data_5XGF # _model_server_result.job_id pep3p1UMy6fhOrH3Y4tqjg _model_server_result.datetime_utc '2025-02-24 02:57:03' _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 5xgf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":301}' # _entry.id 5XGF # _exptl.entry_id 5XGF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 58.693 _entity.id 2 _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 5XGF _cell.length_a 76 _cell.length_b 76 _cell.length_c 144.41 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XGF _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 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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # 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' 7_555 y,x,-z 0 1 0 1 0 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _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 metalc ? metalc1 A OD1 ASP 121 A ASP 100 1_555 B NI NI . A NI 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc2 A O GLY 218 A GLY 197 1_555 B NI NI . A NI 301 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc3 B NI NI . A NI 301 1_555 C O HOH . A HOH 412 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.284 ? metalc ? metalc4 B NI NI . A NI 301 1_555 C O HOH . A HOH 434 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.501 ? metalc ? metalc5 B NI NI . A NI 301 1_555 C O HOH . A HOH 473 7_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.291 ? # _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 5XGF _atom_sites.fract_transf_matrix[1][1] 0.013158 _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] 0.013158 _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] 0.006925 _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 NI A 1 301 1 NI NI . C 3 HOH A 1 401 98 HOH HOH . C 3 HOH A 2 402 52 HOH HOH . C 3 HOH A 3 403 85 HOH HOH . C 3 HOH A 4 404 11 HOH HOH . C 3 HOH A 5 405 110 HOH HOH . C 3 HOH A 6 406 30 HOH HOH . C 3 HOH A 7 407 6 HOH HOH . C 3 HOH A 8 408 54 HOH HOH . C 3 HOH A 9 409 10 HOH HOH . C 3 HOH A 10 410 17 HOH HOH . C 3 HOH A 11 411 33 HOH HOH . C 3 HOH A 12 412 53 HOH HOH . C 3 HOH A 13 413 107 HOH HOH . C 3 HOH A 14 414 29 HOH HOH . C 3 HOH A 15 415 9 HOH HOH . C 3 HOH A 16 416 32 HOH HOH . C 3 HOH A 17 417 58 HOH HOH . C 3 HOH A 18 418 105 HOH HOH . C 3 HOH A 19 419 83 HOH HOH . C 3 HOH A 20 420 25 HOH HOH . C 3 HOH A 21 421 1 HOH HOH . C 3 HOH A 22 422 57 HOH HOH . C 3 HOH A 23 423 20 HOH HOH . C 3 HOH A 24 424 63 HOH HOH . C 3 HOH A 25 425 19 HOH HOH . C 3 HOH A 26 426 7 HOH HOH . C 3 HOH A 27 427 13 HOH HOH . C 3 HOH A 28 428 3 HOH HOH . C 3 HOH A 29 429 41 HOH HOH . C 3 HOH A 30 430 16 HOH HOH . C 3 HOH A 31 431 102 HOH HOH . C 3 HOH A 32 432 4 HOH HOH . C 3 HOH A 33 433 42 HOH HOH . C 3 HOH A 34 434 14 HOH HOH . C 3 HOH A 35 435 2 HOH HOH . C 3 HOH A 36 436 59 HOH HOH . C 3 HOH A 37 437 65 HOH HOH . C 3 HOH A 38 438 18 HOH HOH . C 3 HOH A 39 439 15 HOH HOH . C 3 HOH A 40 440 46 HOH HOH . C 3 HOH A 41 441 77 HOH HOH . C 3 HOH A 42 442 34 HOH HOH . C 3 HOH A 43 443 67 HOH HOH . C 3 HOH A 44 444 36 HOH HOH . C 3 HOH A 45 445 92 HOH HOH . C 3 HOH A 46 446 61 HOH HOH . C 3 HOH A 47 447 47 HOH HOH . C 3 HOH A 48 448 66 HOH HOH . C 3 HOH A 49 449 81 HOH HOH . C 3 HOH A 50 450 12 HOH HOH . C 3 HOH A 51 451 68 HOH HOH . C 3 HOH A 52 452 35 HOH HOH . C 3 HOH A 53 453 8 HOH HOH . C 3 HOH A 54 454 60 HOH HOH . C 3 HOH A 55 455 44 HOH HOH . C 3 HOH A 56 456 39 HOH HOH . C 3 HOH A 57 457 56 HOH HOH . C 3 HOH A 58 458 37 HOH HOH . C 3 HOH A 59 459 64 HOH HOH . C 3 HOH A 60 460 78 HOH HOH . C 3 HOH A 61 461 24 HOH HOH . C 3 HOH A 62 462 82 HOH HOH . C 3 HOH A 63 463 69 HOH HOH . C 3 HOH A 64 464 31 HOH HOH . C 3 HOH A 65 465 23 HOH HOH . C 3 HOH A 66 466 27 HOH HOH . C 3 HOH A 67 467 104 HOH HOH . C 3 HOH A 68 468 28 HOH HOH . C 3 HOH A 69 469 86 HOH HOH . C 3 HOH A 70 470 111 HOH HOH . C 3 HOH A 71 471 43 HOH HOH . C 3 HOH A 72 472 108 HOH HOH . C 3 HOH A 73 473 5 HOH HOH . C 3 HOH A 74 474 21 HOH HOH . C 3 HOH A 75 475 72 HOH HOH . C 3 HOH A 76 476 26 HOH HOH . C 3 HOH A 77 477 45 HOH HOH . C 3 HOH A 78 478 38 HOH HOH . C 3 HOH A 79 479 93 HOH HOH . C 3 HOH A 80 480 101 HOH HOH . C 3 HOH A 81 481 55 HOH HOH . C 3 HOH A 82 482 50 HOH HOH . C 3 HOH A 83 483 49 HOH HOH . C 3 HOH A 84 484 103 HOH HOH . C 3 HOH A 85 485 22 HOH HOH . C 3 HOH A 86 486 89 HOH HOH . C 3 HOH A 87 487 79 HOH HOH . C 3 HOH A 88 488 48 HOH HOH . C 3 HOH A 89 489 62 HOH HOH . C 3 HOH A 90 490 75 HOH HOH . C 3 HOH A 91 491 51 HOH HOH . C 3 HOH A 92 492 74 HOH HOH . C 3 HOH A 93 493 71 HOH HOH . C 3 HOH A 94 494 99 HOH HOH . C 3 HOH A 95 495 94 HOH HOH . C 3 HOH A 96 496 70 HOH HOH . C 3 HOH A 97 497 96 HOH HOH . C 3 HOH A 98 498 90 HOH HOH . C 3 HOH A 99 499 76 HOH HOH . C 3 HOH A 100 500 87 HOH HOH . C 3 HOH A 101 501 88 HOH HOH . C 3 HOH A 102 502 100 HOH HOH . C 3 HOH A 103 503 91 HOH HOH . C 3 HOH A 104 504 73 HOH HOH . C 3 HOH A 105 505 109 HOH HOH . C 3 HOH A 106 506 84 HOH HOH . C 3 HOH A 107 507 106 HOH HOH . C 3 HOH A 108 508 95 HOH HOH . C 3 HOH A 109 509 40 HOH HOH . C 3 HOH A 110 510 97 HOH HOH . C 3 HOH A 111 511 80 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 B _atom_site.label_entity_id 2 _atom_site.Cartn_x -19.033 _atom_site.Cartn_y -6.324 _atom_site.Cartn_z 11.2 _atom_site.occupancy 0.77 _atom_site.B_iso_or_equiv 44.85 _atom_site.pdbx_formal_charge ? _atom_site.auth_atom_id NI _atom_site.auth_comp_id NI _atom_site.auth_seq_id 301 _atom_site.auth_asym_id A _atom_site.pdbx_PDB_model_num 1 # _model_server_stats.io_time_ms 68 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 281 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 1 #