 ? N 0G6 301 H 1 HETATM 2 C CA 0G6 . . . D 4 -44.931 16.627 -13.627 1 56.75 ? CA 0G6 301 H 1 HETATM 3 C C 0G6 . . . D 4 -45.038 17.057 -12.182 1 56.33 ? C 0G6 301 H 1 HETATM 4 O O 0G6 . . . D 4 -45.92 17.833 -11.841 1 55.37 ? O 0G6 301 H 1 HETATM 5 C CB 0G6 . . . D 4 -46.05 15.671 -14.038 1 56.66 ? CB 0G6 301 H 1 HETATM 6 C CG 0G6 . . . D 4 -46.029 14.382 -13.248 1 56.79 ? CG 0G6 301 H 1 HETATM 7 C CD1 0G6 . . . D 4 -44.979 13.472 -13.386 1 56.87 ? CD1 0G6 301 H 1 HETATM 8 C CD2 0G6 . . . D 4 -47.085 14.102 -12.382 1 57.06 ? CD2 0G6 301 H 1 HETATM 9 C CE1 0G6 . . . D 4 -44.984 12.291 -12.645 1 57.21 ? CE1 0G6 301 H 1 HETATM 10 C CE2 0G6 . . . D 4 -47.094 12.921 -11.645 1 56.8 ? CE2 0G6 301 H 1 HETATM 11 C CZ 0G6 . . . D 4 -46.042 12.016 -11.778 1 57.05 ? CZ 0G6 301 H 1 HETATM 12 N N1 0G6 . . . D 4 -44.133 16.568 -11.321 1 56.6 ? N1 0G6 301 H 1 HETATM 13 C CA1 0G6 . . . D 4 -44.208 16.863 -9.884 1 57.32 ? CA1 0G6 301 H 1 HETATM 14 C C1 0G6 . . . D 4 -43.905 18.296 -9.544 1 57.98 ? C1 0G6 301 H 1 HETATM 15 O O1 0G6 . . . D 4 -43.314 19.009 -10.343 1 58.82 ? O1 0G6 301 H 1 HETATM 16 C CB1 0G6 . . . D 4 -43.167 15.96 -9.233 1 56.67 ? CB1 0G6 301 H 1 HETATM 17 C CG1 0G6 . . . D 4 -42.588 15.077 -10.32 1 56.55 ? CG1 0G6 301 H 1 HETATM 18 C CD 0G6 . . . D 4 -42.993 15.709 -11.641 1 56.68 ? CD 0G6 301 H 1 HETATM 19 N N2 0G6 . . . D 4 -44.319 18.711 -8.345 1 57.88 ? N2 0G6 301 H 1 HETATM 20 C CA2 0G6 . . . D 4 -44.317 20.108 -7.939 1 58.44 ? CA2 0G6 301 H 1 HETATM 21 C C2 0G6 . . . D 4 -43.601 20.346 -6.603 1 59.11 ? C2 0G6 301 H 1 HETATM 22 O O2 0G6 . . . D 4 -42.998 21.644 -6.667 1 58.91 ? O2 0G6 301 H 1 HETATM 23 C CB2 0G6 . . . D 4 -45.756 20.607 -7.876 1 57.62 ? CB2 0G6 301 H 1 HETATM 24 C CG2 0G6 . . . D 4 -46.216 21.219 -9.19 1 56.42 ? CG2 0G6 301 H 1 HETATM 25 C CD3 0G6 . . . D 4 -47.593 21.831 -8.989 1 55.29 ? CD3 0G6 301 H 1 HETATM 26 N NE 0G6 . . . D 4 -47.895 22.821 -9.999 1 54.2 ? NE 0G6 301 H 1 HETATM 27 C CZ1 0G6 . . . D 4 -48.878 22.632 -10.87 1 53.94 ? CZ1 0G6 301 H 1 HETATM 28 N NH1 0G6 . . . D 4 -48.601 22.531 -12.167 1 54.2 ? NH1 0G6 301 H 1 HETATM 29 N NH2 0G6 . . . D 4 -50.136 22.554 -10.445 1 53.57 ? NH2 0G6 301 H 1 HETATM 30 C C3 0G6 . . . D 4 -42.489 19.332 -6.319 1 59.57 ? C3 0G6 301 H 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 16 _model_server_stats.create_model_time_ms 20 _model_server_stats.query_time_ms 247 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #