data_4D1D # _model_server_result.job_id sI27XPoXm4_HAnja7ND1ig _model_server_result.datetime_utc '2024-11-22 19:23:46' _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":"B","auth_seq_id":1467}' # _entry.id 4D1D # _exptl.entry_id 4D1D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 240.257 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 5-(2-NAPHTHYLMETHYL)-L-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 2 _struct_asym.id B _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 5NL _chem_comp.mon_nstd_flag . _chem_comp.name 5-(2-NAPHTHYLMETHYL)-L-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 C CA 5NL sing 33 n n C N11 5NL sing 34 n n C O3 5NL doub 35 n n CA N10 5NL sing 36 n n CA C4 5NL sing 37 n n CG CD1 5NL sing 38 n y CG CD2 5NL doub 39 n y CG C4 5NL sing 40 n n CD1 CE1 5NL doub 41 n y CE1 CZ 5NL sing 42 n y CZ CE2 5NL doub 43 n y CZ C6 5NL sing 44 n y CE2 CD2 5NL sing 45 n y CE2 C1 5NL sing 46 n y N10 C2 5NL sing 47 n n C2 N11 5NL sing 48 n n C2 O2 5NL doub 49 n n C1 C3 5NL doub 50 n y C3 C5 5NL sing 51 n y C5 C6 5NL doub 52 n y CA HA 5NL sing 53 n n N11 H11 5NL sing 54 n n N10 H10 5NL sing 55 n n C4 H41C 5NL sing 56 n n C4 H42C 5NL sing 57 n n CD1 HD1 5NL sing 58 n n CD2 HD2 5NL sing 59 n n CE1 HE1 5NL sing 60 n n C6 H6 5NL sing 61 n n C1 H1 5NL sing 62 n n C3 HB 5NL sing 63 n n C5 HC 5NL sing 64 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 C C 5NL . . . B 2 3.037 12.254 -26.176 0.5 144.35 ? C 5NL 1467 A 1 HETATM 2 C CA 5NL . . . B 2 3.383 11.082 -25.361 0.5 146.74 ? CA 5NL 1467 A 1 HETATM 3 C CG 5NL . . . B 2 2.41 9.171 -24.097 0.5 154.03 ? CG 5NL 1467 A 1 HETATM 4 C CD1 5NL . . . B 2 2.821 8.138 -24.928 0.5 154.23 ? CD1 5NL 1467 A 1 HETATM 5 C CE1 5NL . . . B 2 3.078 6.863 -24.398 0.5 157.63 ? CE1 5NL 1467 A 1 HETATM 6 C CZ 5NL . . . B 2 2.925 6.625 -23.037 0.5 161.34 ? CZ 5NL 1467 A 1 HETATM 7 C CE2 5NL . . . B 2 2.517 7.648 -22.203 0.5 161.85 ? CE2 5NL 1467 A 1 HETATM 8 C CD2 5NL . . . B 2 2.259 8.92 -22.73 0.5 157.88 ? CD2 5NL 1467 A 1 HETATM 9 N N10 5NL . . . B 2 4.385 11.482 -24.417 0.5 146.13 ? N10 5NL 1467 A 1 HETATM 10 C C2 5NL . . . B 2 4.668 12.889 -24.632 0.5 143.26 ? C2 5NL 1467 A 1 HETATM 11 N N11 5NL . . . B 2 3.826 13.354 -25.724 0.5 142.09 ? N11 5NL 1467 A 1 HETATM 12 C C1 5NL . . . B 2 2.363 7.413 -20.841 0.5 167.03 ? C1 5NL 1467 A 1 HETATM 13 C C3 5NL . . . B 2 2.621 6.148 -20.318 0.5 171.45 ? C3 5NL 1467 A 1 HETATM 14 C C5 5NL . . . B 2 3.028 5.127 -21.15 0.5 170.13 ? C5 5NL 1467 A 1 HETATM 15 C C6 5NL . . . B 2 3.184 5.36 -22.516 0.5 165.23 ? C6 5NL 1467 A 1 HETATM 16 C C4 5NL . . . B 2 2.131 10.552 -24.663 0.5 150.57 ? C4 5NL 1467 A 1 HETATM 17 O O3 5NL . . . B 2 2.219 12.282 -27.077 0.5 145.1 ? O3 5NL 1467 A 1 HETATM 18 O O2 5NL . . . B 2 5.469 13.562 -24.01 0.5 142.85 ? O2 5NL 1467 A 1 # _model_server_stats.io_time_ms 14 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 243 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 18 #