data_4NGV # _model_server_result.job_id S3ci5eZKZs9KOVHmC3oQEQ _model_server_result.datetime_utc '2024-11-15 04:13:17' _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 4ngv # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4NGV # _exptl.entry_id 4NGV _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 173.04 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'YTTERBIUM (III) ION' _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 4NGV _cell.length_a 78.906 _cell.length_b 78.906 _cell.length_c 37.699 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NGV _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # _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,E,F _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 B N N ? 2 C N N ? 2 D 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 disulf ? disulf1 A SG CYS 6 A CYS 6 1_555 A SG CYS 127 A CYS 127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.019 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.018 ? metalc ? metalc1 A NZ LYS 13 A LYS 13 1_555 C YB YB . A YB 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 3.482 ? metalc ? metalc2 A OE1 GLU 35 A GLU 35 1_555 D YB YB . A YB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.737 ? metalc ? metalc3 A OD1 ASN 46 A ASN 46 1_555 B YB YB . A YB 201 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.349 ? metalc ? metalc4 A OD2 ASP 52 A ASP 52 1_555 B YB YB . A YB 201 1_555 ? ? ? ? B ? ? ? ? ? ? ? 2.096 ? metalc ? metalc5 A OD2 ASP 52 A ASP 52 1_555 B YB YB . A YB 201 1_555 ? ? ? ? A ? ? ? ? ? ? ? 2.528 ? metalc ? metalc6 A OXT LEU 129 A LEU 129 1_555 C YB YB . A YB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.418 ? metalc ? metalc7 A O LEU 129 A LEU 129 1_555 C YB YB . A YB 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.168 ? metalc ? metalc8 B YB YB . A YB 201 1_555 F O HOH . A HOH 301 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.356 ? metalc ? metalc9 B YB YB . A YB 201 1_555 F O HOH . A HOH 301 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.999 ? metalc ? metalc10 B YB YB . A YB 201 1_555 F O HOH . A HOH 302 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.682 ? metalc ? metalc11 B YB YB . A YB 201 1_555 F O HOH . A HOH 303 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.353 ? metalc ? metalc12 B YB YB . A YB 201 1_555 F O HOH . A HOH 303 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.653 ? metalc ? metalc13 B YB YB . A YB 201 1_555 F O HOH . A HOH 304 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.33 ? metalc ? metalc14 B YB YB . A YB 201 1_555 F O HOH . A HOH 307 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.655 ? metalc ? metalc15 B YB YB . A YB 201 1_555 F O HOH . A HOH 307 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.767 ? metalc ? metalc16 C YB YB . A YB 202 1_555 F O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.287 ? metalc ? metalc17 C YB YB . A YB 202 1_555 F O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc18 D YB YB . A YB 203 1_555 F O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc19 D YB YB . A YB 203 1_555 F O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.705 ? metalc ? metalc20 D YB YB . A YB 203 1_555 F O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.766 ? metalc ? metalc21 D YB YB . A YB 203 1_555 F O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.423 ? # _chem_comp.formula 'Yb 3' _chem_comp.formula_weight 173.04 _chem_comp.id YB _chem_comp.mon_nstd_flag . _chem_comp.name 'YTTERBIUM (III) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 4NGV _atom_sites.fract_transf_matrix[1][1] 0.012673 _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] 0.012673 _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] 0.026526 _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 YB A 1 201 201 YB YB . C 2 YB A 1 202 202 YB YB . D 2 YB A 1 203 203 YB YB . E 3 CL A 1 204 204 CL CL . F 4 HOH A 1 301 301 HOH HOH . F 4 HOH A 2 302 302 HOH HOH . F 4 HOH A 3 303 303 HOH HOH . F 4 HOH A 4 304 304 HOH HOH . F 4 HOH A 5 305 305 HOH HOH . F 4 HOH A 6 306 306 HOH HOH . F 4 HOH A 7 307 308 HOH HOH . F 4 HOH A 8 308 309 HOH HOH . F 4 HOH A 9 309 310 HOH HOH . F 4 HOH A 10 310 312 HOH HOH . F 4 HOH A 11 311 313 HOH HOH . F 4 HOH A 12 312 314 HOH HOH . F 4 HOH A 13 313 315 HOH HOH . F 4 HOH A 14 314 316 HOH HOH . F 4 HOH A 15 315 317 HOH HOH . F 4 HOH A 16 316 318 HOH HOH . F 4 HOH A 17 317 319 HOH HOH . F 4 HOH A 18 318 320 HOH HOH . F 4 HOH A 19 319 321 HOH HOH . F 4 HOH A 20 320 322 HOH HOH . F 4 HOH A 21 321 323 HOH HOH . F 4 HOH A 22 322 324 HOH HOH . F 4 HOH A 23 323 325 HOH HOH . F 4 HOH A 24 324 326 HOH HOH . F 4 HOH A 25 325 327 HOH HOH . F 4 HOH A 26 326 328 HOH HOH . F 4 HOH A 27 327 329 HOH HOH . F 4 HOH A 28 328 330 HOH HOH . F 4 HOH A 29 329 331 HOH HOH . F 4 HOH A 30 330 332 HOH HOH . F 4 HOH A 31 331 333 HOH HOH . F 4 HOH A 32 332 334 HOH HOH . F 4 HOH A 33 333 335 HOH HOH . F 4 HOH A 34 334 336 HOH HOH . F 4 HOH A 35 335 337 HOH HOH . F 4 HOH A 36 336 338 HOH HOH . F 4 HOH A 37 337 339 HOH HOH . F 4 HOH A 38 338 340 HOH HOH . F 4 HOH A 39 339 341 HOH HOH . F 4 HOH A 40 340 342 HOH HOH . F 4 HOH A 41 341 343 HOH HOH . F 4 HOH A 42 342 344 HOH HOH . F 4 HOH A 43 343 345 HOH HOH . F 4 HOH A 44 344 346 HOH HOH . F 4 HOH A 45 345 347 HOH HOH . F 4 HOH A 46 346 348 HOH HOH . F 4 HOH A 47 347 349 HOH HOH . F 4 HOH A 48 348 350 HOH HOH . F 4 HOH A 49 349 351 HOH HOH . F 4 HOH A 50 350 352 HOH HOH . F 4 HOH A 51 351 353 HOH HOH . F 4 HOH A 52 352 355 HOH HOH . F 4 HOH A 53 353 357 HOH HOH . F 4 HOH A 54 354 358 HOH HOH . F 4 HOH A 55 355 359 HOH HOH . F 4 HOH A 56 356 360 HOH HOH . F 4 HOH A 57 357 361 HOH HOH . F 4 HOH A 58 358 362 HOH HOH . F 4 HOH A 59 359 363 HOH HOH . F 4 HOH A 60 360 364 HOH HOH . F 4 HOH A 61 361 365 HOH HOH . F 4 HOH A 62 362 366 HOH HOH . F 4 HOH A 63 363 367 HOH HOH . F 4 HOH A 64 364 368 HOH HOH . F 4 HOH A 65 365 369 HOH HOH . F 4 HOH A 66 366 371 HOH HOH . F 4 HOH A 67 367 372 HOH HOH . F 4 HOH A 68 368 373 HOH HOH . F 4 HOH A 69 369 374 HOH HOH . F 4 HOH A 70 370 379 HOH HOH . F 4 HOH A 71 371 381 HOH HOH . F 4 HOH A 72 372 388 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol YB _atom_site.label_atom_id YB _atom_site.label_comp_id YB _atom_site.label_seq_id . _atom_site.label_alt_id . _atom_site.pdbx_PDB_ins_code . _atom_site.label_asym_id C _atom_site.label_entity_id 2 _atom_site.Cartn_x 20.697 _atom_site.Cartn_y 58.208 _atom_site.Cartn_z -9.425 _atom_site.occupancy 0.39 _atom_site.B_iso_or_equiv 37.03 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id YB _atom_site.auth_comp_id YB _atom_site.auth_seq_id 202 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 252 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #