data_5X2R
#
_model_server_result.job_id            YaLF9HCmqJ0uDnqDUecv6A 
_model_server_result.datetime_utc      '2024-11-24 04:31:51' 
_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          5x2r 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Q","auth_seq_id":201}' 
#
_entry.id    5X2R 
#
_exptl.entry_id    5X2R 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              619.336 
_entity.id                          3 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING NI(II)' 
_entity.pdbx_number_of_molecules    6 
_entity.pdbx_parent_entity_id       . 
_entity.pdbx_mutation               ? 
_entity.pdbx_fragment               ? 
_entity.pdbx_ec                     ? 
#
_cell.angle_alpha         90 
_cell.angle_beta          103.28 
_cell.angle_gamma         90 
_cell.entry_id            5X2R 
_cell.length_a            228.768 
_cell.length_b            55.019 
_cell.length_c            138.426 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5X2R 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        5 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'C 1 2 1' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
PISA tetrameric 4 author_and_software_defined_assembly 1 
PISA tetrameric 4 author_and_software_defined_assembly 2 
PISA tetrameric 4 author_and_software_defined_assembly 3 
#
loop_
_pdbx_struct_assembly_gen.asym_id_list
_pdbx_struct_assembly_gen.assembly_id
_pdbx_struct_assembly_gen.oper_expression
A,B,C,D,M,N,O,P 1 1 
E,F,G,H,Q,R,S,T 2 1 
I,J,K,L,U,V,W,X 3 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 
#
loop_
_struct_asym.details
_struct_asym.entity_id
_struct_asym.id
_struct_asym.pdbx_modified
_struct_asym.pdbx_blank_PDB_chainid_flag
? 3 M N N 
? 3 P N N 
? 3 Q N N 
? 3 T N N 
? 3 U N N 
? 3 X 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 87 A HIS 87 1_555 M NI HNI . A HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? 
metalc ? metalc2 B NE2 HIS 92 B HIS 92 1_555 N FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.023 ? 
metalc ? metalc3 C NE2 HIS 87 C HIS 87 1_555 O FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.113 ? 
metalc ? metalc4 D NE2 HIS 92 D HIS 92 1_555 P NI HNI . D HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.095 ? 
metalc ? metalc5 F NE2 HIS 92 F HIS 92 1_555 R FE HEM . F HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? 
metalc ? metalc6 G NE2 HIS 87 G HIS 87 1_555 S FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.188 ? 
metalc ? metalc7 H NE2 HIS 92 H HIS 92 1_555 T NI HNI . H HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? 
metalc ? metalc8 L NE2 HIS 92 L HIS 92 1_555 X NI HNI . L HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.246 ? 
#
_chem_comp.formula           'C34 H32 N4 Ni O4' 
_chem_comp.formula_weight    619.336 
_chem_comp.id                HNI 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PROTOPORPHYRIN IX CONTAINING NI(II)' 
_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
NI NA HNI sing 232 n n 
NI NB HNI sing 233 n n 
NI NC HNI sing 234 n n 
NI ND HNI sing 235 n n 
CHA C1A HNI doub 236 n n 
CHA C4D HNI sing 237 n n 
CHA HHA HNI sing 238 n n 
CHB C4A HNI sing 239 n n 
CHB C1B HNI doub 240 n n 
CHB HHB HNI sing 241 n n 
CHC C4B HNI doub 242 n n 
CHC C1C HNI sing 243 n n 
CHC HHC HNI sing 244 n n 
CHD C4C HNI doub 245 n n 
CHD C1D HNI sing 246 n n 
CHD HHD HNI sing 247 n n 
NA C1A HNI sing 248 n n 
NA C4A HNI doub 249 n n 
C1A C2A HNI sing 250 n n 
C2A C3A HNI doub 251 n n 
C2A CAA HNI sing 252 n n 
C3A C4A HNI sing 253 n n 
C3A CMA HNI sing 254 n n 
CMA HMA1 HNI sing 255 n n 
CMA HMA2 HNI sing 256 n n 
CMA HMA3 HNI sing 257 n n 
CAA CBA HNI sing 258 n n 
CAA HAA1 HNI sing 259 n n 
CAA HAA2 HNI sing 260 n n 
CBA CGA HNI sing 261 n n 
CBA HBA1 HNI sing 262 n n 
CBA HBA2 HNI sing 263 n n 
CGA O1A HNI doub 264 n n 
CGA O2A HNI sing 265 n n 
O2A H2A HNI sing 266 n n 
NB C1B HNI sing 267 n n 
NB C4B HNI sing 268 n n 
C1B C2B HNI sing 269 n n 
C2B C3B HNI doub 270 n n 
C2B CMB HNI sing 271 n n 
C3B C4B HNI sing 272 n n 
C3B CAB HNI sing 273 n n 
CMB HMB1 HNI sing 274 n n 
CMB HMB2 HNI sing 275 n n 
CMB HMB3 HNI sing 276 n n 
CAB CBB HNI doub 277 n n 
CAB HAB HNI sing 278 n n 
CBB HBB1 HNI sing 279 n n 
CBB HBB2 HNI sing 280 n n 
NC C1C HNI doub 281 n n 
NC C4C HNI sing 282 n n 
C1C C2C HNI sing 283 n n 
C2C C3C HNI doub 284 n n 
C2C CMC HNI sing 285 n n 
C3C C4C HNI sing 286 n n 
C3C CAC HNI sing 287 n n 
CMC HMC1 HNI sing 288 n n 
CMC HMC2 HNI sing 289 n n 
CMC HMC3 HNI sing 290 n n 
CAC CBC HNI doub 291 n n 
CAC HAC HNI sing 292 n n 
CBC HBC1 HNI sing 293 n n 
CBC HBC2 HNI sing 294 n n 
ND C1D HNI sing 295 n y 
ND C4D HNI sing 296 n y 
C1D C2D HNI doub 297 n y 
C2D C3D HNI sing 298 n y 
C2D CMD HNI sing 299 n n 
C3D C4D HNI doub 300 n y 
C3D CAD HNI sing 301 n n 
CMD HMD1 HNI sing 302 n n 
CMD HMD2 HNI sing 303 n n 
CMD HMD3 HNI sing 304 n n 
CAD CBD HNI sing 305 n n 
CAD HAD1 HNI sing 306 n n 
CAD HAD2 HNI sing 307 n n 
CBD CGD HNI sing 308 n n 
CBD HBD1 HNI sing 309 n n 
CBD HBD2 HNI sing 310 n n 
CGD O1D HNI doub 311 n n 
CGD O2D HNI sing 312 n n 
O2D H2D HNI sing 313 n n 
#
_atom_sites.entry_id                     5X2R 
_atom_sites.fract_transf_matrix[1][1]    0.004371 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001032 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018176 
_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]    0.007423 
_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
M 3 HNI A 1 201 142 HNI HNI . 
N 4 HEM B 1 201 147 HEM HEM . 
O 4 HEM C 1 201 142 HEM HEM . 
P 3 HNI D 1 201 147 HNI HNI . 
Q 3 HNI E 1 201 142 HNI HNI . 
R 4 HEM F 1 201 147 HEM HEM . 
S 4 HEM G 1 201 142 HEM HEM . 
T 3 HNI H 1 201 147 HNI HNI . 
U 3 HNI I 1 201 142 HNI HNI . 
V 4 HEM J 1 201 147 HEM HEM . 
W 4 HEM K 1 201 142 HEM HEM . 
X 3 HNI L 1 201 147 HNI HNI . 
#
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 NI NI HNI . . . Q 3 -11.856 -25.915 50.912 1 76.22 ? NI HNI 201 E 1 
HETATM 2 C CHA HNI . . . Q 3 -14.904 -25.102 52.129 1 78.08 ? CHA HNI 201 E 1 
HETATM 3 C CHB HNI . . . Q 3 -11.619 -28.286 53.284 1 76.61 ? CHB HNI 201 E 1 
HETATM 4 C CHC HNI . . . Q 3 -9.172 -27.171 49.376 1 76.07 ? CHC HNI 201 E 1 
HETATM 5 C CHD HNI . . . Q 3 -12.299 -23.719 48.397 1 77.65 ? CHD HNI 201 E 1 
HETATM 6 N NA HNI . . . Q 3 -12.964 -26.502 52.396 1 76.69 ? NA HNI 201 E 1 
HETATM 7 C C1A HNI . . . Q 3 -14.2 -26.051 52.792 1 77.27 ? C1A HNI 201 E 1 
HETATM 8 C C2A HNI . . . Q 3 -14.653 -26.69 53.97 1 77.82 ? C2A HNI 201 E 1 
HETATM 9 C C3A HNI . . . Q 3 -13.695 -27.553 54.327 1 77.41 ? C3A HNI 201 E 1 
HETATM 10 C C4A HNI . . . Q 3 -12.701 -27.469 53.335 1 76.54 ? C4A HNI 201 E 1 
HETATM 11 C CMA HNI . . . Q 3 -13.729 -28.478 55.517 1 78.81 ? CMA HNI 201 E 1 
HETATM 12 C CAA HNI . . . Q 3 -15.961 -26.45 54.697 1 79.74 ? CAA HNI 201 E 1 
HETATM 13 C CBA HNI . . . Q 3 -16.932 -27.596 54.38 1 81.51 ? CBA HNI 201 E 1 
HETATM 14 C CGA HNI . . . Q 3 -17.916 -27.766 55.515 1 83.25 ? CGA HNI 201 E 1 
HETATM 15 O O1A HNI . . . Q 3 -18.804 -26.952 55.655 1 85.25 ? O1A HNI 201 E 1 
HETATM 16 O O2A HNI . . . Q 3 -17.808 -28.813 56.367 1 84.12 ? O2A HNI 201 E 1 
HETATM 17 N NB HNI . . . Q 3 -10.627 -27.371 51.276 1 75.56 ? NB HNI 201 E 1 
HETATM 18 C C1B HNI . . . Q 3 -10.647 -28.234 52.302 1 75.94 ? C1B HNI 201 E 1 
HETATM 19 C C2B HNI . . . Q 3 -9.551 -29.135 52.314 1 75.84 ? C2B HNI 201 E 1 
HETATM 20 C C3B HNI . . . Q 3 -8.828 -28.836 51.217 1 75.91 ? C3B HNI 201 E 1 
HETATM 21 C C4B HNI . . . Q 3 -9.564 -27.726 50.567 1 75.62 ? C4B HNI 201 E 1 
HETATM 22 C CMB HNI . . . Q 3 -9.314 -30.18 53.386 1 77.57 ? CMB HNI 201 E 1 
HETATM 23 C CAB HNI . . . Q 3 -7.571 -29.419 50.695 1 76.82 ? CAB HNI 201 E 1 
HETATM 24 C CBB HNI . . . Q 3 -6.929 -30.448 51.243 1 80.03 ? CBB HNI 201 E 1 
HETATM 25 N NC HNI . . . Q 3 -10.938 -25.516 49.271 1 75.98 ? NC HNI 201 E 1 
HETATM 26 C C1C HNI . . . Q 3 -9.814 -26.126 48.775 1 75.62 ? C1C HNI 201 E 1 
HETATM 27 C C2C HNI . . . Q 3 -9.319 -25.441 47.634 1 76.22 ? C2C HNI 201 E 1 
HETATM 28 C C3C HNI . . . Q 3 -10.192 -24.417 47.373 1 76.65 ? C3C HNI 201 E 1 
HETATM 29 C C4C HNI . . . Q 3 -11.209 -24.512 48.369 1 76.49 ? C4C HNI 201 E 1 
HETATM 30 C CMC HNI . . . Q 3 -8.079 -25.8 46.86 1 77.37 ? CMC HNI 201 E 1 
HETATM 31 C CAC HNI . . . Q 3 -10.151 -23.429 46.284 1 77.83 ? CAC HNI 201 E 1 
HETATM 32 C CBC HNI . . . Q 3 -9.04 -22.764 45.976 1 79.75 ? CBC HNI 201 E 1 
HETATM 33 N ND HNI . . . Q 3 -13.278 -24.696 50.387 1 76.94 ? ND HNI 201 E 1 
HETATM 34 C C1D HNI . . . Q 3 -13.274 -23.842 49.37 1 77.49 ? C1D HNI 201 E 1 
HETATM 35 C C2D HNI . . . Q 3 -14.474 -22.988 49.353 1 78.51 ? C2D HNI 201 E 1 
HETATM 36 C C3D HNI . . . Q 3 -15.232 -23.413 50.347 1 78.69 ? C3D HNI 201 E 1 
HETATM 37 C C4D HNI . . . Q 3 -14.468 -24.499 50.981 1 77.67 ? C4D HNI 201 E 1 
HETATM 38 C CMD HNI . . . Q 3 -14.755 -21.889 48.376 1 80.67 ? CMD HNI 201 E 1 
HETATM 39 C CAD HNI . . . Q 3 -16.573 -22.882 50.79 1 80.24 ? CAD HNI 201 E 1 
HETATM 40 C CBD HNI . . . Q 3 -16.46 -21.42 51.248 1 81.67 ? CBD HNI 201 E 1 
HETATM 41 C CGD HNI . . . Q 3 -17.842 -20.876 51.526 1 83.71 ? CGD HNI 201 E 1 
HETATM 42 O O1D HNI . . . Q 3 -18.104 -20.415 52.614 1 84.57 ? O1D HNI 201 E 1 
HETATM 43 O O2D HNI . . . Q 3 -18.783 -20.907 50.566 1 85.11 ? O2D HNI 201 E 1 
#
_model_server_stats.io_time_ms              51 
_model_server_stats.parse_time_ms           14 
_model_server_stats.create_model_time_ms    32 
_model_server_stats.query_time_ms           439 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           43 
#