data_6PX5 # _model_server_result.job_id PkrBk3N3gTRywzZ8LEKMjg _model_server_result.datetime_utc '2024-10-11 03:14:25' _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 6px5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":801}' # _entry.id 6PX5 # _exptl.entry_id 6PX5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.986 _entity.id 5 _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 6PX5 _cell.length_a 100.134 _cell.length_b 100.134 _cell.length_c 118.679 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6PX5 _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 dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,I _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 F _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order 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 3 n C NAG 1 A 1 NAG B 901 NAG 3 n C NAG 2 A 2 NAG B 902 NAG # 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 X CYS 170 1_555 A SG CYS 80 X CYS 248 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.066 ? disulf ? disulf2 A SG CYS 23 X CYS 191 1_555 A SG CYS 63 X CYS 231 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf3 A SG CYS 51 X CYS 219 1_555 A SG CYS 75 X CYS 243 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? disulf ? disulf4 A SG CYS 125 X CYS 293 1_555 B SG CYS 119 B CYS 122 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.083 ? disulf ? disulf5 B SG CYS 28 B CYS 42 1_555 B SG CYS 44 B CYS 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.998 ? disulf ? disulf6 B SG CYS 173 B CYS 168 1_555 B SG CYS 187 B CYS 182 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf7 B SG CYS 201 B CYS 191 1_555 B SG CYS 231 B CYS 220 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? covale ? covale1 B NE2 HIS 43 B HIS 57 1_555 F C3 0G6 . B 0G6 801 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.467 ? covale ? covale2 B ND2 ASN 53 B ASN 60 1_555 C C1 NAG . A NAG 1 1_555 G ? ? ? ? ? ? ? ? ? ? ? 1.475 ? covale ? covale3 C O4 NAG . A NAG 1 1_555 C C1 NAG . A NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.469 ? metalc ? metalc1 A NE2 HIS 19 X HIS 187 1_555 E ZN ZN . X ZN 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc2 A NE2 HIS 19 X HIS 187 1_555 E ZN ZN . X ZN 402 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.979 ? metalc ? metalc3 A OE1 GLU 58 X GLU 226 1_555 D ZN ZN . X ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc4 A OE1 GLU 86 X GLU 254 1_555 D ZN ZN . X ZN 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.962 ? metalc ? metalc5 D ZN ZN . X ZN 401 1_555 H O HOH . X HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.151 ? metalc ? metalc6 D ZN ZN . X ZN 401 1_555 B OD2 ASP 183 B ASP 178 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.024 ? metalc ? metalc7 E ZN ZN . X ZN 402 1_555 B OE2 GLU 94 B GLU 97 1_555 ? ? ? A ? ? ? ? ? ? ? ? 2.082 ? metalc ? metalc8 E ZN ZN . X ZN 402 6_555 B OE2 GLU 94 B GLU 97 1_555 ? ? ? A ? ? ? ? ? ? ? ? 2.128 ? metalc ? metalc9 E ZN ZN . X ZN 402 1_555 I O HOH . B HOH 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.312 ? metalc ? metalc10 E ZN ZN . X ZN 402 1_555 I O HOH . B HOH 901 6_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.315 ? metalc ? metalc11 B O TYR 190 B TYR 184 1_555 G NA NA . B NA 802 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2.411 ? metalc ? metalc12 B O ARG 233 B ARG 221 1_555 G NA NA . B NA 802 1_555 A ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc13 B O LYS 236 B LYS 224 1_555 G NA NA . B NA 802 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.348 ? metalc ? metalc14 G NA NA . B NA 802 1_555 I O HOH . B HOH 904 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.552 ? metalc ? metalc15 G NA NA . B NA 802 1_555 I O HOH . B HOH 905 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc16 G NA NA . B NA 802 1_555 I O HOH . B HOH 907 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.449 ? # _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 6PX5 _atom_sites.fract_transf_matrix[1][1] 0.009987 _atom_sites.fract_transf_matrix[1][2] 0.005766 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011532 _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] 0.008426 _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 ZN X 1 401 804 ZN ZN . E 4 ZN X 1 402 803 ZN ZN . F 5 0G6 B 1 801 801 0G6 0G6 . G 6 NA B 1 802 802 NA NA . H 7 HOH X 1 501 6 HOH HOH . H 7 HOH X 2 502 26 HOH HOH . H 7 HOH X 3 503 14 HOH HOH . H 7 HOH X 4 504 13 HOH HOH . H 7 HOH X 5 505 45 HOH HOH . H 7 HOH X 6 506 51 HOH HOH . H 7 HOH X 7 507 42 HOH HOH . H 7 HOH X 8 508 50 HOH HOH . H 7 HOH X 9 509 37 HOH HOH . H 7 HOH X 10 510 38 HOH HOH . H 7 HOH X 11 511 8 HOH HOH . H 7 HOH X 12 512 27 HOH HOH . H 7 HOH X 13 513 7 HOH HOH . H 7 HOH X 14 514 17 HOH HOH . H 7 HOH X 15 515 25 HOH HOH . H 7 HOH X 16 516 18 HOH HOH . H 7 HOH X 17 517 15 HOH HOH . H 7 HOH X 18 518 12 HOH HOH . H 7 HOH X 19 519 11 HOH HOH . H 7 HOH X 20 520 48 HOH HOH . H 7 HOH X 21 521 36 HOH HOH . H 7 HOH X 22 522 43 HOH HOH . H 7 HOH X 23 523 30 HOH HOH . H 7 HOH X 24 524 47 HOH HOH . H 7 HOH X 25 525 19 HOH HOH . H 7 HOH X 26 526 52 HOH HOH . H 7 HOH X 27 527 35 HOH HOH . I 7 HOH B 1 901 33 HOH HOH . I 7 HOH B 2 902 3 HOH HOH . I 7 HOH B 3 903 41 HOH HOH . I 7 HOH B 4 904 23 HOH HOH . I 7 HOH B 5 905 21 HOH HOH . I 7 HOH B 6 906 49 HOH HOH . I 7 HOH B 7 907 20 HOH HOH . I 7 HOH B 8 908 5 HOH HOH . I 7 HOH B 9 909 53 HOH HOH . I 7 HOH B 10 910 9 HOH HOH . I 7 HOH B 11 911 1 HOH HOH . I 7 HOH B 12 912 2 HOH HOH . I 7 HOH B 13 913 10 HOH HOH . I 7 HOH B 14 914 4 HOH HOH . I 7 HOH B 15 915 39 HOH HOH . I 7 HOH B 16 916 32 HOH HOH . I 7 HOH B 17 917 22 HOH HOH . I 7 HOH B 18 918 44 HOH HOH . I 7 HOH B 19 919 34 HOH HOH . I 7 HOH B 20 920 29 HOH HOH . I 7 HOH B 21 921 40 HOH HOH . I 7 HOH B 22 922 31 HOH HOH . I 7 HOH B 23 923 16 HOH HOH . I 7 HOH B 24 924 28 HOH HOH . I 7 HOH B 25 925 24 HOH HOH . I 7 HOH B 26 926 46 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 . . . F 5 26.892 -48.384 25.035 1 69.48 ? N 0G6 801 B 1 HETATM 2 C CA 0G6 . . . F 5 28.011 -48.838 25.808 1 63.92 ? CA 0G6 801 B 1 HETATM 3 C C 0G6 . . . F 5 29.233 -48.203 25.171 1 66.49 ? C 0G6 801 B 1 HETATM 4 O O 0G6 . . . F 5 29.141 -47.028 24.754 1 58.6 ? O 0G6 801 B 1 HETATM 5 C CB 0G6 . . . F 5 27.653 -48.331 27.205 1 69.68 ? CB 0G6 801 B 1 HETATM 6 C CG 0G6 . . . F 5 28.681 -48.645 28.276 1 72.72 ? CG 0G6 801 B 1 HETATM 7 C CD1 0G6 . . . F 5 29.067 -49.976 28.512 1 70.85 ? CD1 0G6 801 B 1 HETATM 8 C CD2 0G6 . . . F 5 29.236 -47.603 29.013 1 64.58 ? CD2 0G6 801 B 1 HETATM 9 C CE1 0G6 . . . F 5 30.006 -50.261 29.488 1 66.11 ? CE1 0G6 801 B 1 HETATM 10 C CE2 0G6 . . . F 5 30.177 -47.901 29.988 1 68.19 ? CE2 0G6 801 B 1 HETATM 11 C CZ 0G6 . . . F 5 30.555 -49.218 30.225 1 68.7 ? CZ 0G6 801 B 1 HETATM 12 N N1 0G6 . . . F 5 30.353 -48.954 25.06 1 62.53 ? N1 0G6 801 B 1 HETATM 13 C CA1 0G6 . . . F 5 31.597 -48.403 24.491 1 64.94 ? CA1 0G6 801 B 1 HETATM 14 C C1 0G6 . . . F 5 31.387 -48.124 23.031 1 68.79 ? C1 0G6 801 B 1 HETATM 15 O O1 0G6 . . . F 5 30.415 -48.613 22.471 1 80.81 ? O1 0G6 801 B 1 HETATM 16 C CB1 0G6 . . . F 5 32.698 -49.467 24.627 1 60.89 ? CB1 0G6 801 B 1 HETATM 17 C CG1 0G6 . . . F 5 32.043 -50.656 25.301 1 65.33 ? CG1 0G6 801 B 1 HETATM 18 C CD 0G6 . . . F 5 30.527 -50.363 25.414 1 61.14 ? CD 0G6 801 B 1 HETATM 19 N N2 0G6 . . . F 5 32.265 -47.314 22.437 1 69.1 ? N2 0G6 801 B 1 HETATM 20 C CA2 0G6 . . . F 5 32.084 -46.785 21.085 1 68.49 ? CA2 0G6 801 B 1 HETATM 21 C C2 0G6 . . . F 5 33.192 -47.039 20.066 1 62.62 ? C2 0G6 801 B 1 HETATM 22 O O2 0G6 . . . F 5 32.593 -47.832 19.069 1 65.56 ? O2 0G6 801 B 1 HETATM 23 C CB2 0G6 . . . F 5 31.872 -45.261 21.185 1 66.66 ? CB2 0G6 801 B 1 HETATM 24 C CG2 0G6 . . . F 5 30.399 -44.97 21.406 1 63.44 ? CG2 0G6 801 B 1 HETATM 25 C CD3 0G6 . . . F 5 30.081 -43.492 21.436 1 64.87 ? CD3 0G6 801 B 1 HETATM 26 N NE 0G6 . . . F 5 28.634 -43.305 21.444 1 69.6 ? NE 0G6 801 B 1 HETATM 27 C CZ1 0G6 . . . F 5 28.05 -42.096 21.452 1 72.14 ? CZ1 0G6 801 B 1 HETATM 28 N NH1 0G6 . . . F 5 28.764 -40.957 21.436 1 58.03 ? NH1 0G6 801 B 1 HETATM 29 N NH2 0G6 . . . F 5 26.707 -42.046 21.496 1 79.87 ? NH2 0G6 801 B 1 HETATM 30 C C3 0G6 . . . F 5 34.472 -47.679 20.589 1 64.06 ? C3 0G6 801 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 28 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 303 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #