data_6QF7 # _model_server_result.job_id Xd2OoeSa_COaJrHSh033RA _model_server_result.datetime_utc '2025-07-16 06:51:30' _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 6qf7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":703}' # _entry.id 6QF7 # _exptl.entry_id 6QF7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 453.986 _entity.id 6 _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 2 _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 6QF7 _cell.length_a 131.45 _cell.length_b 131.45 _cell.length_c 238.35 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QF7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id ? dimeric 2 author_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,F,H,I 1 1 C,D,E,G,J 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 I N N ? 6 J N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 3 oligosaccharide 4 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 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 4 2 1 GLC GLC C1 O1 . O4 HO4 . 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 E NAG 1 E 1 NAG D 701 NAG 3 n E NAG 2 E 2 NAG D 702 NAG 4 n F GLC 1 F 1 GLC A 401 MAL 4 n F GLC 2 F 2 GLC A 401 MAL 4 n G GLC 1 G 1 GLC C 401 MAL 4 n G GLC 2 G 2 GLC C 401 MAL # 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 B SG CYS 12 B CYS 341 1_555 B SG CYS 129 B CYS 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.831 ? disulf ? disulf2 B SG CYS 40 B CYS 378 1_555 B SG CYS 56 B CYS 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf3 B SG CYS 48 B CYS 386 1_555 B SG CYS 118 B CYS 456 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 79 B CYS 417 1_555 B SG CYS 82 B CYS 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.045 ? disulf ? disulf5 B SG CYS 143 B CYS 481 1_555 B SG CYS 212 B CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? disulf ? disulf6 B SG CYS 175 B CYS 513 1_555 B SG CYS 191 B CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf7 B SG CYS 202 B CYS 540 1_555 B SG CYS 229 B CYS 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.025 ? disulf ? disulf8 D SG CYS 12 D CYS 340 1_555 D SG CYS 129 D CYS 467 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.062 ? disulf ? disulf9 D SG CYS 40 D CYS 378 1_555 D SG CYS 56 D CYS 394 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf10 D SG CYS 48 D CYS 386 1_555 D SG CYS 118 D CYS 456 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf11 D SG CYS 79 D CYS 417 1_555 D SG CYS 82 D CYS 420 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf12 D SG CYS 143 D CYS 481 1_555 D SG CYS 212 D CYS 550 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf13 D SG CYS 175 D CYS 513 1_555 D SG CYS 191 D CYS 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf14 D SG CYS 202 D CYS 540 1_555 D SG CYS 229 D CYS 568 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? covale ? covale1 B NE2 HIS 55 B HIS 393 1_555 I C3 0G6 . B 0G6 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.519 ? covale ? covale2 B ND2 ASN 76 B ASN 414 1_555 H C1 NAG . B NAG 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 B OG SER 206 B SER 544 1_555 I C2 0G6 . B 0G6 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.533 ? covale ? covale4 D NE2 HIS 55 D HIS 393 1_555 J C3 0G6 . D 0G6 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale5 D OG SER 206 D SER 544 1_555 J C2 0G6 . D 0G6 703 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.428 ? covale ? covale7 F O4 GLC . F GLC 1 1_555 F C1 GLC . F GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 sing covale ? covale8 G O4 GLC . G GLC 1 1_555 G C1 GLC . G GLC 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 sing # _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 6QF7 _atom_sites.fract_transf_matrix[1][1] 0.007607 _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] 0.007607 _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] 0.004196 _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 H 5 NAG B 1 701 701 NAG NAG . I 6 0G6 B 1 702 711 0G6 0G6 . J 6 0G6 D 1 703 711 0G6 0G6 . # 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 . . . J 6 17.617 63.01 261.589 1 19.34 ? N 0G6 703 D 1 HETATM 2 C CA 0G6 . . . J 6 17.336 63.515 262.919 1 19.4 ? CA 0G6 703 D 1 HETATM 3 C C 0G6 . . . J 6 18.626 63.817 263.622 1 19.24 ? C 0G6 703 D 1 HETATM 4 O O 0G6 . . . J 6 18.678 64.688 264.474 1 19.33 ? O 0G6 703 D 1 HETATM 5 C CB 0G6 . . . J 6 16.504 64.787 262.815 1 19.5 ? CB 0G6 703 D 1 HETATM 6 C CG 0G6 . . . J 6 17.371 65.915 262.306 0.6 19.56 ? CG 0G6 703 D 1 HETATM 7 C CD1 0G6 . . . J 6 18.086 65.763 261.123 1 19.58 ? CD1 0G6 703 D 1 HETATM 8 C CD2 0G6 . . . J 6 17.453 67.105 263.02 1 19.51 ? CD2 0G6 703 D 1 HETATM 9 C CE1 0G6 . . . J 6 18.883 66.801 260.655 1 19.56 ? CE1 0G6 703 D 1 HETATM 10 C CE2 0G6 . . . J 6 18.251 68.143 262.551 1 19.52 ? CE2 0G6 703 D 1 HETATM 11 C CZ 0G6 . . . J 6 18.966 67.991 261.369 1 19.57 ? CZ 0G6 703 D 1 HETATM 12 N N1 0G6 . . . J 6 19.681 63.091 263.263 1 18.88 ? N1 0G6 703 D 1 HETATM 13 C CA1 0G6 . . . J 6 19.904 61.773 263.851 1 18.5 ? CA1 0G6 703 D 1 HETATM 14 C C1 0G6 . . . J 6 19.826 61.815 265.348 1 17.86 ? C1 0G6 703 D 1 HETATM 15 O O1 0G6 . . . J 6 18.902 62.386 265.905 1 18.07 ? O1 0G6 703 D 1 HETATM 16 C CB1 0G6 . . . J 6 21.312 61.381 263.426 1 18.65 ? CB1 0G6 703 D 1 HETATM 17 C CG1 0G6 . . . J 6 21.812 62.441 262.461 1 18.83 ? CG1 0G6 703 D 1 HETATM 18 C CD 0G6 . . . J 6 20.706 63.473 262.295 1 18.89 ? CD 0G6 703 D 1 HETATM 19 N N2 0G6 . . . J 6 20.805 61.206 266.011 1 16.85 ? N2 0G6 703 D 1 HETATM 20 C CA2 0G6 . . . J 6 21.278 61.702 267.289 1 15.42 ? CA2 0G6 703 D 1 HETATM 21 C C2 0G6 . . . J 6 22.486 60.894 267.748 1 14.3 ? C2 0G6 703 D 1 HETATM 22 O O2 0G6 . . . J 6 23.686 61.536 267.304 1 14.33 ? O2 0G6 703 D 1 HETATM 23 C CB2 0G6 . . . J 6 20.156 61.639 268.319 1 16.9 ? CB2 0G6 703 D 1 HETATM 24 C CG2 0G6 . . . J 6 19.204 60.487 268.021 0.5 17.75 ? CG2 0G6 703 D 1 HETATM 25 C CD3 0G6 . . . J 6 18.254 60.247 269.188 0.2 18.31 ? CD3 0G6 703 D 1 HETATM 26 N NE 0G6 . . . J 6 16.869 60.212 268.763 1 18.69 ? NE 0G6 703 D 1 HETATM 27 C CZ1 0G6 . . . J 6 15.961 61.035 269.282 1 18.89 ? CZ1 0G6 703 D 1 HETATM 28 N NH1 0G6 . . . J 6 15.23 60.647 270.325 1 18.93 ? NH1 0G6 703 D 1 HETATM 29 N NH2 0G6 . . . J 6 15.784 62.246 268.757 1 18.99 ? NH2 0G6 703 D 1 HETATM 30 C C3 0G6 . . . J 6 22.435 59.474 267.195 1 14 ? C3 0G6 703 D 1 # _model_server_stats.io_time_ms 1214 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 341 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 30 #