data_5VZP
#
_model_server_result.job_id            K1GjtYcoz1c5kvbtwYAm_Q 
_model_server_result.datetime_utc      '2024-10-19 22:35:13' 
_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          5vzp 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"J","auth_seq_id":209}' 
#
_entry.id    5VZP 
#
_exptl.entry_id    5VZP 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              46.005 
_entity.id                          5 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'NITRITE ION' 
_entity.pdbx_number_of_molecules    7 
_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         120 
_cell.entry_id            5VZP 
_cell.length_a            90.132 
_cell.length_b            90.132 
_cell.length_c            45.248 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5VZP 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        168 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 6' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? monomeric 1 author_defined_assembly 1 
PISA trimeric 3 software_defined_assembly 2 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 1 1 
A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q 2 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' 2_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 90.132 156.113203 0 
3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -90.132 156.113203 0 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 5 E N N 
? 5 F N N 
? 5 H N N 
? 5 I N N 
? 5 J N N 
? 5 K N N 
? 5 M 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
metalc ? metalc1 A NE2 HIS 94 A HIS 93 1_555 B FE HEM . A HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? 
metalc ? metalc2 B FE HEM . A HEM 201 1_555 D N NO . A NO 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.964 ? 
metalc ? metalc3 B FE HEM . A HEM 201 1_555 D O NO . A NO 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.796 ? 
#
_chem_comp.formula           'N O2 -1' 
_chem_comp.formula_weight    46.005 
_chem_comp.id                NO2 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'NITRITE ION' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     ? 
#
loop_
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.comp_id
_chem_comp_bond.value_order
_chem_comp_bond.pdbx_ordinal
_chem_comp_bond.pdbx_stereo_config
_chem_comp_bond.pdbx_aromatic_flag
N O1 NO2 doub 320 n n 
N O2 NO2 sing 321 n n 
#
_atom_sites.entry_id                     5VZP 
_atom_sites.fract_transf_matrix[1][1]    0.011095 
_atom_sites.fract_transf_matrix[1][2]    0.006406 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.012811 
_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]    0.0221 
_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 HEM A 1 201 154 HEM HEM . 
C 3 SO4 A 1 202 1 SO4 SO4 . 
D 4 NO A 1 203 82 NO NO . 
E 5 NO2 A 1 204 5657 NO2 NO2 . 
F 5 NO2 A 1 205 5657 NO2 NO2 . 
G 6 GOL A 1 206 3968 GOL GOL . 
H 5 NO2 A 1 207 5657 NO2 NO2 . 
I 5 NO2 A 1 208 5657 NO2 NO2 . 
J 5 NO2 A 1 209 5657 NO2 NO2 . 
K 5 NO2 A 1 210 5657 NO2 NO2 . 
L 3 SO4 A 1 211 6920 SO4 SO4 . 
M 5 NO2 A 1 212 5657 NO2 NO2 . 
N 3 SO4 A 1 213 6920 SO4 SO4 . 
O 6 GOL A 1 214 3968 GOL GOL . 
P 6 GOL A 1 215 3968 GOL GOL . 
Q 7 HOH A 1 301 154 HOH HOH . 
Q 7 HOH A 2 302 110 HOH HOH . 
Q 7 HOH A 3 303 82 HOH HOH . 
Q 7 HOH A 4 304 92 HOH HOH . 
Q 7 HOH A 5 305 129 HOH HOH . 
Q 7 HOH A 6 306 148 HOH HOH . 
Q 7 HOH A 7 307 53 HOH HOH . 
Q 7 HOH A 8 308 60 HOH HOH . 
Q 7 HOH A 9 309 87 HOH HOH . 
Q 7 HOH A 10 310 62 HOH HOH . 
Q 7 HOH A 11 311 30 HOH HOH . 
Q 7 HOH A 12 312 134 HOH HOH . 
Q 7 HOH A 13 313 45 HOH HOH . 
Q 7 HOH A 14 314 152 HOH HOH . 
Q 7 HOH A 15 315 51 HOH HOH . 
Q 7 HOH A 16 316 100 HOH HOH . 
Q 7 HOH A 17 317 107 HOH HOH . 
Q 7 HOH A 18 318 133 HOH HOH . 
Q 7 HOH A 19 319 119 HOH HOH . 
Q 7 HOH A 20 320 56 HOH HOH . 
Q 7 HOH A 21 321 80 HOH HOH . 
Q 7 HOH A 22 322 157 HOH HOH . 
Q 7 HOH A 23 323 130 HOH HOH . 
Q 7 HOH A 24 324 70 HOH HOH . 
Q 7 HOH A 25 325 120 HOH HOH . 
Q 7 HOH A 26 326 34 HOH HOH . 
Q 7 HOH A 27 327 91 HOH HOH . 
Q 7 HOH A 28 328 79 HOH HOH . 
Q 7 HOH A 29 329 24 HOH HOH . 
Q 7 HOH A 30 330 11 HOH HOH . 
Q 7 HOH A 31 331 115 HOH HOH . 
Q 7 HOH A 32 332 125 HOH HOH . 
Q 7 HOH A 33 333 12 HOH HOH . 
Q 7 HOH A 34 334 117 HOH HOH . 
Q 7 HOH A 35 335 38 HOH HOH . 
Q 7 HOH A 36 336 98 HOH HOH . 
Q 7 HOH A 37 337 52 HOH HOH . 
Q 7 HOH A 38 338 50 HOH HOH . 
Q 7 HOH A 39 339 3 HOH HOH . 
Q 7 HOH A 40 340 39 HOH HOH . 
Q 7 HOH A 41 341 6 HOH HOH . 
Q 7 HOH A 42 342 57 HOH HOH . 
Q 7 HOH A 43 343 93 HOH HOH . 
Q 7 HOH A 44 344 40 HOH HOH . 
Q 7 HOH A 45 345 58 HOH HOH . 
Q 7 HOH A 46 346 137 HOH HOH . 
Q 7 HOH A 47 347 89 HOH HOH . 
Q 7 HOH A 48 348 144 HOH HOH . 
Q 7 HOH A 49 349 44 HOH HOH . 
Q 7 HOH A 50 350 55 HOH HOH . 
Q 7 HOH A 51 351 17 HOH HOH . 
Q 7 HOH A 52 352 68 HOH HOH . 
Q 7 HOH A 53 353 75 HOH HOH . 
Q 7 HOH A 54 354 37 HOH HOH . 
Q 7 HOH A 55 355 69 HOH HOH . 
Q 7 HOH A 56 356 33 HOH HOH . 
Q 7 HOH A 57 357 16 HOH HOH . 
Q 7 HOH A 58 358 10 HOH HOH . 
Q 7 HOH A 59 359 1 HOH HOH . 
Q 7 HOH A 60 360 61 HOH HOH . 
Q 7 HOH A 61 361 54 HOH HOH . 
Q 7 HOH A 62 362 42 HOH HOH . 
Q 7 HOH A 63 363 94 HOH HOH . 
Q 7 HOH A 64 364 32 HOH HOH . 
Q 7 HOH A 65 365 66 HOH HOH . 
Q 7 HOH A 66 366 105 HOH HOH . 
Q 7 HOH A 67 367 121 HOH HOH . 
Q 7 HOH A 68 368 114 HOH HOH . 
Q 7 HOH A 69 369 71 HOH HOH . 
Q 7 HOH A 70 370 106 HOH HOH . 
Q 7 HOH A 71 371 8 HOH HOH . 
Q 7 HOH A 72 372 21 HOH HOH . 
Q 7 HOH A 73 373 65 HOH HOH . 
Q 7 HOH A 74 374 99 HOH HOH . 
Q 7 HOH A 75 375 126 HOH HOH . 
Q 7 HOH A 76 376 15 HOH HOH . 
Q 7 HOH A 77 377 85 HOH HOH . 
Q 7 HOH A 78 378 76 HOH HOH . 
Q 7 HOH A 79 379 27 HOH HOH . 
Q 7 HOH A 80 380 41 HOH HOH . 
Q 7 HOH A 81 381 150 HOH HOH . 
Q 7 HOH A 82 382 78 HOH HOH . 
Q 7 HOH A 83 383 81 HOH HOH . 
Q 7 HOH A 84 384 127 HOH HOH . 
Q 7 HOH A 85 385 155 HOH HOH . 
Q 7 HOH A 86 386 14 HOH HOH . 
Q 7 HOH A 87 387 19 HOH HOH . 
Q 7 HOH A 88 388 43 HOH HOH . 
Q 7 HOH A 89 389 22 HOH HOH . 
Q 7 HOH A 90 390 103 HOH HOH . 
Q 7 HOH A 91 391 5 HOH HOH . 
Q 7 HOH A 92 392 139 HOH HOH . 
Q 7 HOH A 93 393 13 HOH HOH . 
Q 7 HOH A 94 394 23 HOH HOH . 
Q 7 HOH A 95 395 7 HOH HOH . 
Q 7 HOH A 96 396 9 HOH HOH . 
Q 7 HOH A 97 397 20 HOH HOH . 
Q 7 HOH A 98 398 104 HOH HOH . 
Q 7 HOH A 99 399 116 HOH HOH . 
Q 7 HOH A 100 400 112 HOH HOH . 
Q 7 HOH A 101 401 135 HOH HOH . 
Q 7 HOH A 102 402 143 HOH HOH . 
Q 7 HOH A 103 403 26 HOH HOH . 
Q 7 HOH A 104 404 29 HOH HOH . 
Q 7 HOH A 105 405 88 HOH HOH . 
Q 7 HOH A 106 406 138 HOH HOH . 
Q 7 HOH A 107 407 67 HOH HOH . 
Q 7 HOH A 108 408 102 HOH HOH . 
Q 7 HOH A 109 409 31 HOH HOH . 
Q 7 HOH A 110 410 59 HOH HOH . 
Q 7 HOH A 111 411 109 HOH HOH . 
Q 7 HOH A 112 412 64 HOH HOH . 
Q 7 HOH A 113 413 108 HOH HOH . 
Q 7 HOH A 114 414 90 HOH HOH . 
Q 7 HOH A 115 415 25 HOH HOH . 
Q 7 HOH A 116 416 153 HOH HOH . 
Q 7 HOH A 117 417 63 HOH HOH . 
Q 7 HOH A 118 418 140 HOH HOH . 
Q 7 HOH A 119 419 131 HOH HOH . 
Q 7 HOH A 120 420 72 HOH HOH . 
Q 7 HOH A 121 421 132 HOH HOH . 
Q 7 HOH A 122 422 136 HOH HOH . 
Q 7 HOH A 123 423 84 HOH HOH . 
Q 7 HOH A 124 424 156 HOH HOH . 
Q 7 HOH A 125 425 149 HOH HOH . 
Q 7 HOH A 126 426 77 HOH HOH . 
Q 7 HOH A 127 427 122 HOH HOH . 
Q 7 HOH A 128 428 101 HOH HOH . 
Q 7 HOH A 129 429 83 HOH HOH . 
Q 7 HOH A 130 430 141 HOH HOH . 
Q 7 HOH A 131 431 95 HOH HOH . 
Q 7 HOH A 132 432 124 HOH HOH . 
Q 7 HOH A 133 433 123 HOH HOH . 
Q 7 HOH A 134 434 158 HOH HOH . 
Q 7 HOH A 135 435 47 HOH HOH . 
Q 7 HOH A 136 436 151 HOH HOH . 
Q 7 HOH A 137 437 113 HOH HOH . 
Q 7 HOH A 138 438 146 HOH HOH . 
Q 7 HOH A 139 439 49 HOH HOH . 
Q 7 HOH A 140 440 128 HOH HOH . 
Q 7 HOH A 141 441 96 HOH HOH . 
Q 7 HOH A 142 442 86 HOH HOH . 
Q 7 HOH A 143 443 97 HOH HOH . 
Q 7 HOH A 144 444 142 HOH HOH . 
Q 7 HOH A 145 445 111 HOH HOH . 
Q 7 HOH A 146 446 145 HOH HOH . 
#
loop_
_atom_site.group_PDB
_atom_site.id
_atom_site.type_symbol
_atom_site.label_atom_id
_atom_site.label_comp_id
_atom_site.label_seq_id
_atom_site.label_alt_id
_atom_site.pdbx_PDB_ins_code
_atom_site.label_asym_id
_atom_site.label_entity_id
_atom_site.Cartn_x
_atom_site.Cartn_y
_atom_site.Cartn_z
_atom_site.occupancy
_atom_site.B_iso_or_equiv
_atom_site.pdbx_formal_charge
_atom_site.auth_atom_id
_atom_site.auth_comp_id
_atom_site.auth_seq_id
_atom_site.auth_asym_id
_atom_site.pdbx_PDB_model_num
HETATM 1 N N NO2 . . . J 5 -0.742 86.743 -9.719 1 41.11 ? N NO2 209 A 1 
HETATM 2 O O1 NO2 . . . J 5 -0.195 86.077 -8.863 1 42.27 ? O1 NO2 209 A 1 
HETATM 3 O O2 NO2 . . . J 5 -0.977 86.249 -11.042 1 44.32 ? O2 NO2 209 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           10 
_model_server_stats.create_model_time_ms    3 
_model_server_stats.query_time_ms           265 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           3 
#