data_5YHA
#
_model_server_result.job_id            T9TggERlyRbDy2VLIUXpdA 
_model_server_result.datetime_utc      '2025-07-07 06:23:24' 
_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          5yha 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"H","auth_seq_id":307}' 
#
_entry.id    5YHA 
#
_exptl.entry_id    5YHA 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              106.42 
_entity.id                          4 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PALLADIUM ION' 
_entity.pdbx_number_of_molecules    5 
_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            5YHA 
_cell.length_a            103.19 
_cell.length_b            103.19 
_cell.length_c            103.19 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5YHA 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        197 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'I 2 3' 
#
_pdbx_struct_assembly.method_details        PISA 
_pdbx_struct_assembly.oligomeric_details    trimeric 
_pdbx_struct_assembly.oligomeric_count      3 
_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,J,K,L 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2,3 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 5_555 z,x,y 0 0 1 1 0 0 0 1 0 0 0 0 
3 'crystal symmetry operation' 9_555 y,z,x 0 1 0 0 0 1 1 0 0 0 0 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 4 F N N 
? 4 G N N 
? 4 H N N 
? 4 I N N 
? 4 J 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
covale ? covale1 A C ACE 1 A ACE 1 1_555 A N ALA 2 A ALA 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.333 ? 
metalc ? metalc1 A NZ LYS 66 A LYS 66 1_555 G PD PD . A PD 306 5_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.8 ? 
metalc ? metalc2 A ND1 HIS 76 A HIS 76 1_555 F PD PD . A PD 305 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? 
metalc ? metalc3 A ND1 HIS 76 A HIS 76 1_555 F PD PD . A PD 305 2_665 ? ? ? ? ? ? ? ? ? ? ? ? 2.117 ? 
metalc ? metalc4 A NE2 HIS 170 A HIS 170 1_555 H PD PD . A PD 307 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc5 A SG CYS 204 A CYS 204 1_555 I PD PD . A PD 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.485 ? 
metalc ? metalc6 A SG CYS 211 A CYS 211 1_555 C PD PLL . A PLL 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.187 ? 
metalc ? metalc7 A SG CYS 211 A CYS 211 1_555 D PD PLL . A PLL 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? 
metalc ? metalc8 A SG CYS 211 A CYS 211 1_555 G PD PD . A PD 306 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc9 A NE2 HIS 238 A HIS 238 1_555 E PD PLL . A PLL 304 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.529 ? 
metalc ? metalc10 A ND1 HIS 238 A HIS 238 1_555 J PD PD . A PD 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.725 ? 
metalc ? metalc11 E PD PLL . A PLL 304 1_555 L O HOH . A HOH 411 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.235 ? 
metalc ? metalc12 I PD PD . A PD 308 1_555 L O HOH . A HOH 509 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? 
#
_chem_comp.formula           'Pd 2' 
_chem_comp.formula_weight    106.42 
_chem_comp.id                PD 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PALLADIUM ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
_atom_sites.entry_id                     5YHA 
_atom_sites.fract_transf_matrix[1][1]    0.009691 
_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]    0.009691 
_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]    0.009691 
_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 CL A 1 301 249 CL CL . 
C 3 PLL A 1 302 1 PLL PLL . 
D 3 PLL A 1 303 2 PLL PLL . 
E 3 PLL A 1 304 3 PLL PLL . 
F 4 PD A 1 305 1 PD PD . 
G 4 PD A 1 306 2 PD PD . 
H 4 PD A 1 307 3 PD PD . 
I 4 PD A 1 308 4 PD PD . 
J 4 PD A 1 309 5 PD PD . 
K 5 EDO A 1 310 1 EDO EDO . 
L 6 HOH A 1 401 400 HOH HOH . 
L 6 HOH A 2 402 348 HOH HOH . 
L 6 HOH A 3 403 380 HOH HOH . 
L 6 HOH A 4 404 360 HOH HOH . 
L 6 HOH A 5 405 301 HOH HOH . 
L 6 HOH A 6 406 365 HOH HOH . 
L 6 HOH A 7 407 362 HOH HOH . 
L 6 HOH A 8 408 296 HOH HOH . 
L 6 HOH A 9 409 345 HOH HOH . 
L 6 HOH A 10 410 314 HOH HOH . 
L 6 HOH A 11 411 398 HOH HOH . 
L 6 HOH A 12 412 387 HOH HOH . 
L 6 HOH A 13 413 309 HOH HOH . 
L 6 HOH A 14 414 384 HOH HOH . 
L 6 HOH A 15 415 363 HOH HOH . 
L 6 HOH A 16 416 383 HOH HOH . 
L 6 HOH A 17 417 355 HOH HOH . 
L 6 HOH A 18 418 320 HOH HOH . 
L 6 HOH A 19 419 307 HOH HOH . 
L 6 HOH A 20 420 388 HOH HOH . 
L 6 HOH A 21 421 392 HOH HOH . 
L 6 HOH A 22 422 375 HOH HOH . 
L 6 HOH A 23 423 292 HOH HOH . 
L 6 HOH A 24 424 343 HOH HOH . 
L 6 HOH A 25 425 401 HOH HOH . 
L 6 HOH A 26 426 270 HOH HOH . 
L 6 HOH A 27 427 282 HOH HOH . 
L 6 HOH A 28 428 389 HOH HOH . 
L 6 HOH A 29 429 318 HOH HOH . 
L 6 HOH A 30 430 312 HOH HOH . 
L 6 HOH A 31 431 284 HOH HOH . 
L 6 HOH A 32 432 346 HOH HOH . 
L 6 HOH A 33 433 342 HOH HOH . 
L 6 HOH A 34 434 256 HOH HOH . 
L 6 HOH A 35 435 305 HOH HOH . 
L 6 HOH A 36 436 341 HOH HOH . 
L 6 HOH A 37 437 385 HOH HOH . 
L 6 HOH A 38 438 255 HOH HOH . 
L 6 HOH A 39 439 322 HOH HOH . 
L 6 HOH A 40 440 396 HOH HOH . 
L 6 HOH A 41 441 376 HOH HOH . 
L 6 HOH A 42 442 279 HOH HOH . 
L 6 HOH A 43 443 354 HOH HOH . 
L 6 HOH A 44 444 382 HOH HOH . 
L 6 HOH A 45 445 374 HOH HOH . 
L 6 HOH A 46 446 369 HOH HOH . 
L 6 HOH A 47 447 370 HOH HOH . 
L 6 HOH A 48 448 336 HOH HOH . 
L 6 HOH A 49 449 364 HOH HOH . 
L 6 HOH A 50 450 373 HOH HOH . 
L 6 HOH A 51 451 265 HOH HOH . 
L 6 HOH A 52 452 278 HOH HOH . 
L 6 HOH A 53 453 344 HOH HOH . 
L 6 HOH A 54 454 395 HOH HOH . 
L 6 HOH A 55 455 321 HOH HOH . 
L 6 HOH A 56 456 377 HOH HOH . 
L 6 HOH A 57 457 295 HOH HOH . 
L 6 HOH A 58 458 359 HOH HOH . 
L 6 HOH A 59 459 281 HOH HOH . 
L 6 HOH A 60 460 266 HOH HOH . 
L 6 HOH A 61 461 368 HOH HOH . 
L 6 HOH A 62 462 303 HOH HOH . 
L 6 HOH A 63 463 325 HOH HOH . 
L 6 HOH A 64 464 317 HOH HOH . 
L 6 HOH A 65 465 275 HOH HOH . 
L 6 HOH A 66 466 356 HOH HOH . 
L 6 HOH A 67 467 358 HOH HOH . 
L 6 HOH A 68 468 274 HOH HOH . 
L 6 HOH A 69 469 297 HOH HOH . 
L 6 HOH A 70 470 371 HOH HOH . 
L 6 HOH A 71 471 304 HOH HOH . 
L 6 HOH A 72 472 347 HOH HOH . 
L 6 HOH A 73 473 378 HOH HOH . 
L 6 HOH A 74 474 257 HOH HOH . 
L 6 HOH A 75 475 381 HOH HOH . 
L 6 HOH A 76 476 339 HOH HOH . 
L 6 HOH A 77 477 361 HOH HOH . 
L 6 HOH A 78 478 258 HOH HOH . 
L 6 HOH A 79 479 259 HOH HOH . 
L 6 HOH A 80 480 338 HOH HOH . 
L 6 HOH A 81 481 280 HOH HOH . 
L 6 HOH A 82 482 386 HOH HOH . 
L 6 HOH A 83 483 391 HOH HOH . 
L 6 HOH A 84 484 298 HOH HOH . 
L 6 HOH A 85 485 291 HOH HOH . 
L 6 HOH A 86 486 337 HOH HOH . 
L 6 HOH A 87 487 379 HOH HOH . 
L 6 HOH A 88 488 313 HOH HOH . 
L 6 HOH A 89 489 393 HOH HOH . 
L 6 HOH A 90 490 276 HOH HOH . 
L 6 HOH A 91 491 330 HOH HOH . 
L 6 HOH A 92 492 353 HOH HOH . 
L 6 HOH A 93 493 323 HOH HOH . 
L 6 HOH A 94 494 310 HOH HOH . 
L 6 HOH A 95 495 271 HOH HOH . 
L 6 HOH A 96 496 283 HOH HOH . 
L 6 HOH A 97 497 315 HOH HOH . 
L 6 HOH A 98 498 349 HOH HOH . 
L 6 HOH A 99 499 394 HOH HOH . 
L 6 HOH A 100 500 316 HOH HOH . 
L 6 HOH A 101 501 397 HOH HOH . 
L 6 HOH A 102 502 402 HOH HOH . 
L 6 HOH A 103 503 340 HOH HOH . 
L 6 HOH A 104 504 263 HOH HOH . 
L 6 HOH A 105 505 299 HOH HOH . 
L 6 HOH A 106 506 302 HOH HOH . 
L 6 HOH A 107 507 267 HOH HOH . 
L 6 HOH A 108 508 357 HOH HOH . 
L 6 HOH A 109 509 399 HOH HOH . 
L 6 HOH A 110 510 311 HOH HOH . 
L 6 HOH A 111 511 319 HOH HOH . 
#
_atom_site.group_PDB             HETATM 
_atom_site.id                    1 
_atom_site.type_symbol           PD 
_atom_site.label_atom_id         PD 
_atom_site.label_comp_id         PD 
_atom_site.label_seq_id          . 
_atom_site.label_alt_id          . 
_atom_site.pdbx_PDB_ins_code     . 
_atom_site.label_asym_id         H 
_atom_site.label_entity_id       4 
_atom_site.Cartn_x               42.556 
_atom_site.Cartn_y               51.109 
_atom_site.Cartn_z               8 
_atom_site.occupancy             0.5 
_atom_site.B_iso_or_equiv        53.99 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          PD 
_atom_site.auth_comp_id          PD 
_atom_site.auth_seq_id           307 
_atom_site.auth_asym_id          A 
_atom_site.pdbx_PDB_model_num    1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           7 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           1 
#