data_3PMH # _model_server_result.job_id NdrpgtA7YcDDmlKm4M7D0w _model_server_result.datetime_utc '2024-12-02 02:37:59' _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 3pmh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 3PMH # _exptl.entry_id 3PMH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 450.962 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-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 3PMH _cell.length_a 67.657 _cell.length_b 67.657 _cell.length_c 329.73 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PMH _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details trimeric _pdbx_struct_assembly.oligomeric_count 3 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F _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 5 _struct_asym.id E _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 4 _pdbx_entity_branch.type oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 4 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 3 2 MAN NAG C1 O1 . O4 HO4 . sing 3 ? 4 4 3 MAN MAN C1 O1 . O3 HO3 . sing 4 ? 4 5 3 MAN MAN C1 O1 . O6 HO6 . sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 4 n D NAG 1 C 1 NAG B 501 NAG 4 n D NAG 2 C 2 NAG B 502 NAG 4 n D MAN 3 C 3 MAN B 503 MAN 4 n D MAN 4 C 4 MAN B 508 MAN 4 n D MAN 5 C 5 MAN B 504 MAN # 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 A CYS 1 1_555 B SG CYS 119 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf2 B SG CYS 28 B CYS 42 1_555 B SG CYS 44 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf3 B SG CYS 173 B CYS 168 1_555 B SG CYS 187 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 201 B CYS 191 1_555 B SG CYS 231 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf5 C SG CYS 4 G CYS 4 1_555 C SG CYS 17 G CYS 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf6 C SG CYS 209 G CYS 209 1_555 C SG CYS 248 G CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 C SG CYS 211 G CYS 211 1_555 C SG CYS 264 G CYS 264 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? covale ? covale1 B ND2 ASN 53 B ASN 60 1_555 D C1 NAG . C NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.459 ? covale ? covale2 C ND2 ASN 159 G ASN 159 1_555 F C1 NAG . G NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 C C TYS 276 G TYS 276 1_555 C N ASP 277 G ASP 277 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale4 C C TYS 279 G TYS 279 1_555 C N PRO 280 G PRO 280 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.345 ? covale ? covale5 D O4 NAG . C NAG 1 1_555 D C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.391 ? covale ? covale6 D O4 NAG . C NAG 2 1_555 D C1 MAN . C MAN 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.407 ? covale ? covale7 D O3 MAN . C MAN 3 1_555 D C1 MAN . C MAN 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.405 ? covale ? covale8 D O6 MAN . C MAN 3 1_555 D C1 MAN . C MAN 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.409 ? # _chem_comp.formula 'C21 H31 Cl N6 O3' _chem_comp.formula_weight 450.962 _chem_comp.id 0G7 _chem_comp.mon_nstd_flag . _chem_comp.name D-phenylalanyl-N-[(3S)-6-carbamimidamido-1-chloro-2-oxohexan-3-yl]-L-prolinamide _chem_comp.type peptide-like _chem_comp.pdbx_synonyms 'd-Phe-Pro-Arg chloromethylketone (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 C O 0G7 doub 1 n n N CA 0G7 sing 2 n n N HN 0G7 sing 3 n n N HNA 0G7 sing 4 n n C1 CA1 0G7 sing 5 n n C1 O1 0G7 doub 6 n n N1 C 0G7 sing 7 n n N1 CA1 0G7 sing 8 n n C2 CA2 0G7 sing 9 n n C2 O2 0G7 doub 10 n n N2 C1 0G7 sing 11 n n N2 HN2 0G7 sing 12 n n C3 C2 0G7 sing 13 n n C3 CL1 0G7 sing 14 n n C3 H3 0G7 sing 15 n n C3 H3A 0G7 sing 16 n n CA C 0G7 sing 17 n n CA CB 0G7 sing 18 n n CA HA 0G7 sing 19 n n CB CG 0G7 sing 20 n n CB HB 0G7 sing 21 n n CB HBA 0G7 sing 22 n n CD N1 0G7 sing 23 n n CD CG1 0G7 sing 24 n n NE CD3 0G7 sing 25 n n NE CZ1 0G7 sing 26 n n NE HNE 0G7 sing 27 n n CG CD1 0G7 doub 28 n y CG CD2 0G7 sing 29 n y CZ HZ 0G7 sing 30 n n CA1 HA1 0G7 sing 31 n n CA2 N2 0G7 sing 32 n n CA2 CB2 0G7 sing 33 n n CA2 HA2 0G7 sing 34 n n CB1 CA1 0G7 sing 35 n n CB1 HB1 0G7 sing 36 n n CB1 HB1A 0G7 sing 37 n n CB2 HB2 0G7 sing 38 n n CB2 HB2A 0G7 sing 39 n n CD1 CE1 0G7 sing 40 n y CD1 HD1 0G7 sing 41 n n CD2 CE2 0G7 doub 42 n y CD2 HD2 0G7 sing 43 n n CD3 CG2 0G7 sing 44 n n CD3 HD3 0G7 sing 45 n n CD3 HD3A 0G7 sing 46 n n CE1 CZ 0G7 doub 47 n y CE1 HE1 0G7 sing 48 n n CE2 CZ 0G7 sing 49 n y CE2 HE2 0G7 sing 50 n n CG1 CB1 0G7 sing 51 n n CG2 CB2 0G7 sing 52 n n CG2 HG2 0G7 sing 53 n n CG2 HG2A 0G7 sing 54 n n NH1 HNH1 0G7 sing 55 n n NH1 HNHA 0G7 sing 56 n n NH2 CZ1 0G7 doub 57 n n NH2 HNH2 0G7 sing 58 n n CZ1 NH1 0G7 sing 59 n n CD HD 0G7 sing 60 n n CD H29 0G7 sing 61 n n CG1 HG1 0G7 sing 62 n n CG1 H31 0G7 sing 63 n n # _atom_sites.entry_id 3PMH _atom_sites.fract_transf_matrix[1][1] 0.01478 _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] 0.01478 _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] 0.003033 _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 E 5 0G7 B 1 301 700 0G7 0G7 . F 6 NAG G 1 601 601 NAG NAG . # 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 0G7 . . . E 5 25.413 -16.83 124.585 1 56.99 ? N 0G7 301 B 1 HETATM 2 C CA 0G7 . . . E 5 24.143 -16.108 124.388 1 46.32 ? CA 0G7 301 B 1 HETATM 3 C C 0G7 . . . E 5 23.166 -17.014 123.573 1 42.31 ? C 0G7 301 B 1 HETATM 4 O O 0G7 . . . E 5 23.57 -17.526 122.525 1 43.52 ? O 0G7 301 B 1 HETATM 5 C CB 0G7 . . . E 5 23.707 -15.787 125.83 1 40.77 ? CB 0G7 301 B 1 HETATM 6 C CG 0G7 . . . E 5 23.601 -16.975 126.731 1 36.93 ? CG 0G7 301 B 1 HETATM 7 C CD1 0G7 . . . E 5 24.515 -18.021 126.672 1 36.05 ? CD1 0G7 301 B 1 HETATM 8 C CD2 0G7 . . . E 5 22.534 -17.064 127.616 1 36.11 ? CD2 0G7 301 B 1 HETATM 9 C CE1 0G7 . . . E 5 24.346 -19.141 127.484 1 36.64 ? CE1 0G7 301 B 1 HETATM 10 C CE2 0G7 . . . E 5 22.354 -18.175 128.427 1 32.8 ? CE2 0G7 301 B 1 HETATM 11 C CZ 0G7 . . . E 5 23.256 -19.215 128.362 1 33.05 ? CZ 0G7 301 B 1 HETATM 12 N N1 0G7 . . . E 5 21.883 -17.178 123.977 1 35.97 ? N1 0G7 301 B 1 HETATM 13 C CA1 0G7 . . . E 5 21.009 -18.054 123.174 1 36.22 ? CA1 0G7 301 B 1 HETATM 14 C C1 0G7 . . . E 5 20.843 -17.595 121.727 1 40.25 ? C1 0G7 301 B 1 HETATM 15 O O1 0G7 . . . E 5 20.627 -16.395 121.469 1 44.61 ? O1 0G7 301 B 1 HETATM 16 C CB1 0G7 . . . E 5 19.677 -18.012 123.928 1 27.27 ? CB1 0G7 301 B 1 HETATM 17 C CG1 0G7 . . . E 5 20.037 -17.464 125.266 1 25.43 ? CG1 0G7 301 B 1 HETATM 18 C CD 0G7 . . . E 5 21.066 -16.448 124.948 1 29.09 ? CD 0G7 301 B 1 HETATM 19 N N2 0G7 . . . E 5 20.923 -18.537 120.786 1 38.91 ? N2 0G7 301 B 1 HETATM 20 C CA2 0G7 . . . E 5 20.797 -18.174 119.376 1 38.32 ? CA2 0G7 301 B 1 HETATM 21 C C2 0G7 . . . E 5 19.513 -18.656 118.709 1 38.79 ? C2 0G7 301 B 1 HETATM 22 O O2 0G7 . . . E 5 18.954 -19.721 119.09 1 41.58 ? O2 0G7 301 B 1 HETATM 23 C CB2 0G7 . . . E 5 22.042 -18.649 118.632 1 33.53 ? CB2 0G7 301 B 1 HETATM 24 C CG2 0G7 . . . E 5 23.274 -17.901 119.128 1 27.01 ? CG2 0G7 301 B 1 HETATM 25 C CD3 0G7 . . . E 5 24.529 -18.284 118.402 1 34.42 ? CD3 0G7 301 B 1 HETATM 26 N NE 0G7 . . . E 5 25.51 -17.204 118.419 1 34.21 ? NE 0G7 301 B 1 HETATM 27 C CZ1 0G7 . . . E 5 26.7 -17.282 117.835 1 36.21 ? CZ1 0G7 301 B 1 HETATM 28 N NH1 0G7 . . . E 5 27.048 -18.391 117.197 1 39.7 ? NH1 0G7 301 B 1 HETATM 29 N NH2 0G7 . . . E 5 27.531 -16.254 117.875 1 33.92 ? NH2 0G7 301 B 1 HETATM 30 C C3 0G7 . . . E 5 19.037 -18.05 117.729 1 31.73 ? C3 0G7 301 B 1 HETATM 31 CL CL1 0G7 . . . E 5 17.992 -16.543 117.763 1 20.34 ? CL1 0G7 301 B 1 # _model_server_stats.io_time_ms 52 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 257 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 31 #