data_7LKC # _model_server_result.job_id DtqyQoi_ne2XqEI_L8qaAw _model_server_result.datetime_utc '2024-11-23 06:40:26' _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 7lkc # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":102}' # _entry.id 7LKC # _exptl.entry_id 7LKC _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 161.199 _entity.id 4 _entity.src_method nat _entity.type non-polymer _entity.pdbx_description (2~{S},4~{S},5~{R},6~{S})-4-azanyl-5-methoxy-6-methyl-oxan-2-ol _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 7LKC _cell.length_a 20.72 _cell.length_b 32.251 _cell.length_c 37.941 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7LKC _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall 'P 2ac 2ab' _symmetry.space_group_name_H-M 'P 21 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 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,C,E,F,G,H,L 1 1 B,D,I,J,K,M 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 ? 4 F N N ? 4 J N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 RAM _pdbx_entity_branch_link.comp_id_2 BGC _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 O2 _pdbx_entity_branch_link.leaving_atom_id_2 HO2 _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 2 n C BGC 1 G 1 BGC A 10 BGC 2 n C RAM 2 G 2 RAM A 11 RAM 2 n D BGC 1 K 1 BGC B 10 BGC 2 n D RAM 2 K 2 RAM B 11 RAM # 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 0UZ 1 A 0UZ 1 1_555 A N HTY 2 A HTY 2 1_555 ? A ? ? ? ? ? ? ? ? ? ? 1.324 ? covale ? covale2 A C 0UZ 1 A 0UZ 1 1_555 A N HTY 2 A HTY 2 1_555 ? B ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale3 A C HTY 2 A HTY 2 1_555 A N PHE 3 A PHE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.327 ? covale ? covale4 A OH HTY 2 A HTY 2 1_555 A C3 GHP 4 A GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.412 ? covale ? covale5 A C PHE 3 A PHE 3 1_555 A N GHP 4 A GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale6 A C GHP 4 A GHP 4 1_555 A N GHP 5 A GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.321 ? covale ? covale7 A C5 GHP 4 A GHP 4 1_555 A OCZ OMY 6 A OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.426 ? covale ? covale8 A O4 GHP 4 A GHP 4 1_555 C C1 BGC . G BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.423 sing covale ? covale9 A C GHP 5 A GHP 5 1_555 A N OMY 6 A OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? covale ? covale10 A C3 GHP 5 A GHP 5 1_555 A CG1 3FG 7 A 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.499 ? covale ? covale11 A C OMY 6 A OMY 6 1_555 A N 3FG 7 A 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.326 ? covale ? covale12 A ODE OMY 6 A OMY 6 1_555 F C1 YBJ . A YBJ 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.378 ? covale ? covale13 A OD1 3FG 7 A 3FG 7 1_555 E C1 MAN . A MAN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.38 sing covale ? covale14 B C 0UZ 1 B 0UZ 1 1_555 B N HTY 2 B HTY 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.325 ? covale ? covale15 B C HTY 2 B HTY 2 1_555 B N PHE 3 B PHE 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale16 B OH HTY 2 B HTY 2 1_555 B C3 GHP 4 B GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.41 ? covale ? covale17 B C PHE 3 B PHE 3 1_555 B N GHP 4 B GHP 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale18 B C GHP 4 B GHP 4 1_555 B N GHP 5 B GHP 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.328 ? covale ? covale19 B C5 GHP 4 B GHP 4 1_555 B OCZ OMY 6 B OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale20 B O4 GHP 4 B GHP 4 1_555 D C1 BGC . K BGC 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.379 sing covale ? covale21 B C GHP 5 B GHP 5 1_555 B N OMY 6 B OMY 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale22 B C3 GHP 5 B GHP 5 1_555 B CG1 3FG 7 B 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.504 ? covale ? covale23 B C OMY 6 B OMY 6 1_555 B N 3FG 7 B 3FG 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale24 B ODE OMY 6 B OMY 6 1_555 J C1 YBJ . B YBJ 102 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.425 ? covale ? covale25 B OD1 3FG 7 B 3FG 7 1_555 I C1 MAN . B MAN 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.381 sing covale ? covale26 C O2 BGC . G BGC 1 1_555 C C1 RAM . G RAM 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.401 ? covale ? covale27 D O2 BGC . K BGC 1 1_555 D C1 RAM . K RAM 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.387 ? # _chem_comp.formula 'C7 H15 N O3' _chem_comp.formula_weight 161.199 _chem_comp.id YBJ _chem_comp.mon_nstd_flag . _chem_comp.name (2~{S},4~{S},5~{R},6~{S})-4-azanyl-5-methoxy-6-methyl-oxan-2-ol _chem_comp.type non-polymer _chem_comp.pdbx_synonyms L-actinosamine # 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 C5 YBJ sing 215 n n O C5 YBJ sing 216 n n O C1 YBJ sing 217 n n C5 C4 YBJ sing 218 n n C6 O2 YBJ sing 219 n n C4 O2 YBJ sing 220 n n C4 C3 YBJ sing 221 n n C1 C2 YBJ sing 222 n n C2 C3 YBJ sing 223 n n C3 N YBJ sing 224 n n C1 H9 YBJ sing 225 n n C2 H8 YBJ sing 226 n n C2 H7 YBJ sing 227 n n C3 H2 YBJ sing 228 n n C4 H1 YBJ sing 229 n n C5 H YBJ sing 230 n n N H10 YBJ sing 231 n n N H11 YBJ sing 232 n n C H4 YBJ sing 233 n n C H6 YBJ sing 234 n n C H5 YBJ sing 235 n n C6 H13 YBJ sing 236 n n C6 H12 YBJ sing 237 n n C6 H14 YBJ sing 238 n n C1 O1 YBJ sing 239 n n O1 H3 YBJ sing 240 n n # _atom_sites.entry_id 7LKC _atom_sites.fract_transf_matrix[1][1] 0.048263 _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] 0.031007 _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] 0.026357 _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 3 MAN A 1 101 9 MAN MAN . F 4 YBJ A 1 102 8 YBJ CIM . G 5 FMT A 1 103 1 FMT FMT . H 6 CL A 1 104 3 CL CL . I 3 MAN B 1 101 9 MAN MAN . J 4 YBJ B 1 102 8 YBJ CIM . K 5 FMT B 1 103 2 FMT FMT . L 7 HOH A 1 201 1 HOH HOH . L 7 HOH A 2 202 50 HOH HOH . L 7 HOH A 3 203 21 HOH HOH . L 7 HOH A 4 204 30 HOH HOH . L 7 HOH A 5 205 29 HOH HOH . L 7 HOH A 6 206 53 HOH HOH . L 7 HOH A 7 207 20 HOH HOH . L 7 HOH A 8 208 39 HOH HOH . L 7 HOH A 9 209 45 HOH HOH . L 7 HOH A 10 210 48 HOH HOH . L 7 HOH A 11 211 49 HOH HOH . L 7 HOH A 12 212 28 HOH HOH . L 7 HOH A 13 213 8 HOH HOH . L 7 HOH A 14 214 6 HOH HOH . L 7 HOH A 15 215 16 HOH HOH . L 7 HOH A 16 216 43 HOH HOH . L 7 HOH A 17 217 51 HOH HOH . L 7 HOH A 18 218 41 HOH HOH . M 7 HOH B 1 201 9 HOH HOH . M 7 HOH B 2 202 17 HOH HOH . M 7 HOH B 3 203 46 HOH HOH . M 7 HOH B 4 204 40 HOH HOH . M 7 HOH B 5 205 13 HOH HOH . M 7 HOH B 6 206 7 HOH HOH . M 7 HOH B 7 207 12 HOH HOH . M 7 HOH B 8 208 42 HOH HOH . M 7 HOH B 9 209 37 HOH HOH . M 7 HOH B 10 210 19 HOH HOH . M 7 HOH B 11 211 22 HOH HOH . M 7 HOH B 12 212 38 HOH HOH . M 7 HOH B 13 213 3 HOH HOH . M 7 HOH B 14 214 18 HOH HOH . M 7 HOH B 15 215 52 HOH HOH . M 7 HOH B 16 216 54 HOH HOH . M 7 HOH B 17 217 5 HOH HOH . M 7 HOH B 18 218 24 HOH HOH . M 7 HOH B 19 219 27 HOH HOH . M 7 HOH B 20 220 14 HOH HOH . M 7 HOH B 21 221 36 HOH HOH . M 7 HOH B 22 222 34 HOH HOH . M 7 HOH B 23 223 11 HOH HOH . M 7 HOH B 24 224 25 HOH HOH . M 7 HOH B 25 225 35 HOH HOH . M 7 HOH B 26 226 2 HOH HOH . M 7 HOH B 27 227 47 HOH HOH . M 7 HOH B 28 228 26 HOH HOH . M 7 HOH B 29 229 4 HOH HOH . M 7 HOH B 30 230 31 HOH HOH . M 7 HOH B 31 231 10 HOH HOH . M 7 HOH B 32 232 15 HOH HOH . M 7 HOH B 33 233 44 HOH HOH . M 7 HOH B 34 234 32 HOH HOH . M 7 HOH B 35 235 23 HOH HOH . M 7 HOH B 36 236 33 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 C C1 YBJ . . . J 4 24.936 16.112 9.978 1 9.51 ? C1 YBJ 102 B 1 HETATM 2 C C2 YBJ . . . J 4 25.6 17.468 9.786 1 10.11 ? C2 YBJ 102 B 1 HETATM 3 C C3 YBJ . . . J 4 25.773 18.168 11.122 1 11.39 ? C3 YBJ 102 B 1 HETATM 4 C C4 YBJ . . . J 4 26.518 17.243 12.072 1 12.43 ? C4 YBJ 102 B 1 HETATM 5 C C5 YBJ . . . J 4 25.819 15.89 12.2 1 11.42 ? C5 YBJ 102 B 1 HETATM 6 N N YBJ . . . J 4 26.51 19.439 10.969 1 12.07 ? N YBJ 102 B 1 HETATM 7 C C YBJ . . . J 4 26.654 14.937 13.047 1 12.04 ? C YBJ 102 B 1 HETATM 8 O O YBJ . . . J 4 25.635 15.302 10.917 1 10.22 ? O YBJ 102 B 1 HETATM 9 C C6 YBJ . . . J 4 25.551 18.323 14.047 1 16.56 ? C6 YBJ 102 B 1 HETATM 10 O O2 YBJ . . . J 4 26.707 17.86 13.353 1 14.98 ? O2 YBJ 102 B 1 HETATM 11 H H9 YBJ . . . J 4 24.947 15.603 9.004 1 11.41 ? H9 YBJ 102 B 1 HETATM 12 H H8 YBJ . . . J 4 26.575 17.334 9.312 1 12.13 ? H8 YBJ 102 B 1 HETATM 13 H H7 YBJ . . . J 4 24.987 18.085 9.125 1 12.13 ? H7 YBJ 102 B 1 HETATM 14 H H2 YBJ . . . J 4 24.782 18.41 11.529 1 13.67 ? H2 YBJ 102 B 1 HETATM 15 H H1 YBJ . . . J 4 27.514 17.057 11.646 1 14.92 ? H1 YBJ 102 B 1 HETATM 16 H H YBJ . . . J 4 24.842 16.059 12.675 1 13.7 ? H YBJ 102 B 1 HETATM 17 H H10 YBJ . . . J 4 25.844 20.219 11.089 1 14.49 ? H10 YBJ 102 B 1 HETATM 18 H H11 YBJ . . . J 4 26.916 19.483 10.023 1 14.49 ? H11 YBJ 102 B 1 HETATM 19 H H4 YBJ . . . J 4 26.774 15.341 14.019 1 14.45 ? H4 YBJ 102 B 1 HETATM 20 H H6 YBJ . . . J 4 26.165 14 13.112 1 14.45 ? H6 YBJ 102 B 1 HETATM 21 H H5 YBJ . . . J 4 27.605 14.808 12.6 1 14.45 ? H5 YBJ 102 B 1 HETATM 22 H H13 YBJ . . . J 4 25.397 19.349 13.833 1 19.87 ? H13 YBJ 102 B 1 HETATM 23 H H12 YBJ . . . J 4 24.705 17.767 13.735 1 19.87 ? H12 YBJ 102 B 1 HETATM 24 H H14 YBJ . . . J 4 25.691 18.198 15.089 1 19.87 ? H14 YBJ 102 B 1 # _model_server_stats.io_time_ms 55 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 24 #