data_7KWF # _model_server_result.job_id -m90Y83dQz5qX0sIUdILNw _model_server_result.datetime_utc '2024-10-10 06:29:05' _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 7kwf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":301}' # _entry.id 7KWF # _exptl.entry_id 7KWF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 318.412 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid' _entity.pdbx_number_of_molecules 3 _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 7KWF _cell.length_a 85.26 _cell.length_b 226.72 _cell.length_c 201.53 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7KWF _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 author_and_software_defined_assembly 1 PISA tetrameric 4 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,I,J 1 1,2 B,D,E,F,G,H,K,L,M,N,O 2 1 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 3_554 -x,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 0 0 -100.765 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 G N N ? 3 I N N ? 3 L N 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 covale ? covale1 A C VAL 177 A VAL 165 1_555 A N KPI 178 A KPI 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C KPI 178 A KPI 166 1_555 A N GLU 179 A GLU 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale3 B C VAL 177 B VAL 165 1_555 B N KPI 178 B KPI 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale4 B C KPI 178 B KPI 166 1_555 B N GLU 179 B GLU 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale5 F C VAL 177 F VAL 165 1_555 F N KPI 178 F KPI 166 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale6 F C KPI 178 F KPI 166 1_555 F N GLU 179 F GLU 167 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? # _chem_comp.formula 'C14 H30 N4 O4' _chem_comp.formula_weight 318.412 _chem_comp.id 3VN _chem_comp.mon_nstd_flag . _chem_comp.name '(2R,5R)-2,5-diamino-2,5-bis(4-aminobutyl)hexanedioic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms bis-Lysine # 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 N10 C09 3VN sing 1 n n C09 C08 3VN sing 2 n n C08 C07 3VN sing 3 n n C07 C06 3VN sing 4 n n O04 C03 3VN doub 5 n n C06 C02 3VN sing 6 n n O05 C03 3VN sing 7 n n C03 C02 3VN sing 8 n n N01 C02 3VN sing 9 n n C02 C11 3VN sing 10 n n C11 C12 3VN sing 11 n n C12 C13 3VN sing 12 n n C13 N14 3VN sing 13 n n C13 C15 3VN sing 14 n n C13 C20 3VN sing 15 n n C15 C16 3VN sing 16 n n C20 O21 3VN doub 17 n n C20 O22 3VN sing 18 n n C16 C17 3VN sing 19 n n C17 C18 3VN sing 20 n n C18 N19 3VN sing 21 n n N01 H1 3VN sing 22 n n N01 H2 3VN sing 23 n n O05 H4 3VN sing 24 n n C06 H5 3VN sing 25 n n C07 H6 3VN sing 26 n n C08 H7 3VN sing 27 n n C08 H8 3VN sing 28 n n C09 H9 3VN sing 29 n n C09 H10 3VN sing 30 n n N10 H11 3VN sing 31 n n N10 H12 3VN sing 32 n n C11 H14 3VN sing 33 n n C12 H15 3VN sing 34 n n N14 H16 3VN sing 35 n n N14 H17 3VN sing 36 n n C15 H19 3VN sing 37 n n C15 H20 3VN sing 38 n n C16 H21 3VN sing 39 n n C17 H22 3VN sing 40 n n C18 H23 3VN sing 41 n n C18 H24 3VN sing 42 n n N19 H25 3VN sing 43 n n N19 H26 3VN sing 44 n n O22 H28 3VN sing 45 n n C06 H3 3VN sing 46 n n C07 H29 3VN sing 47 n n C11 H13 3VN sing 48 n n C12 H30 3VN sing 49 n n C16 H18 3VN sing 50 n n C17 H31 3VN sing 51 n n # _atom_sites.entry_id 7KWF _atom_sites.fract_transf_matrix[1][1] 0.011729 _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] 0.004411 _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] 0.004962 _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 G 3 3VN B 1 301 3 3VN 3VN . H 4 ACT B 1 302 1 ACT ACT . I 3 3VN C 1 301 1 3VN 3VN . J 5 PEG C 1 302 1 PEG PEG . K 5 PEG D 1 301 2 PEG PEG . L 3 3VN E 1 301 2 3VN 3VN . M 6 PGE E 1 302 1 PGE PGE . N 4 ACT F 1 301 3 ACT ACT . O 6 PGE F 1 302 2 PGE PGE . # 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 N01 3VN . . . L 3 -24.319 26.32 15.959 1 52.13 ? N01 3VN 301 E 1 HETATM 2 C C02 3VN . . . L 3 -24.31 24.911 15.688 1 50.87 ? C02 3VN 301 E 1 HETATM 3 C C03 3VN . . . L 3 -25.707 24.346 15.934 1 46.39 ? C03 3VN 301 E 1 HETATM 4 O O04 3VN . . . L 3 -26.084 23.308 15.345 1 44.03 ? O04 3VN 301 E 1 HETATM 5 O O05 3VN . . . L 3 -26.486 24.933 16.734 1 44.72 ? O05 3VN 301 E 1 HETATM 6 C C06 3VN . . . L 3 -23.265 24.215 16.634 1 50.44 ? C06 3VN 301 E 1 HETATM 7 C C07 3VN . . . L 3 -22.91 22.782 16.114 1 47.95 ? C07 3VN 301 E 1 HETATM 8 C C08 3VN . . . L 3 -21.662 22.262 16.893 1 45.66 ? C08 3VN 301 E 1 HETATM 9 C C09 3VN . . . L 3 -22.001 20.907 17.559 1 42.95 ? C09 3VN 301 E 1 HETATM 10 N N10 3VN . . . L 3 -22.402 21.144 18.939 1 41.07 ? N10 3VN 301 E 1 HETATM 11 C C11 3VN . . . L 3 -23.911 24.674 14.2 1 52.06 ? C11 3VN 301 E 1 HETATM 12 C C12 3VN . . . L 3 -24.871 25.5 13.283 1 50.97 ? C12 3VN 301 E 1 HETATM 13 C C13 3VN . . . L 3 -25.026 24.768 11.92 1 48.84 ? C13 3VN 301 E 1 HETATM 14 N N14 3VN . . . L 3 -25.213 23.346 12.151 1 51.49 ? N14 3VN 301 E 1 HETATM 15 C C15 3VN . . . L 3 -23.76 24.987 11.068 1 49.41 ? C15 3VN 301 E 1 HETATM 16 C C16 3VN . . . L 3 -23.607 26.519 10.731 1 48.2 ? C16 3VN 301 E 1 HETATM 17 C C17 3VN . . . L 3 -22.634 26.687 9.555 1 47 ? C17 3VN 301 E 1 HETATM 18 C C18 3VN . . . L 3 -23.011 27.969 8.769 1 47.59 ? C18 3VN 301 E 1 HETATM 19 N N19 3VN . . . L 3 -24.397 27.861 8.307 1 48.06 ? N19 3VN 301 E 1 HETATM 20 C C20 3VN . . . L 3 -26.227 25.316 11.206 1 41.75 ? C20 3VN 301 E 1 HETATM 21 O O21 3VN . . . L 3 -26.805 26.353 11.632 1 38.91 ? O21 3VN 301 E 1 HETATM 22 O O22 3VN . . . L 3 -26.661 24.731 10.177 1 38.85 ? O22 3VN 301 E 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 29 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 268 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 22 #