data_1SDW # _model_server_result.job_id JiYumYDgwJ3yQvI7ZfojSw _model_server_result.datetime_utc '2025-07-31 07:37:17' _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 1sdw # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":359}' # _entry.id 1SDW # _exptl.entry_id 1SDW _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'NICKEL (II) ION' _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 1SDW _cell.length_a 69.478 _cell.length_b 68.979 _cell.length_c 82.108 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1SDW _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 ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_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,M,N,O _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 3 _struct_asym.id D _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 5 A CYS 47 1_555 A SG CYS 144 A CYS 186 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf2 A SG CYS 39 A CYS 81 1_555 A SG CYS 84 A CYS 126 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf3 A SG CYS 72 A CYS 114 1_555 A SG CYS 89 A CYS 131 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? disulf ? disulf4 A SG CYS 185 A CYS 227 1_555 A SG CYS 292 A CYS 334 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.038 ? disulf ? disulf5 A SG CYS 251 A CYS 293 1_555 A SG CYS 273 A CYS 315 1_555 ? A ? ? ? ? ? ? ? ? ? ? 2.023 ? metalc ? metalc1 A ND1 HIS 65 A HIS 107 1_555 B CU CU . A CU 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.82 ? metalc ? metalc2 A ND1 HIS 66 A HIS 108 1_555 B CU CU . A CU 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? metalc ? metalc3 A ND1 HIS 130 A HIS 172 1_555 B CU CU . A CU 357 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.092 ? metalc ? metalc4 A NE2 HIS 193 A HIS 235 1_555 D NI NI . A NI 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? metalc ? metalc5 A NE2 HIS 200 A HIS 242 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.11 ? metalc ? metalc6 A NE2 HIS 202 A HIS 244 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.125 ? metalc ? metalc7 A NE2 HIS 263 A HIS 305 4_456 D NI NI . A NI 359 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? metalc ? metalc8 A SD MET 272 A MET 314 1_555 C CU CU . A CU 358 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.27 ? metalc ? metalc9 C CU CU . A CU 358 1_555 E O1 OXY . A OXY 360 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc10 D NI NI . A NI 359 1_555 O O HOH . A HOH 361 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc11 D NI NI . A NI 359 1_555 O O HOH . A HOH 362 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.975 ? metalc ? metalc12 D NI NI . A NI 359 1_555 I O1 GOL . A GOL 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc13 D NI NI . A NI 359 1_555 I O2 GOL . A GOL 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.985 ? # _chem_comp.formula 'Ni 2' _chem_comp.formula_weight 58.693 _chem_comp.id NI _chem_comp.mon_nstd_flag . _chem_comp.name 'NICKEL (II) ION' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1SDW _atom_sites.fract_transf_matrix[1][1] 0.014393 _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] 0.014497 _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] 0.012179 _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 CU A 1 357 357 CU CU . C 2 CU A 1 358 358 CU CU . D 3 NI A 1 359 359 NI NI . E 4 OXY A 1 360 360 OXY O2 . F 5 IYT A 1 701 701 IYT IYT . G 5 IYT A 1 702 702 IYT IYT . H 5 IYT A 1 703 703 IYT IYT . I 6 GOL A 1 363 363 GOL GOL . J 6 GOL A 1 364 364 GOL GOL . K 6 GOL A 1 365 365 GOL GOL . L 6 GOL A 1 366 366 GOL GOL . M 6 GOL A 1 367 367 GOL GOL . N 6 GOL A 1 368 368 GOL GOL . O 7 HOH A 1 361 361 HOH HOH . O 7 HOH A 2 362 362 HOH HOH . O 7 HOH A 3 400 400 HOH HOH . O 7 HOH A 4 401 401 HOH HOH . O 7 HOH A 5 402 402 HOH HOH . O 7 HOH A 6 403 403 HOH HOH . O 7 HOH A 7 404 404 HOH HOH . O 7 HOH A 8 405 405 HOH HOH . O 7 HOH A 9 406 406 HOH HOH . O 7 HOH A 10 407 407 HOH HOH . O 7 HOH A 11 408 408 HOH HOH . O 7 HOH A 12 409 409 HOH HOH . O 7 HOH A 13 410 410 HOH HOH . O 7 HOH A 14 411 411 HOH HOH . O 7 HOH A 15 412 412 HOH HOH . O 7 HOH A 16 413 413 HOH HOH . O 7 HOH A 17 414 414 HOH HOH . O 7 HOH A 18 415 415 HOH HOH . O 7 HOH A 19 416 416 HOH HOH . O 7 HOH A 20 417 417 HOH HOH . O 7 HOH A 21 418 418 HOH HOH . O 7 HOH A 22 419 419 HOH HOH . O 7 HOH A 23 420 420 HOH HOH . O 7 HOH A 24 421 421 HOH HOH . O 7 HOH A 25 422 422 HOH HOH . O 7 HOH A 26 423 423 HOH HOH . O 7 HOH A 27 424 424 HOH HOH . O 7 HOH A 28 425 425 HOH HOH . O 7 HOH A 29 426 426 HOH HOH . O 7 HOH A 30 427 427 HOH HOH . O 7 HOH A 31 428 428 HOH HOH . O 7 HOH A 32 429 429 HOH HOH . O 7 HOH A 33 430 430 HOH HOH . O 7 HOH A 34 431 431 HOH HOH . O 7 HOH A 35 432 432 HOH HOH . O 7 HOH A 36 433 433 HOH HOH . O 7 HOH A 37 434 434 HOH HOH . O 7 HOH A 38 435 435 HOH HOH . O 7 HOH A 39 436 436 HOH HOH . O 7 HOH A 40 437 437 HOH HOH . O 7 HOH A 41 438 438 HOH HOH . O 7 HOH A 42 439 439 HOH HOH . O 7 HOH A 43 440 440 HOH HOH . O 7 HOH A 44 441 441 HOH HOH . O 7 HOH A 45 442 442 HOH HOH . O 7 HOH A 46 443 443 HOH HOH . O 7 HOH A 47 444 444 HOH HOH . O 7 HOH A 48 445 445 HOH HOH . O 7 HOH A 49 446 446 HOH HOH . O 7 HOH A 50 447 447 HOH HOH . O 7 HOH A 51 448 448 HOH HOH . O 7 HOH A 52 449 449 HOH HOH . O 7 HOH A 53 450 450 HOH HOH . O 7 HOH A 54 451 451 HOH HOH . O 7 HOH A 55 452 452 HOH HOH . O 7 HOH A 56 453 453 HOH HOH . O 7 HOH A 57 454 454 HOH HOH . O 7 HOH A 58 455 455 HOH HOH . O 7 HOH A 59 456 456 HOH HOH . O 7 HOH A 60 457 457 HOH HOH . O 7 HOH A 61 458 458 HOH HOH . O 7 HOH A 62 459 459 HOH HOH . O 7 HOH A 63 460 460 HOH HOH . O 7 HOH A 64 461 461 HOH HOH . O 7 HOH A 65 462 462 HOH HOH . O 7 HOH A 66 463 463 HOH HOH . O 7 HOH A 67 464 464 HOH HOH . O 7 HOH A 68 465 465 HOH HOH . O 7 HOH A 69 466 466 HOH HOH . O 7 HOH A 70 467 467 HOH HOH . O 7 HOH A 71 468 468 HOH HOH . O 7 HOH A 72 469 469 HOH HOH . O 7 HOH A 73 470 470 HOH HOH . O 7 HOH A 74 471 471 HOH HOH . O 7 HOH A 75 472 472 HOH HOH . O 7 HOH A 76 473 473 HOH HOH . O 7 HOH A 77 474 474 HOH HOH . O 7 HOH A 78 475 475 HOH HOH . O 7 HOH A 79 476 476 HOH HOH . O 7 HOH A 80 477 477 HOH HOH . O 7 HOH A 81 478 478 HOH HOH . O 7 HOH A 82 479 479 HOH HOH . O 7 HOH A 83 480 480 HOH HOH . O 7 HOH A 84 481 481 HOH HOH . O 7 HOH A 85 482 482 HOH HOH . O 7 HOH A 86 483 483 HOH HOH . O 7 HOH A 87 484 484 HOH HOH . O 7 HOH A 88 485 485 HOH HOH . O 7 HOH A 89 486 486 HOH HOH . O 7 HOH A 90 487 487 HOH HOH . O 7 HOH A 91 488 488 HOH HOH . O 7 HOH A 92 489 489 HOH HOH . O 7 HOH A 93 490 490 HOH HOH . O 7 HOH A 94 491 491 HOH HOH . O 7 HOH A 95 492 492 HOH HOH . O 7 HOH A 96 493 493 HOH HOH . O 7 HOH A 97 494 494 HOH HOH . O 7 HOH A 98 495 495 HOH HOH . O 7 HOH A 99 496 496 HOH HOH . O 7 HOH A 100 497 497 HOH HOH . O 7 HOH A 101 498 498 HOH HOH . O 7 HOH A 102 499 499 HOH HOH . O 7 HOH A 103 500 500 HOH HOH . O 7 HOH A 104 501 501 HOH HOH . O 7 HOH A 105 502 502 HOH HOH . O 7 HOH A 106 503 503 HOH HOH . O 7 HOH A 107 504 504 HOH HOH . O 7 HOH A 108 505 505 HOH HOH . O 7 HOH A 109 506 506 HOH HOH . O 7 HOH A 110 507 507 HOH HOH . O 7 HOH A 111 508 508 HOH HOH . O 7 HOH A 112 509 509 HOH HOH . O 7 HOH A 113 510 510 HOH HOH . O 7 HOH A 114 511 511 HOH HOH . O 7 HOH A 115 512 512 HOH HOH . O 7 HOH A 116 513 513 HOH HOH . O 7 HOH A 117 514 514 HOH HOH . O 7 HOH A 118 515 515 HOH HOH . O 7 HOH A 119 516 516 HOH HOH . O 7 HOH A 120 517 517 HOH HOH . O 7 HOH A 121 518 518 HOH HOH . O 7 HOH A 122 519 519 HOH HOH . O 7 HOH A 123 520 520 HOH HOH . O 7 HOH A 124 521 521 HOH HOH . O 7 HOH A 125 522 522 HOH HOH . O 7 HOH A 126 523 523 HOH HOH . O 7 HOH A 127 524 524 HOH HOH . O 7 HOH A 128 525 525 HOH HOH . O 7 HOH A 129 526 526 HOH HOH . O 7 HOH A 130 527 527 HOH HOH . O 7 HOH A 131 528 528 HOH HOH . O 7 HOH A 132 529 529 HOH HOH . O 7 HOH A 133 530 530 HOH HOH . O 7 HOH A 134 531 531 HOH HOH . O 7 HOH A 135 532 532 HOH HOH . O 7 HOH A 136 533 533 HOH HOH . O 7 HOH A 137 534 534 HOH HOH . O 7 HOH A 138 535 535 HOH HOH . O 7 HOH A 139 536 536 HOH HOH . O 7 HOH A 140 537 537 HOH HOH . O 7 HOH A 141 538 538 HOH HOH . O 7 HOH A 142 539 539 HOH HOH . O 7 HOH A 143 540 540 HOH HOH . O 7 HOH A 144 541 541 HOH HOH . O 7 HOH A 145 542 542 HOH HOH . O 7 HOH A 146 543 543 HOH HOH . O 7 HOH A 147 544 544 HOH HOH . O 7 HOH A 148 545 545 HOH HOH . O 7 HOH A 149 546 546 HOH HOH . O 7 HOH A 150 547 547 HOH HOH . O 7 HOH A 151 548 548 HOH HOH . O 7 HOH A 152 549 549 HOH HOH . O 7 HOH A 153 550 550 HOH HOH . O 7 HOH A 154 551 551 HOH HOH . O 7 HOH A 155 552 552 HOH HOH . O 7 HOH A 156 553 553 HOH HOH . O 7 HOH A 157 554 554 HOH HOH . O 7 HOH A 158 555 555 HOH HOH . O 7 HOH A 159 556 556 HOH HOH . O 7 HOH A 160 557 557 HOH HOH . O 7 HOH A 161 558 558 HOH HOH . O 7 HOH A 162 559 559 HOH HOH . O 7 HOH A 163 560 560 HOH HOH . O 7 HOH A 164 561 561 HOH HOH . O 7 HOH A 165 562 562 HOH HOH . O 7 HOH A 166 563 563 HOH HOH . O 7 HOH A 167 564 564 HOH HOH . O 7 HOH A 168 565 565 HOH HOH . O 7 HOH A 169 566 566 HOH HOH . O 7 HOH A 170 567 567 HOH HOH . O 7 HOH A 171 568 568 HOH HOH . O 7 HOH A 172 569 569 HOH HOH . O 7 HOH A 173 570 570 HOH HOH . O 7 HOH A 174 571 571 HOH HOH . O 7 HOH A 175 572 572 HOH HOH . O 7 HOH A 176 573 573 HOH HOH . O 7 HOH A 177 574 574 HOH HOH . O 7 HOH A 178 575 575 HOH HOH . O 7 HOH A 179 576 576 HOH HOH . O 7 HOH A 180 577 577 HOH HOH . # _atom_site.group_PDB HETATM _atom_site.id 1 _atom_site.type_symbol NI _atom_site.label_atom_id NI _atom_site.label_comp_id NI _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 3 _atom_site.Cartn_x 23.037 _atom_site.Cartn_y 7.874 _atom_site.Cartn_z 49.278 _atom_site.occupancy 1 _atom_site.B_iso_or_equiv 32.72 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 359 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 355 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #