data_5GZF
#
_model_server_result.job_id            wXLfnSPNR2Ym1UdBfmWDsw 
_model_server_result.datetime_utc      '2024-12-23 06:12:42' 
_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          5gzf 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":203}' 
#
_entry.id    5GZF 
#
_exptl.entry_id    5GZF 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              58.693 
_entity.id                          4 
_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            5GZF 
_cell.length_a            48.871 
_cell.length_b            48.871 
_cell.length_c            159.725 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5GZF 
_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        ? 
_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 
_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                      4 
_struct_asym.id                             D 
_struct_asym.pdbx_modified                  N 
_struct_asym.pdbx_blank_PDB_chainid_flag    N 
#
_pdbx_entity_branch.entity_id    2 
_pdbx_entity_branch.type         oligosaccharide 
#
_pdbx_entity_branch_link.link_id                     1 
_pdbx_entity_branch_link.details                     ? 
_pdbx_entity_branch_link.entity_id                   2 
_pdbx_entity_branch_link.entity_branch_list_num_1    2 
_pdbx_entity_branch_link.entity_branch_list_num_2    1 
_pdbx_entity_branch_link.comp_id_1                   GAL 
_pdbx_entity_branch_link.comp_id_2                   BGC 
_pdbx_entity_branch_link.atom_id_1                   C1 
_pdbx_entity_branch_link.leaving_atom_id_1           O1 
_pdbx_entity_branch_link.atom_stereo_config_1        . 
_pdbx_entity_branch_link.atom_id_2                   O4 
_pdbx_entity_branch_link.leaving_atom_id_2           HO4 
_pdbx_entity_branch_link.atom_stereo_config_2        . 
_pdbx_entity_branch_link.value_order                 sing 
#
loop_
_pdbx_branch_scheme.entity_id
_pdbx_branch_scheme.hetero
_pdbx_branch_scheme.asym_id
_pdbx_branch_scheme.mon_id
_pdbx_branch_scheme.num
_pdbx_branch_scheme.pdb_asym_id
_pdbx_branch_scheme.pdb_seq_num
_pdbx_branch_scheme.pdb_mon_id
_pdbx_branch_scheme.auth_asym_id
_pdbx_branch_scheme.auth_seq_num
_pdbx_branch_scheme.auth_mon_id
2 n B BGC 1 B 1 BGC C 1 B4H 
2 n B GAL 2 B 2 GAL C 1 B4H 
#
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 B O4 BGC . B BGC 1 1_555 B C1 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.403 sing 
metalc ? metalc1 A OD1 ASP 28 A ASP 25 1_555 D NI NI . A NI 203 5_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? 
metalc ? metalc2 A NE2 HIS 41 A HIS 38 1_555 D NI NI . A NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.242 ? 
metalc ? metalc3 A NE2 HIS 150 A HIS 147 1_555 D NI NI . A NI 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.227 ? 
metalc ? metalc4 C NA NA . A NA 202 1_555 B O3 GAL . B GAL 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.084 ? 
metalc ? metalc5 D NI NI . A NI 203 1_555 E O HOH . A HOH 340 5_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? 
metalc ? metalc6 D NI NI . A NI 203 1_555 E O HOH . A HOH 356 5_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? 
#
_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                     5GZF 
_atom_sites.fract_transf_matrix[1][1]    0.020462 
_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]    0.020462 
_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]    0.006261 
_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
C 3 NA A 1 202 1 NA NA . 
D 4 NI A 1 203 1 NI NI . 
E 5 HOH A 1 301 80 HOH HOH . 
E 5 HOH A 2 302 32 HOH HOH . 
E 5 HOH A 3 303 79 HOH HOH . 
E 5 HOH A 4 304 18 HOH HOH . 
E 5 HOH A 5 305 50 HOH HOH . 
E 5 HOH A 6 306 38 HOH HOH . 
E 5 HOH A 7 307 36 HOH HOH . 
E 5 HOH A 8 308 41 HOH HOH . 
E 5 HOH A 9 309 1 HOH HOH . 
E 5 HOH A 10 310 5 HOH HOH . 
E 5 HOH A 11 311 3 HOH HOH . 
E 5 HOH A 12 312 47 HOH HOH . 
E 5 HOH A 13 313 53 HOH HOH . 
E 5 HOH A 14 314 22 HOH HOH . 
E 5 HOH A 15 315 71 HOH HOH . 
E 5 HOH A 16 316 49 HOH HOH . 
E 5 HOH A 17 317 29 HOH HOH . 
E 5 HOH A 18 318 15 HOH HOH . 
E 5 HOH A 19 319 21 HOH HOH . 
E 5 HOH A 20 320 20 HOH HOH . 
E 5 HOH A 21 321 55 HOH HOH . 
E 5 HOH A 22 322 14 HOH HOH . 
E 5 HOH A 23 323 35 HOH HOH . 
E 5 HOH A 24 324 60 HOH HOH . 
E 5 HOH A 25 325 73 HOH HOH . 
E 5 HOH A 26 326 37 HOH HOH . 
E 5 HOH A 27 327 56 HOH HOH . 
E 5 HOH A 28 328 4 HOH HOH . 
E 5 HOH A 29 329 67 HOH HOH . 
E 5 HOH A 30 330 7 HOH HOH . 
E 5 HOH A 31 331 44 HOH HOH . 
E 5 HOH A 32 332 9 HOH HOH . 
E 5 HOH A 33 333 23 HOH HOH . 
E 5 HOH A 34 334 27 HOH HOH . 
E 5 HOH A 35 335 17 HOH HOH . 
E 5 HOH A 36 336 42 HOH HOH . 
E 5 HOH A 37 337 8 HOH HOH . 
E 5 HOH A 38 338 64 HOH HOH . 
E 5 HOH A 39 339 81 HOH HOH . 
E 5 HOH A 40 340 33 HOH HOH . 
E 5 HOH A 41 341 51 HOH HOH . 
E 5 HOH A 42 342 25 HOH HOH . 
E 5 HOH A 43 343 6 HOH HOH . 
E 5 HOH A 44 344 59 HOH HOH . 
E 5 HOH A 45 345 13 HOH HOH . 
E 5 HOH A 46 346 72 HOH HOH . 
E 5 HOH A 47 347 86 HOH HOH . 
E 5 HOH A 48 348 43 HOH HOH . 
E 5 HOH A 49 349 34 HOH HOH . 
E 5 HOH A 50 350 89 HOH HOH . 
E 5 HOH A 51 351 24 HOH HOH . 
E 5 HOH A 52 352 69 HOH HOH . 
E 5 HOH A 53 353 39 HOH HOH . 
E 5 HOH A 54 354 87 HOH HOH . 
E 5 HOH A 55 355 12 HOH HOH . 
E 5 HOH A 56 356 28 HOH HOH . 
E 5 HOH A 57 357 11 HOH HOH . 
E 5 HOH A 58 358 70 HOH HOH . 
E 5 HOH A 59 359 88 HOH HOH . 
E 5 HOH A 60 360 61 HOH HOH . 
E 5 HOH A 61 361 65 HOH HOH . 
E 5 HOH A 62 362 77 HOH HOH . 
E 5 HOH A 63 363 57 HOH HOH . 
E 5 HOH A 64 364 10 HOH HOH . 
E 5 HOH A 65 365 75 HOH HOH . 
E 5 HOH A 66 366 76 HOH HOH . 
E 5 HOH A 67 367 26 HOH HOH . 
E 5 HOH A 68 368 66 HOH HOH . 
E 5 HOH A 69 369 63 HOH HOH . 
E 5 HOH A 70 370 83 HOH HOH . 
E 5 HOH A 71 371 58 HOH HOH . 
E 5 HOH A 72 372 52 HOH HOH . 
E 5 HOH A 73 373 16 HOH HOH . 
E 5 HOH A 74 374 85 HOH HOH . 
E 5 HOH A 75 375 40 HOH HOH . 
E 5 HOH A 76 376 30 HOH HOH . 
E 5 HOH A 77 377 78 HOH HOH . 
E 5 HOH A 78 378 2 HOH HOH . 
E 5 HOH A 79 379 68 HOH HOH . 
E 5 HOH A 80 380 45 HOH HOH . 
E 5 HOH A 81 381 46 HOH HOH . 
E 5 HOH A 82 382 82 HOH HOH . 
E 5 HOH A 83 383 54 HOH HOH . 
E 5 HOH A 84 384 74 HOH HOH . 
E 5 HOH A 85 385 31 HOH HOH . 
E 5 HOH A 86 386 84 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       4 
_atom_site.Cartn_x               -21.424 
_atom_site.Cartn_y               21.939 
_atom_site.Cartn_z               -15.695 
_atom_site.occupancy             1 
_atom_site.B_iso_or_equiv        48.64 
_atom_site.pdbx_formal_charge    ? 
_atom_site.auth_atom_id          NI 
_atom_site.auth_comp_id          NI 
_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              15 
_model_server_stats.parse_time_ms           22 
_model_server_stats.create_model_time_ms    7 
_model_server_stats.query_time_ms           394 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           1 
#