data_3SBK # _model_server_result.job_id G78TH-SeDn511Rekwnvndw _model_server_result.datetime_utc '2024-12-26 18:53:47' _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 3sbk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":302}' # _entry.id 3SBK # _exptl.entry_id 3SBK _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 120 _cell.entry_id 3SBK _cell.length_a 77.233 _cell.length_b 77.233 _cell.length_c 168.433 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SBK _symmetry.cell_setting ? _symmetry.Int_Tables_number 179 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 65 2 2' # _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,D _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 7 A CYS 22 1_555 A SG CYS 139 A CYS 157 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf2 A SG CYS 28 A CYS 42 1_555 A SG CYS 44 A CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? disulf ? disulf3 A SG CYS 76 A CYS 91 1_555 A SG CYS 232 A CYS 245 1_555 ? ? ? E ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf4 A SG CYS 120 A CYS 136 1_555 A SG CYS 186 A CYS 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf5 A SG CYS 150 A CYS 168 1_555 A SG CYS 165 A CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.017 ? disulf ? disulf6 A SG CYS 176 A CYS 191 1_555 A SG CYS 201 A CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? covale ? covale1 A NE2 HIS 43 A HIS 57 1_555 C C3 0G6 . A 0G6 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? covale ? covale2 A OG SER 180 A SER 195 1_555 C C2 0G6 . A 0G6 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.429 ? covale ? covale3 A ND2 ASN 227 A ASN 245 1_555 B C1 NAG . A NAG 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.461 ? # _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 3SBK _atom_sites.fract_transf_matrix[1][1] 0.012948 _atom_sites.fract_transf_matrix[1][2] 0.007475 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.014951 _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] 0.005937 _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 NAG A 1 301 301 NAG NAG . C 3 0G6 A 1 302 301 0G6 DPN . D 4 HOH A 1 1 1 HOH HOH . D 4 HOH A 2 3 3 HOH HOH . D 4 HOH A 3 4 4 HOH HOH . D 4 HOH A 4 5 5 HOH HOH . D 4 HOH A 5 6 6 HOH HOH . D 4 HOH A 6 7 7 HOH HOH . D 4 HOH A 7 8 8 HOH HOH . D 4 HOH A 8 9 9 HOH HOH . D 4 HOH A 9 10 10 HOH HOH . D 4 HOH A 10 11 11 HOH HOH . D 4 HOH A 11 12 12 HOH HOH . D 4 HOH A 12 13 13 HOH HOH . D 4 HOH A 13 14 14 HOH HOH . D 4 HOH A 14 15 15 HOH HOH . D 4 HOH A 15 246 16 HOH HOH . D 4 HOH A 16 247 17 HOH HOH . D 4 HOH A 17 248 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 N N 0G6 . . . C 3 1.153 -37.313 -10.179 1 55.01 ? N 0G6 302 A 1 HETATM 2 C CA 0G6 . . . C 3 2.005 -36.115 -10.461 1 54.63 ? CA 0G6 302 A 1 HETATM 3 C C 0G6 . . . C 3 1.526 -34.889 -9.704 1 54.51 ? C 0G6 302 A 1 HETATM 4 O O 0G6 . . . C 3 0.983 -35.005 -8.593 1 54.85 ? O 0G6 302 A 1 HETATM 5 C CB 0G6 . . . C 3 3.505 -36.4 -10.241 1 54.76 ? CB 0G6 302 A 1 HETATM 6 C CG 0G6 . . . C 3 4.197 -35.546 -9.189 1 53.82 ? CG 0G6 302 A 1 HETATM 7 C CD1 0G6 . . . C 3 4.778 -34.332 -9.515 1 52.86 ? CD1 0G6 302 A 1 HETATM 8 C CD2 0G6 . . . C 3 4.377 -36.024 -7.897 1 52.71 ? CD2 0G6 302 A 1 HETATM 9 C CE1 0G6 . . . C 3 5.455 -33.588 -8.557 1 51.22 ? CE1 0G6 302 A 1 HETATM 10 C CE2 0G6 . . . C 3 5.055 -35.291 -6.938 1 50.52 ? CE2 0G6 302 A 1 HETATM 11 C CZ 0G6 . . . C 3 5.585 -34.065 -7.267 1 50.22 ? CZ 0G6 302 A 1 HETATM 12 N N1 0G6 . . . C 3 1.705 -33.715 -10.335 1 53.59 ? N1 0G6 302 A 1 HETATM 13 C CA1 0G6 . . . C 3 1.315 -32.415 -9.793 1 52.88 ? CA1 0G6 302 A 1 HETATM 14 C C1 0G6 . . . C 3 -0.192 -32.374 -9.52 1 50.24 ? C1 0G6 302 A 1 HETATM 15 O O1 0G6 . . . C 3 -1.01 -32.562 -10.426 1 51.02 ? O1 0G6 302 A 1 HETATM 16 C CB1 0G6 . . . C 3 1.718 -31.433 -10.906 1 52.99 ? CB1 0G6 302 A 1 HETATM 17 C CG1 0G6 . . . C 3 1.699 -32.258 -12.165 1 53.5 ? CG1 0G6 302 A 1 HETATM 18 C CD 0G6 . . . C 3 2.136 -33.629 -11.742 1 53.64 ? CD 0G6 302 A 1 HETATM 19 N N2 0G6 . . . C 3 -0.096 -31.515 -8.502 1 43.74 ? N2 0G6 302 A 1 HETATM 20 C CA2 0G6 . . . C 3 -1.44 -31.211 -8.005 1 39.59 ? CA2 0G6 302 A 1 HETATM 21 C C2 0G6 . . . C 3 -1.787 -29.749 -8.273 1 38.44 ? C2 0G6 302 A 1 HETATM 22 O O2 0G6 . . . C 3 -3.202 -29.646 -8.257 1 37.95 ? O2 0G6 302 A 1 HETATM 23 C CB2 0G6 . . . C 3 -1.508 -31.677 -6.546 1 39.35 ? CB2 0G6 302 A 1 HETATM 24 C CG2 0G6 . . . C 3 -2.1 -33.077 -6.494 1 36.93 ? CG2 0G6 302 A 1 HETATM 25 C CD3 0G6 . . . C 3 -1.536 -33.889 -5.332 1 41.39 ? CD3 0G6 302 A 1 HETATM 26 N NE 0G6 . . . C 3 -2.339 -35.049 -4.973 1 43.21 ? NE 0G6 302 A 1 HETATM 27 C CZ1 0G6 . . . C 3 -2.108 -36.038 -4.082 1 44.42 ? CZ1 0G6 302 A 1 HETATM 28 N NH1 0G6 . . . C 3 -1.526 -35.836 -2.973 1 39.3 ? NH1 0G6 302 A 1 HETATM 29 N NH2 0G6 . . . C 3 -2.544 -37.281 -4.365 1 42.57 ? NH2 0G6 302 A 1 HETATM 30 C C3 0G6 . . . C 3 -1.307 -29.202 -9.62 1 36.79 ? C3 0G6 302 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 365 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 30 #