data_2VDB # _model_server_result.job_id qofYhpM4k8AoiYi7SFMx_g _model_server_result.datetime_utc '2024-10-11 01:29:44' _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 2vdb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"I","auth_seq_id":1591}' # _entry.id 2VDB # _exptl.entry_id 2VDB _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 230.259 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid' _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 93 _cell.angle_gamma 90 _cell.entry_id 2VDB _cell.length_a 190.507 _cell.length_b 49.462 _cell.length_c 79.933 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VDB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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,E,F,G,H,I _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 4 _struct_asym.id I _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 disulf ? disulf1 A SG CYS 48 A CYS 53 1_555 A SG CYS 57 A CYS 62 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.474 ? disulf ? disulf2 A SG CYS 70 A CYS 75 1_555 A SG CYS 86 A CYS 91 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf3 A SG CYS 85 A CYS 90 1_555 A SG CYS 96 A CYS 101 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 A SG CYS 119 A CYS 124 1_555 A SG CYS 164 A CYS 169 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf5 A SG CYS 163 A CYS 168 1_555 A SG CYS 172 A CYS 177 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf6 A SG CYS 195 A CYS 200 1_555 A SG CYS 241 A CYS 246 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf7 A SG CYS 240 A CYS 245 1_555 A SG CYS 248 A CYS 253 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf8 A SG CYS 260 A CYS 265 1_555 A SG CYS 274 A CYS 279 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf9 A SG CYS 273 A CYS 278 1_555 A SG CYS 284 A CYS 289 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.081 ? disulf ? disulf10 A SG CYS 311 A CYS 316 1_555 A SG CYS 356 A CYS 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf11 A SG CYS 355 A CYS 360 1_555 A SG CYS 364 A CYS 369 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf12 A SG CYS 387 A CYS 392 1_555 A SG CYS 433 A CYS 438 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf13 A SG CYS 432 A CYS 437 1_555 A SG CYS 443 A CYS 448 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf14 A SG CYS 456 A CYS 461 1_555 A SG CYS 472 A CYS 477 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf15 A SG CYS 471 A CYS 476 1_555 A SG CYS 482 A CYS 487 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? disulf ? disulf16 A SG CYS 509 A CYS 514 1_555 A SG CYS 554 A CYS 559 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? disulf ? disulf17 A SG CYS 553 A CYS 558 1_555 A SG CYS 562 A CYS 567 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? # _chem_comp.formula 'C14 H14 O3' _chem_comp.formula_weight 230.259 _chem_comp.id NPS _chem_comp.mon_nstd_flag . _chem_comp.name '(2S)-2-(6-methoxynaphthalen-2-yl)propanoic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms NAPROXEN # 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 O C15 NPS sing 266 n n C15 OXT NPS doub 267 n n C15 C14 NPS sing 268 n n C14 C10 NPS sing 269 n n C14 C8 NPS sing 270 n n C8 C7 NPS sing 271 n y C8 C11 NPS doub 272 n y C7 C4 NPS doub 273 n y C4 C3 NPS sing 274 n y C4 C5 NPS sing 275 n y C3 C2 NPS doub 276 n y C2 C1 NPS sing 277 n y C11 C13 NPS sing 278 n y C13 C5 NPS doub 279 n y C5 C6 NPS sing 280 n y C6 C1 NPS doub 281 n y C1 O2 NPS sing 282 n n O2 C12 NPS sing 283 n n O H NPS sing 284 n n C14 H14 NPS sing 285 n n C10 H101 NPS sing 286 n n C10 H102 NPS sing 287 n n C10 H103 NPS sing 288 n n C7 H7 NPS sing 289 n n C11 H11 NPS sing 290 n n C3 H3 NPS sing 291 n n C2 H2 NPS sing 292 n n C13 H13 NPS sing 293 n n C6 H6 NPS sing 294 n n C12 H121 NPS sing 295 n n C12 H122 NPS sing 296 n n C12 H123 NPS sing 297 n n # _atom_sites.entry_id 2VDB _atom_sites.fract_transf_matrix[1][1] 0.005249 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000275 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020218 _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] 0.012528 _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 C 3 DKA A 1 1585 1585 DKA DKA . D 3 DKA A 1 1586 1586 DKA DKA . E 3 DKA A 1 1587 1587 DKA DKA . F 3 DKA A 1 1588 1588 DKA DKA . G 3 DKA A 1 1589 1589 DKA DKA . H 3 DKA A 1 1590 1590 DKA DKA . I 4 NPS A 1 1591 1591 NPS NPS . # 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 NPS . . . I 4 15.291 -5.214 27.936 1 54.62 ? C1 NPS 1591 A 1 HETATM 2 O O2 NPS . . . I 4 16.022 -6.335 27.788 1 54.29 ? O2 NPS 1591 A 1 HETATM 3 C C2 NPS . . . I 4 15.561 -4.057 27.255 1 54.09 ? C2 NPS 1591 A 1 HETATM 4 C C14 NPS . . . I 4 10.842 -0.984 29.783 1 56.55 ? C14 NPS 1591 A 1 HETATM 5 C C3 NPS . . . I 4 14.771 -2.943 27.447 1 54.74 ? C3 NPS 1591 A 1 HETATM 6 C C4 NPS . . . I 4 13.702 -2.975 28.32 1 55.26 ? C4 NPS 1591 A 1 HETATM 7 C C5 NPS . . . I 4 13.442 -4.224 29.023 1 55.41 ? C5 NPS 1591 A 1 HETATM 8 C C6 NPS . . . I 4 14.246 -5.292 28.809 1 55.11 ? C6 NPS 1591 A 1 HETATM 9 C C7 NPS . . . I 4 12.863 -1.905 28.563 1 55.48 ? C7 NPS 1591 A 1 HETATM 10 C C8 NPS . . . I 4 11.823 -2.048 29.471 1 55.95 ? C8 NPS 1591 A 1 HETATM 11 C C10 NPS . . . I 4 10.245 -0.441 28.507 1 57.32 ? C10 NPS 1591 A 1 HETATM 12 C C13 NPS . . . I 4 12.411 -4.33 29.898 1 55.57 ? C13 NPS 1591 A 1 HETATM 13 C C11 NPS . . . I 4 11.611 -3.244 30.1 1 55.53 ? C11 NPS 1591 A 1 HETATM 14 C C12 NPS . . . I 4 17.047 -6.392 26.853 1 54.29 ? C12 NPS 1591 A 1 HETATM 15 O O NPS . . . I 4 11.531 1.221 30.127 1 58.16 ? O NPS 1591 A 1 HETATM 16 O OXT NPS . . . I 4 11.18 0.026 31.854 1 57.06 ? OXT NPS 1591 A 1 HETATM 17 C C15 NPS . . . I 4 11.225 0.156 30.646 1 57.04 ? C15 NPS 1591 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 293 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #