data_4D1D # _model_server_result.job_id LqqbLfAA-ychJUM1gFzy7Q _model_server_result.datetime_utc '2024-11-22 19:47:06' _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 4d1d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1468}' # _entry.id 4D1D # _exptl.entry_id 4D1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 240.257 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-(2-NAPHTHYLMETHYL)-D-HYDANTOIN _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 4D1D _cell.length_a 87.6 _cell.length_b 106.9 _cell.length_c 106.8 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D1D _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 metalc ? metalc1 A O ALA 38 A ALA 38 1_555 D NA NA . A NA 1471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.445 ? metalc ? metalc2 A O ILE 41 A ILE 41 1_555 D NA NA . A NA 1471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.606 ? metalc ? metalc3 A O ALA 309 A ALA 309 1_555 D NA NA . A NA 1471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc4 A OG SER 312 A SER 312 1_555 D NA NA . A NA 1471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.582 ? metalc ? metalc5 A OG1 THR 313 A THR 313 1_555 D NA NA . A NA 1471 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.298 ? # _chem_comp.formula 'C14 H12 N2 O2' _chem_comp.formula_weight 240.257 _chem_comp.id 5ND _chem_comp.mon_nstd_flag . _chem_comp.name 5-(2-NAPHTHYLMETHYL)-D-HYDANTOIN _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 CA 5ND sing 1 n n N10 C2 5ND sing 2 n n CA CB 5ND sing 3 n n CA C 5ND sing 4 n n CB CG 5ND sing 5 n n CG CD1 5ND sing 6 n y CG CD2 5ND doub 7 n y CD1 CE1 5ND doub 8 n y CE1 CZ 5ND sing 9 n y CZ CE2 5ND doub 10 n y CZ C6 5ND sing 11 n y CE2 CD2 5ND sing 12 n y CE2 C1 5ND sing 13 n y C N11 5ND sing 14 n n C O3 5ND doub 15 n n N11 C2 5ND sing 16 n n C2 O2 5ND doub 17 n n C1 C3 5ND doub 18 n y C3 C5 5ND sing 19 n y C5 C6 5ND doub 20 n y N10 H10 5ND sing 21 n n CA HA 5ND sing 22 n n CB HB1C 5ND sing 23 n n CB HB2C 5ND sing 24 n n CD1 HD1 5ND sing 25 n n CD2 HD2 5ND sing 26 n n CE1 HE1 5ND sing 27 n n C6 H6 5ND sing 28 n n C1 H1 5ND sing 29 n n N11 H11 5ND sing 30 n n C3 H3 5ND sing 31 n n C5 H5 5ND sing 32 n n # _atom_sites.entry_id 4D1D _atom_sites.fract_transf_matrix[1][1] 0.011416 _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] 0.009355 _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] 0.009363 _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 B 2 5NL A 1 1467 1467 5NL 5NL . C 3 5ND A 1 1468 1468 5ND 5ND . D 4 NA A 1 1471 1471 NA NA . # 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 N10 5ND . . . C 3 4.047 11.8 -24.141 0.5 143.88 ? N10 5ND 1468 A 1 HETATM 2 C CA 5ND . . . C 3 2.853 11.317 -24.754 0.5 145.56 ? CA 5ND 1468 A 1 HETATM 3 C CB 5ND . . . C 3 3.045 9.902 -25.199 0.5 147.76 ? CB 5ND 1468 A 1 HETATM 4 C CG 5ND . . . C 3 2.833 8.989 -24.043 0.5 151.73 ? CG 5ND 1468 A 1 HETATM 5 C CD1 5ND . . . C 3 2.068 9.398 -22.959 0.5 154.2 ? CD1 5ND 1468 A 1 HETATM 6 C CE1 5ND . . . C 3 1.877 8.556 -21.879 0.5 159.49 ? CE1 5ND 1468 A 1 HETATM 7 C CZ 5ND . . . C 3 2.451 7.297 -21.869 0.5 161.66 ? CZ 5ND 1468 A 1 HETATM 8 C CE2 5ND . . . C 3 3.218 6.88 -22.944 0.5 158.52 ? CE2 5ND 1468 A 1 HETATM 9 C CD2 5ND . . . C 3 3.406 7.727 -24.027 0.5 153.91 ? CD2 5ND 1468 A 1 HETATM 10 C C 5ND . . . C 3 2.565 12.163 -25.916 0.5 143.51 ? C 5ND 1468 A 1 HETATM 11 N N11 5ND . . . C 3 3.579 13.156 -26 0.5 140.63 ? N11 5ND 1468 A 1 HETATM 12 C C2 5ND . . . C 3 4.505 12.947 -24.901 0.5 140.94 ? C2 5ND 1468 A 1 HETATM 13 O O2 5ND . . . C 3 5.502 13.618 -24.663 0.5 140.17 ? O2 5ND 1468 A 1 HETATM 14 O O3 5ND . . . C 3 1.618 12.036 -26.678 0.5 145.14 ? O3 5ND 1468 A 1 HETATM 15 C C1 5ND . . . C 3 3.794 5.622 -22.936 0.5 160.83 ? C1 5ND 1468 A 1 HETATM 16 C C3 5ND . . . C 3 3.603 4.783 -21.854 0.5 166.09 ? C3 5ND 1468 A 1 HETATM 17 C C5 5ND . . . C 3 2.834 5.2 -20.778 0.5 169.91 ? C5 5ND 1468 A 1 HETATM 18 C C6 5ND . . . C 3 2.259 6.455 -20.785 0.5 167.79 ? C6 5ND 1468 A 1 # _model_server_stats.io_time_ms 12 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 305 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 18 #