data_1PFX # _model_server_result.job_id 3weJq1CI9DXUNMogI2vL7g _model_server_result.datetime_utc '2025-03-27 00:21:37' _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 1pfx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 1PFX # _exptl.entry_id 1PFX _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.986 _entity.id 3 _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 90 _cell.entry_id 1PFX _cell.length_a 128.75 _cell.length_b 128.75 _cell.length_c 77.2 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1PFX _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_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 3 _struct_asym.id C _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 26 C CYS 42 1_555 A SG CYS 42 C CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? disulf ? disulf2 A SG CYS 109 C CYS 122 1_555 B SG CYS 132 L CYS 132 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.041 ? disulf ? disulf3 A SG CYS 156 C CYS 168 1_555 A SG CYS 170 C CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf4 A SG CYS 181 C CYS 191 1_555 A SG CYS 209 C CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? disulf ? disulf5 B SG CYS 18 L CYS 18 1_555 B SG CYS 23 L CYS 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf6 B SG CYS 51 L CYS 51 1_555 B SG CYS 62 L CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? disulf ? disulf7 B SG CYS 56 L CYS 56 1_555 B SG CYS 71 L CYS 71 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.02 ? disulf ? disulf8 B SG CYS 73 L CYS 73 1_555 B SG CYS 82 L CYS 82 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf9 B SG CYS 88 L CYS 88 1_555 B SG CYS 99 L CYS 99 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf10 B SG CYS 95 L CYS 95 1_555 B SG CYS 109 L CYS 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf11 B SG CYS 111 L CYS 111 1_555 B SG CYS 124 L CYS 124 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.035 ? covale ? covale1 A OG SER 185 C SER 195 1_555 C C2 0G6 . C 0G6 301 1_555 ? ? ? ? A ? ? ? ? ? ? ? 1.41 ? covale ? covale2 B C CGU 8 L CGU 8 1_555 B N PHE 9 L PHE 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale3 B C CGU 15 L CGU 15 1_555 B N ARG 16 L ARG 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 B C CGU 17 L CGU 17 1_555 B N CYS 18 L CYS 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale5 B C CGU 21 L CGU 21 1_555 B N LYS 22 L LYS 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale6 B C CGU 27 L CGU 27 1_555 B N ALA 28 L ALA 28 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale7 B C CGU 30 L CGU 30 1_555 B N VAL 31 L VAL 31 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale8 B C CGU 33 L CGU 33 1_555 B N ASN 34 L ASN 34 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.339 ? covale ? covale9 B C CGU 36 L CGU 36 1_555 B N LYS 37 L LYS 37 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? covale ? covale10 B C CGU 40 L CGU 40 1_555 B N PHE 41 L PHE 41 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.344 ? covale ? covale11 B C LYS 63 L LYS 63 1_555 B N BHD 64 L BHD 64 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.337 ? covale ? covale12 B C BHD 64 L BHD 64 1_555 B N ASP 65 L ASP 65 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? # _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 1PFX _atom_sites.fract_transf_matrix[1][1] 0.007767 _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] 0.007767 _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] 0.012953 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id C _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id 0G6 _pdbx_nonpoly_scheme.pdb_strand_id C _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 1 _pdbx_nonpoly_scheme.pdb_mon_id 0G6 _pdbx_nonpoly_scheme.auth_mon_id PHE _pdbx_nonpoly_scheme.pdb_ins_code . # 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 . . . C 3 120.98 176.464 96.459 1 74.74 ? N 0G6 301 C 1 HETATM 2 C CA 0G6 . . . C 3 120.857 176.702 97.917 1 74.74 ? CA 0G6 301 C 1 HETATM 3 C C 0G6 . . . C 3 121.283 175.483 98.702 1 74.74 ? C 0G6 301 C 1 HETATM 4 O O 0G6 . . . C 3 122.388 174.974 98.508 1 74.74 ? O 0G6 301 C 1 HETATM 5 C CB 0G6 . . . C 3 121.683 177.91 98.333 1 80 ? CB 0G6 301 C 1 HETATM 6 C CG 0G6 . . . C 3 120.853 179.076 98.737 1 80 ? CG 0G6 301 C 1 HETATM 7 C CD1 0G6 . . . C 3 120.218 179.853 97.779 1 80 ? CD1 0G6 301 C 1 HETATM 8 C CD2 0G6 . . . C 3 120.67 179.379 100.078 1 80 ? CD2 0G6 301 C 1 HETATM 9 C CE1 0G6 . . . C 3 119.41 180.916 98.148 1 80 ? CE1 0G6 301 C 1 HETATM 10 C CE2 0G6 . . . C 3 119.864 180.438 100.458 1 80 ? CE2 0G6 301 C 1 HETATM 11 C CZ 0G6 . . . C 3 119.232 181.21 99.492 1 80 ? CZ 0G6 301 C 1 HETATM 12 N N1 0G6 . . . C 3 120.426 175.016 99.625 1 10 ? N1 0G6 301 C 1 HETATM 13 C CA1 0G6 . . . C 3 120.767 173.838 100.419 1 10 ? CA1 0G6 301 C 1 HETATM 14 C C1 0G6 . . . C 3 120.701 172.623 99.509 1 10 ? C1 0G6 301 C 1 HETATM 15 O O1 0G6 . . . C 3 119.891 172.594 98.582 1 10 ? O1 0G6 301 C 1 HETATM 16 C CB1 0G6 . . . C 3 119.676 173.826 101.493 1 27.58 ? CB1 0G6 301 C 1 HETATM 17 C CG1 0G6 . . . C 3 118.51 174.385 100.782 1 27.58 ? CG1 0G6 301 C 1 HETATM 18 C CD 0G6 . . . C 3 119.105 175.541 100.013 1 27.58 ? CD 0G6 301 C 1 HETATM 19 N N2 0G6 . . . C 3 121.586 171.657 99.742 1 10 ? N2 0G6 301 C 1 HETATM 20 C CA2 0G6 . . . C 3 121.63 170.45 98.934 1 10 ? CA2 0G6 301 C 1 HETATM 21 C C2 0G6 . A . C 3 121.176 169.234 99.724 1 10 ? C2 0G6 301 C 1 HETATM 22 C C2 0G6 . B . C 3 120.011 169.358 100.734 0 10 ? C2 0G6 301 C 1 HETATM 23 O O2 0G6 . A . C 3 120.883 168.337 98.624 1 10 ? O2 0G6 301 C 1 HETATM 24 O O2 0G6 . B . C 3 119.925 168.376 98.471 0 20 ? O2 0G6 301 C 1 HETATM 25 C CB2 0G6 . . . C 3 123.048 170.214 98.396 1 10 ? CB2 0G6 301 C 1 HETATM 26 C CG2 0G6 . . . C 3 123.562 171.299 97.476 1 10 ? CG2 0G6 301 C 1 HETATM 27 C CD3 0G6 . . . C 3 124.799 171.986 98.046 1 10 ? CD3 0G6 301 C 1 HETATM 28 N NE 0G6 . . . C 3 125.396 172.932 97.1 1 10 ? NE 0G6 301 C 1 HETATM 29 C CZ1 0G6 . . . C 3 126.704 173.064 96.902 1 10 ? CZ1 0G6 301 C 1 HETATM 30 N NH1 0G6 . . . C 3 127.156 173.91 95.986 1 10 ? NH1 0G6 301 C 1 HETATM 31 N NH2 0G6 . . . C 3 127.564 172.32 97.59 1 10 ? NH2 0G6 301 C 1 HETATM 32 H H2 0G6 . . . C 3 120.606 177.274 95.933 0 20 ? H2 0G6 301 C 1 HETATM 33 H H3 0G6 . . . C 3 121.969 176.215 96.257 0 20 ? H3 0G6 301 C 1 HETATM 34 H H 0G6 . . . C 3 120.368 175.638 96.353 0 20 ? H 0G6 301 C 1 HETATM 35 H H1 0G6 . . . C 3 122.249 171.73 100.464 0 20 ? H1 0G6 301 C 1 HETATM 36 H HE 0G6 . . . C 3 124.771 173.486 96.581 0 20 ? HE 0G6 301 C 1 HETATM 37 H HH11 0G6 . . . C 3 128.13 174.01 95.805 0 20 ? HH11 0G6 301 C 1 HETATM 38 H HH12 0G6 . . . C 3 126.563 174.468 95.387 0 20 ? HH12 0G6 301 C 1 HETATM 39 H HH21 0G6 . . . C 3 127.235 171.651 98.26 0 20 ? HH21 0G6 301 C 1 HETATM 40 H HH22 0G6 . . . C 3 128.554 172.365 97.468 0 20 ? HH22 0G6 301 C 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 21 _model_server_stats.create_model_time_ms 12 _model_server_stats.query_time_ms 346 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 40 #