data_5X2S
#
_model_server_result.job_id            vHLBTrjckeWzO6ZIWIN0oA 
_model_server_result.datetime_utc      '2024-10-31 06:17:03' 
_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          5x2s 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"Y","auth_seq_id":201}' 
#
_entry.id    5X2S 
#
_exptl.entry_id    5X2S 
_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          103.18 
_cell.angle_gamma         90 
_cell.entry_id            5X2S 
_cell.length_a            228.603 
_cell.length_b            54.598 
_cell.length_c            138.444 
_cell.Z_PDB               24 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 5X2S 
_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
? tetrameric 4 author_defined_assembly 1 
? tetrameric 4 author_defined_assembly 2 
? tetrameric 4 author_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,Z,AA,BA 1 1 
E,F,G,H,Q,R,S,T,CA,DA,EA,FA 2 1 
I,J,K,L,U,V,W,X,Y,GA,HA,IA,JA 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 Y 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 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc2 B NE2 HIS 92 B HIS 92 1_555 N FE HEM . B HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.1 ? 
metalc ? metalc3 C NE2 HIS 87 C HIS 87 1_555 O FE HEM . C HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.34 ? 
metalc ? metalc4 D NE2 HIS 92 D HIS 92 1_555 P NI HNI . D HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.2 ? 
metalc ? metalc5 F NE2 HIS 92 F HIS 92 1_555 R FE HEM . F HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.224 ? 
metalc ? metalc6 G NE2 HIS 87 G HIS 87 1_555 S FE HEM . G HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.718 ? 
metalc ? metalc7 H NE2 HIS 92 H HIS 92 1_555 T NI HNI . H HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? 
metalc ? metalc8 J NE2 HIS 92 J HIS 92 1_555 W FE HEM . J HEM 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.995 ? 
metalc ? metalc9 L NE2 HIS 92 L HIS 92 1_555 Y NI HNI . L HNI 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.741 ? 
#
_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                     5X2S 
_atom_sites.fract_transf_matrix[1][1]    0.004374 
_atom_sites.fract_transf_matrix[1][2]    0 
_atom_sites.fract_transf_matrix[1][3]    0.001024 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.018316 
_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]    0.007419 
_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 5 PEM I 1 202 1 PEM PEM . 
W 4 HEM J 1 201 147 HEM HEM . 
X 4 HEM K 1 201 142 HEM HEM . 
Y 3 HNI L 1 201 147 HNI HNI . 
Z 6 HOH A 1 301 51 HOH HOH . 
Z 6 HOH A 2 302 1 HOH HOH . 
AA 6 HOH B 1 301 10 HOH HOH . 
AA 6 HOH B 2 302 9 HOH HOH . 
BA 6 HOH D 1 301 24 HOH HOH . 
BA 6 HOH D 2 302 34 HOH HOH . 
BA 6 HOH D 3 303 53 HOH HOH . 
CA 6 HOH E 1 301 17 HOH HOH . 
CA 6 HOH E 2 302 64 HOH HOH . 
CA 6 HOH E 3 303 47 HOH HOH . 
DA 6 HOH F 1 301 48 HOH HOH . 
DA 6 HOH F 2 302 60 HOH HOH . 
EA 6 HOH G 1 301 8 HOH HOH . 
EA 6 HOH G 2 302 65 HOH HOH . 
EA 6 HOH G 3 303 21 HOH HOH . 
FA 6 HOH H 1 301 55 HOH HOH . 
FA 6 HOH H 2 302 68 HOH HOH . 
FA 6 HOH H 3 303 63 HOH HOH . 
GA 6 HOH I 1 301 7 HOH HOH . 
GA 6 HOH I 2 302 43 HOH HOH . 
GA 6 HOH I 3 303 40 HOH HOH . 
GA 6 HOH I 4 304 5 HOH HOH . 
HA 6 HOH J 1 301 15 HOH HOH . 
HA 6 HOH J 2 302 18 HOH HOH . 
HA 6 HOH J 3 303 31 HOH HOH . 
HA 6 HOH J 4 304 2 HOH HOH . 
HA 6 HOH J 5 305 66 HOH HOH . 
IA 6 HOH K 1 301 57 HOH HOH . 
IA 6 HOH K 2 302 32 HOH HOH . 
IA 6 HOH K 3 303 20 HOH HOH . 
IA 6 HOH K 4 304 12 HOH HOH . 
IA 6 HOH K 5 305 37 HOH HOH . 
JA 6 HOH L 1 301 44 HOH HOH . 
JA 6 HOH L 2 302 45 HOH HOH . 
JA 6 HOH L 3 303 33 HOH HOH . 
JA 6 HOH L 4 304 3 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 NI NI HNI . . . Y 3 -3.106 -1.331 74.891 1 83.97 ? NI HNI 201 L 1 
HETATM 2 C CHA HNI . . . Y 3 -5.535 -0.706 72.574 1 87.34 ? CHA HNI 201 L 1 
HETATM 3 C CHB HNI . . . Y 3 -5.061 -3.828 76.118 1 83.65 ? CHB HNI 201 L 1 
HETATM 4 C CHC HNI . . . Y 3 -1.096 -1.58 77.567 1 82.33 ? CHC HNI 201 L 1 
HETATM 5 C CHD HNI . . . Y 3 -1.46 1.433 73.887 1 86.82 ? CHD HNI 201 L 1 
HETATM 6 N NA HNI . . . Y 3 -4.927 -2.068 74.476 1 84.62 ? NA HNI 201 L 1 
HETATM 7 C C1A HNI . . . Y 3 -5.785 -1.704 73.479 1 85.86 ? C1A HNI 201 L 1 
HETATM 8 C C2A HNI . . . Y 3 -6.937 -2.569 73.403 1 86.46 ? C2A HNI 201 L 1 
HETATM 9 C C3A HNI . . . Y 3 -6.822 -3.448 74.462 1 85.47 ? C3A HNI 201 L 1 
HETATM 10 C C4A HNI . . . Y 3 -5.585 -3.119 75.086 1 84.14 ? C4A HNI 201 L 1 
HETATM 11 C CMA HNI . . . Y 3 -7.748 -4.571 74.854 1 86.93 ? CMA HNI 201 L 1 
HETATM 12 C CAA HNI . . . Y 3 -8.068 -2.486 72.384 1 89.09 ? CAA HNI 201 L 1 
HETATM 13 C CBA HNI . . . Y 3 -8.248 -3.834 71.628 1 91.75 ? CBA HNI 201 L 1 
HETATM 14 C CGA HNI . . . Y 3 -8.885 -3.63 70.263 1 94.84 ? CGA HNI 201 L 1 
HETATM 15 O O1A HNI . . . Y 3 -9.758 -4.391 69.867 1 97.23 ? O1A HNI 201 L 1 
HETATM 16 O O2A HNI . . . Y 3 -8.475 -2.585 69.497 1 96.68 ? O2A HNI 201 L 1 
HETATM 17 N NB HNI . . . Y 3 -3.04 -2.515 76.46 1 82.29 ? NB HNI 201 L 1 
HETATM 18 C C1B HNI . . . Y 3 -3.867 -3.506 76.776 1 82.57 ? C1B HNI 201 L 1 
HETATM 19 C C2B HNI . . . Y 3 -3.504 -4.212 77.967 1 81.99 ? C2B HNI 201 L 1 
HETATM 20 C C3B HNI . . . Y 3 -2.4 -3.581 78.43 1 81.7 ? C3B HNI 201 L 1 
HETATM 21 C C4B HNI . . . Y 3 -2.155 -2.479 77.456 1 81.82 ? C4B HNI 201 L 1 
HETATM 22 C CMB HNI . . . Y 3 -4.221 -5.393 78.58 1 83.78 ? CMB HNI 201 L 1 
HETATM 23 C CAB HNI . . . Y 3 -1.656 -3.924 79.654 1 82.1 ? CAB HNI 201 L 1 
HETATM 24 C CBB HNI . . . Y 3 -0.34 -3.791 79.76 1 85.59 ? CBB HNI 201 L 1 
HETATM 25 N NC HNI . . . Y 3 -1.575 -0.275 75.574 1 83.57 ? NC HNI 201 L 1 
HETATM 26 C C1C HNI . . . Y 3 -0.837 -0.55 76.69 1 82.5 ? C1C HNI 201 L 1 
HETATM 27 C C2C HNI . . . Y 3 0.247 0.359 76.842 1 83.37 ? C2C HNI 201 L 1 
HETATM 28 C C3C HNI . . . Y 3 0.147 1.255 75.749 1 84.66 ? C3C HNI 201 L 1 
HETATM 29 C C4C HNI . . . Y 3 -1.004 0.835 75.008 1 84.76 ? C4C HNI 201 L 1 
HETATM 30 C CMC HNI . . . Y 3 1.229 0.291 77.987 1 84.06 ? CMC HNI 201 L 1 
HETATM 31 C CAC HNI . . . Y 3 0.985 2.413 75.422 1 86.47 ? CAC HNI 201 L 1 
HETATM 32 C CBC HNI . . . Y 3 1.403 3.216 76.404 1 88.38 ? CBC HNI 201 L 1 
HETATM 33 N ND HNI . . . Y 3 -3.406 0.038 73.486 1 85.82 ? ND HNI 201 L 1 
HETATM 34 C C1D HNI . . . Y 3 -2.606 1.053 73.201 1 86.86 ? C1D HNI 201 L 1 
HETATM 35 C C2D HNI . . . Y 3 -3.078 1.82 72.05 1 88.89 ? C2D HNI 201 L 1 
HETATM 36 C C3D HNI . . . Y 3 -4.225 1.225 71.647 1 89.14 ? C3D HNI 201 L 1 
HETATM 37 C C4D HNI . . . Y 3 -4.431 0.12 72.612 1 87.11 ? C4D HNI 201 L 1 
HETATM 38 C CMD HNI . . . Y 3 -2.374 2.999 71.453 1 91.94 ? CMD HNI 201 L 1 
HETATM 39 C CAD HNI . . . Y 3 -5.1 1.692 70.511 1 91.87 ? CAD HNI 201 L 1 
HETATM 40 C CBD HNI . . . Y 3 -5.609 0.628 69.54 1 94.29 ? CBD HNI 201 L 1 
HETATM 41 C CGD HNI . . . Y 3 -6.19 1.342 68.336 1 97.6 ? CGD HNI 201 L 1 
HETATM 42 O O1D HNI . . . Y 3 -5.546 2.168 67.709 1 99.49 ? O1D HNI 201 L 1 
HETATM 43 O O2D HNI . . . Y 3 -7.441 1.04 67.957 1 99.07 ? O2D HNI 201 L 1 
#
_model_server_stats.io_time_ms              30 
_model_server_stats.parse_time_ms           12 
_model_server_stats.create_model_time_ms    14 
_model_server_stats.query_time_ms           307 
_model_server_stats.encode_time_ms          3 
_model_server_stats.element_count           43 
#