data_4NGZ # _model_server_result.job_id SLnoYk-hr6dnauiTX54onw _model_server_result.datetime_utc '2024-11-23 12:52:13' _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 4ngz # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":203}' # _entry.id 4NGZ # _exptl.entry_id 4NGZ _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 4NGZ _cell.length_a 78.589 _cell.length_b 78.589 _cell.length_c 37.017 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4NGZ _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,G,H _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 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 30 A CYS 30 1_555 A SG CYS 115 A CYS 115 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.016 ? disulf ? disulf3 A SG CYS 64 A CYS 64 1_555 A SG CYS 80 A CYS 80 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.037 ? disulf ? disulf4 A SG CYS 76 A CYS 76 1_555 A SG CYS 94 A CYS 94 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? metalc ? metalc1 A OD1 ASN 46 A ASN 46 1_555 B YB YB . A YB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.265 ? metalc ? metalc2 A OD2 ASP 52 A ASP 52 1_555 B YB YB . A YB 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc3 A OD2 ASP 101 A ASP 101 1_555 D YB YB . A YB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.166 ? metalc ? metalc4 A OD1 ASP 101 A ASP 101 1_555 D YB YB . A YB 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.736 ? metalc ? metalc5 A OXT LEU 129 A LEU 129 1_555 C YB YB . A YB 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.281 ? metalc ? metalc6 A O LEU 129 A LEU 129 1_555 C YB YB . A YB 202 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.965 ? metalc ? metalc7 A OXT LEU 129 A LEU 129 1_555 C YB YB . A YB 202 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.297 ? metalc ? metalc8 A O LEU 129 A LEU 129 1_555 C YB YB . A YB 202 1_555 ? B ? ? ? ? ? ? ? ? ? ? 2.986 ? metalc ? metalc9 B YB YB . A YB 201 1_555 H O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.189 ? metalc ? metalc10 B YB YB . A YB 201 1_555 H O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.279 ? metalc ? metalc11 B YB YB . A YB 201 1_555 H O HOH . A HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.073 ? metalc ? metalc12 B YB YB . A YB 201 1_555 H O HOH . A HOH 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.197 ? metalc ? metalc13 B YB YB . A YB 201 1_555 H O HOH . A HOH 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.229 ? metalc ? metalc14 C YB YB . A YB 202 1_555 H O HOH . A HOH 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.208 ? metalc ? metalc15 C YB YB . A YB 202 1_555 H O HOH . A HOH 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc16 D YB YB . A YB 203 1_555 H O HOH . A HOH 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.158 ? metalc ? metalc17 D YB YB . A YB 203 1_555 H O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.203 ? metalc ? metalc18 D YB YB . A YB 203 1_555 H O HOH . A HOH 310 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.185 ? metalc ? metalc19 D YB YB . A YB 203 1_555 H O HOH . A HOH 311 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.216 ? metalc ? metalc20 D YB YB . A YB 203 1_555 H O HOH . A HOH 312 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.213 ? metalc ? metalc21 D YB YB . A YB 203 1_555 H O HOH . A HOH 381 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.217 ? # _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 4NGZ _atom_sites.fract_transf_matrix[1][1] 0.012724 _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] 0.012724 _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] 0.027015 _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 3 CL A 1 205 205 CL CL . G 3 CL A 1 206 206 CL CL . H 4 HOH A 1 301 301 HOH HOH . H 4 HOH A 2 302 302 HOH HOH . H 4 HOH A 3 303 303 HOH HOH . H 4 HOH A 4 304 304 HOH HOH . H 4 HOH A 5 305 305 HOH HOH . H 4 HOH A 6 306 306 HOH HOH . H 4 HOH A 7 307 307 HOH HOH . H 4 HOH A 8 308 308 HOH HOH . H 4 HOH A 9 309 309 HOH HOH . H 4 HOH A 10 310 310 HOH HOH . H 4 HOH A 11 311 311 HOH HOH . H 4 HOH A 12 312 312 HOH HOH . H 4 HOH A 13 313 313 HOH HOH . H 4 HOH A 14 314 314 HOH HOH . H 4 HOH A 15 315 315 HOH HOH . H 4 HOH A 16 316 316 HOH HOH . H 4 HOH A 17 317 317 HOH HOH . H 4 HOH A 18 318 318 HOH HOH . H 4 HOH A 19 319 319 HOH HOH . H 4 HOH A 20 320 320 HOH HOH . H 4 HOH A 21 321 321 HOH HOH . H 4 HOH A 22 322 322 HOH HOH . H 4 HOH A 23 323 323 HOH HOH . H 4 HOH A 24 324 324 HOH HOH . H 4 HOH A 25 325 325 HOH HOH . H 4 HOH A 26 326 326 HOH HOH . H 4 HOH A 27 327 327 HOH HOH . H 4 HOH A 28 328 328 HOH HOH . H 4 HOH A 29 329 329 HOH HOH . H 4 HOH A 30 330 330 HOH HOH . H 4 HOH A 31 331 331 HOH HOH . H 4 HOH A 32 332 332 HOH HOH . H 4 HOH A 33 333 333 HOH HOH . H 4 HOH A 34 334 334 HOH HOH . H 4 HOH A 35 335 335 HOH HOH . H 4 HOH A 36 336 336 HOH HOH . H 4 HOH A 37 337 337 HOH HOH . H 4 HOH A 38 338 338 HOH HOH . H 4 HOH A 39 339 339 HOH HOH . H 4 HOH A 40 340 340 HOH HOH . H 4 HOH A 41 341 341 HOH HOH . H 4 HOH A 42 342 342 HOH HOH . H 4 HOH A 43 343 343 HOH HOH . H 4 HOH A 44 344 344 HOH HOH . H 4 HOH A 45 345 345 HOH HOH . H 4 HOH A 46 346 346 HOH HOH . H 4 HOH A 47 347 347 HOH HOH . H 4 HOH A 48 348 348 HOH HOH . H 4 HOH A 49 349 349 HOH HOH . H 4 HOH A 50 350 350 HOH HOH . H 4 HOH A 51 351 351 HOH HOH . H 4 HOH A 52 352 352 HOH HOH . H 4 HOH A 53 353 353 HOH HOH . H 4 HOH A 54 354 354 HOH HOH . H 4 HOH A 55 355 355 HOH HOH . H 4 HOH A 56 356 356 HOH HOH . H 4 HOH A 57 357 357 HOH HOH . H 4 HOH A 58 358 358 HOH HOH . H 4 HOH A 59 359 359 HOH HOH . H 4 HOH A 60 360 360 HOH HOH . H 4 HOH A 61 361 362 HOH HOH . H 4 HOH A 62 362 363 HOH HOH . H 4 HOH A 63 363 364 HOH HOH . H 4 HOH A 64 364 365 HOH HOH . H 4 HOH A 65 365 366 HOH HOH . H 4 HOH A 66 366 367 HOH HOH . H 4 HOH A 67 367 368 HOH HOH . H 4 HOH A 68 368 369 HOH HOH . H 4 HOH A 69 369 370 HOH HOH . H 4 HOH A 70 370 371 HOH HOH . H 4 HOH A 71 371 372 HOH HOH . H 4 HOH A 72 372 373 HOH HOH . H 4 HOH A 73 373 374 HOH HOH . H 4 HOH A 74 374 375 HOH HOH . H 4 HOH A 75 375 376 HOH HOH . H 4 HOH A 76 376 377 HOH HOH . H 4 HOH A 77 377 378 HOH HOH . H 4 HOH A 78 378 379 HOH HOH . H 4 HOH A 79 379 380 HOH HOH . H 4 HOH A 80 380 381 HOH HOH . H 4 HOH A 81 381 382 HOH HOH . H 4 HOH A 82 382 383 HOH HOH . H 4 HOH A 83 383 384 HOH HOH . H 4 HOH A 84 384 385 HOH HOH . H 4 HOH A 85 385 386 HOH HOH . H 4 HOH A 86 386 387 HOH HOH . H 4 HOH A 87 387 388 HOH HOH . H 4 HOH A 88 388 389 HOH HOH . H 4 HOH A 89 389 390 HOH HOH . H 4 HOH A 90 390 391 HOH HOH . H 4 HOH A 91 391 392 HOH HOH . H 4 HOH A 92 392 393 HOH HOH . H 4 HOH A 93 393 394 HOH HOH . H 4 HOH A 94 394 395 HOH HOH . H 4 HOH A 95 395 396 HOH HOH . H 4 HOH A 96 396 397 HOH HOH . H 4 HOH A 97 397 398 HOH HOH . H 4 HOH A 98 398 399 HOH HOH . H 4 HOH A 99 399 400 HOH HOH . H 4 HOH A 100 400 401 HOH HOH . H 4 HOH A 101 401 402 HOH HOH . H 4 HOH A 102 402 403 HOH HOH . H 4 HOH A 103 403 406 HOH HOH . H 4 HOH A 104 404 407 HOH HOH . H 4 HOH A 105 405 408 HOH HOH . H 4 HOH A 106 406 409 HOH HOH . H 4 HOH A 107 407 410 HOH HOH . H 4 HOH A 108 408 412 HOH HOH . H 4 HOH A 109 409 413 HOH HOH . H 4 HOH A 110 410 414 HOH HOH . H 4 HOH A 111 411 415 HOH HOH . H 4 HOH A 112 412 416 HOH HOH . H 4 HOH A 113 413 417 HOH HOH . H 4 HOH A 114 414 418 HOH HOH . H 4 HOH A 115 415 420 HOH HOH . H 4 HOH A 116 416 421 HOH HOH . H 4 HOH A 117 417 425 HOH HOH . H 4 HOH A 118 418 427 HOH HOH . H 4 HOH A 119 419 428 HOH HOH . H 4 HOH A 120 420 431 HOH HOH . H 4 HOH A 121 421 437 HOH HOH . H 4 HOH A 122 422 438 HOH HOH . H 4 HOH A 123 423 439 HOH HOH . H 4 HOH A 124 424 441 HOH HOH . H 4 HOH A 125 425 442 HOH HOH . H 4 HOH A 126 426 443 HOH HOH . H 4 HOH A 127 427 445 HOH HOH . H 4 HOH A 128 428 447 HOH HOH . H 4 HOH A 129 429 448 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 D _atom_site.label_entity_id 2 _atom_site.Cartn_x -0.773 _atom_site.Cartn_y 53.334 _atom_site.Cartn_z 16.049 _atom_site.occupancy 0.67 _atom_site.B_iso_or_equiv 35.29 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id YB _atom_site.auth_comp_id YB _atom_site.auth_seq_id 203 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 43 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 334 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #