data_5X2R
#
_model_server_result.job_id            RYZb0-9ZiX02AIyY9uKw1Q 
_model_server_result.datetime_utc      '2024-11-27 22:00:01' 
_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":"X","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 . . . X 3 -3.083 -0.324 74.862 1 90.66 ? NI HNI 201 L 1 
HETATM 2 C CHA HNI . . . X 3 -5.524 0.578 72.766 1 92.37 ? CHA HNI 201 L 1 
HETATM 3 C CHB HNI . . . X 3 -5.146 -2.666 76.166 1 91.11 ? CHB HNI 201 L 1 
HETATM 4 C CHC HNI . . . X 3 -0.983 -0.815 77.435 1 90.45 ? CHC HNI 201 L 1 
HETATM 5 C CHD HNI . . . X 3 -1.364 2.469 74.009 1 91.93 ? CHD HNI 201 L 1 
HETATM 6 N NA HNI . . . X 3 -4.892 -0.922 74.516 1 91.14 ? NA HNI 201 L 1 
HETATM 7 C C1A HNI . . . X 3 -5.78 -0.456 73.59 1 91.66 ? C1A HNI 201 L 1 
HETATM 8 C C2A HNI . . . X 3 -6.972 -1.205 73.566 1 92.2 ? C2A HNI 201 L 1 
HETATM 9 C C3A HNI . . . X 3 -6.857 -2.142 74.512 1 91.87 ? C3A HNI 201 L 1 
HETATM 10 C C4A HNI . . . X 3 -5.601 -1.949 75.11 1 91.01 ? C4A HNI 201 L 1 
HETATM 11 C CMA HNI . . . X 3 -7.9 -3.16 74.883 1 93.31 ? CMA HNI 201 L 1 
HETATM 12 C CAA HNI . . . X 3 -8.166 -0.986 72.67 1 94.03 ? CAA HNI 201 L 1 
HETATM 13 C CBA HNI . . . X 3 -7.834 -1.229 71.191 1 95.98 ? CBA HNI 201 L 1 
HETATM 14 C CGA HNI . . . X 3 -8.87 -0.598 70.28 1 97.6 ? CGA HNI 201 L 1 
HETATM 15 O O1A HNI . . . X 3 -8.902 -0.932 69.117 1 99.69 ? O1A HNI 201 L 1 
HETATM 16 O O2A HNI . . . X 3 -9.749 0.323 70.736 1 98.38 ? O2A HNI 201 L 1 
HETATM 17 N NB HNI . . . X 3 -3.018 -1.545 76.392 1 90.04 ? NB HNI 201 L 1 
HETATM 18 C C1B HNI . . . X 3 -3.918 -2.464 76.759 1 90.38 ? C1B HNI 201 L 1 
HETATM 19 C C2B HNI . . . X 3 -3.513 -3.256 77.861 1 90.32 ? C2B HNI 201 L 1 
HETATM 20 C C3B HNI . . . X 3 -2.325 -2.796 78.242 1 90.31 ? C3B HNI 201 L 1 
HETATM 21 C C4B HNI . . . X 3 -2.059 -1.656 77.317 1 90.02 ? C4B HNI 201 L 1 
HETATM 22 C CMB HNI . . . X 3 -4.285 -4.4 78.484 1 92 ? CMB HNI 201 L 1 
HETATM 23 C CAB HNI . . . X 3 -1.533 -3.32 79.377 1 91.14 ? CAB HNI 201 L 1 
HETATM 24 C CBB HNI . . . X 3 -0.23 -3.129 79.539 1 93.78 ? CBB HNI 201 L 1 
HETATM 25 N NC HNI . . . X 3 -1.513 0.593 75.536 1 90.4 ? NC HNI 201 L 1 
HETATM 26 C C1C HNI . . . X 3 -0.738 0.241 76.612 1 89.98 ? C1C HNI 201 L 1 
HETATM 27 C C2C HNI . . . X 3 0.35 1.113 76.781 1 90.58 ? C2C HNI 201 L 1 
HETATM 28 C C3C HNI . . . X 3 0.275 2.045 75.793 1 90.98 ? C3C HNI 201 L 1 
HETATM 29 C C4C HNI . . . X 3 -0.901 1.726 75.045 1 90.83 ? C4C HNI 201 L 1 
HETATM 30 C CMC HNI . . . X 3 1.395 1.017 77.858 1 91.72 ? CMC HNI 201 L 1 
HETATM 31 C CAC HNI . . . X 3 1.201 3.17 75.564 1 92.09 ? CAC HNI 201 L 1 
HETATM 32 C CBC HNI . . . X 3 1.28 4.182 76.426 1 94.02 ? CBC HNI 201 L 1 
HETATM 33 N ND HNI . . . X 3 -3.332 1.112 73.579 1 91.26 ? ND HNI 201 L 1 
HETATM 34 C C1D HNI . . . X 3 -2.511 2.135 73.319 1 91.73 ? C1D HNI 201 L 1 
HETATM 35 C C2D HNI . . . X 3 -2.969 2.934 72.155 1 92.67 ? C2D HNI 201 L 1 
HETATM 36 C C3D HNI . . . X 3 -4.151 2.419 71.802 1 92.86 ? C3D HNI 201 L 1 
HETATM 37 C C4D HNI . . . X 3 -4.369 1.301 72.753 1 91.93 ? C4D HNI 201 L 1 
HETATM 38 C CMD HNI . . . X 3 -2.225 4.094 71.542 1 94.73 ? CMD HNI 201 L 1 
HETATM 39 C CAD HNI . . . X 3 -5.063 2.83 70.657 1 94.46 ? CAD HNI 201 L 1 
HETATM 40 C CBD HNI . . . X 3 -5.395 1.598 69.782 1 96.03 ? CBD HNI 201 L 1 
HETATM 41 C CGD HNI . . . X 3 -6.297 1.882 68.607 1 97.98 ? CGD HNI 201 L 1 
HETATM 42 O O1D HNI . . . X 3 -5.82 2.015 67.495 1 99.15 ? O1D HNI 201 L 1 
HETATM 43 O O2D HNI . . . X 3 -7.627 1.975 68.8 1 98.95 ? O2D HNI 201 L 1 
#
_model_server_stats.io_time_ms              152 
_model_server_stats.parse_time_ms           11 
_model_server_stats.create_model_time_ms    23 
_model_server_stats.query_time_ms           269 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#