data_8Q2F
#
_model_server_result.job_id            WzTXYTV7WOSjUrzi34utog 
_model_server_result.datetime_utc      '2025-01-19 11:24:22' 
_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          8q2f 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"VA","auth_seq_id":501}' 
#
_entry.id    8Q2F 
#
_exptl.entry_id    8Q2F 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              616.487 
_entity.id                          2 
_entity.src_method                  syn 
_entity.type                        non-polymer 
_entity.pdbx_description            'PROTOPORPHYRIN IX CONTAINING FE' 
_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          90 
_cell.angle_gamma         90 
_cell.entry_id            8Q2F 
_cell.length_a            167.44 
_cell.length_b            167.44 
_cell.length_c            364.743 
_cell.Z_PDB               48 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 8Q2F 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
loop_
_pdbx_struct_assembly.method_details
_pdbx_struct_assembly.oligomeric_details
_pdbx_struct_assembly.oligomeric_count
_pdbx_struct_assembly.details
_pdbx_struct_assembly.id
? dimeric 2 author_defined_assembly 1 
? dimeric 2 author_defined_assembly 2 
? dimeric 2 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,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X 1 1 
C,D,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA,JA,KA 2 1 
E,F,LA,MA,NA,OA,PA,QA,RA,SA,TA,UA,VA,WA,XA,YA,ZA,AB 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
? 2 G N N 
? 2 P N N 
? 2 Y N N 
? 2 DA N N 
? 2 LA N N 
? 2 VA 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 SG CYS 401 A CYS 400 1_555 G FE HEM . A HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.299 ? 
metalc ? metalc2 B SG CYS 401 B CYS 400 1_555 P FE HEM . B HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.316 ? 
metalc ? metalc3 C SG CYS 401 C CYS 400 1_555 Y FE HEM . C HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.303 ? 
metalc ? metalc4 D SG CYS 401 D CYS 400 1_555 DA FE HEM . D HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? 
metalc ? metalc5 E SG CYS 401 E CYS 400 1_555 LA FE HEM . E HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.33 ? 
metalc ? metalc6 F SG CYS 401 F CYS 400 1_555 VA FE HEM . F HEM 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.306 ? 
#
_chem_comp.formula           'C34 H32 Fe N4 O4' 
_chem_comp.formula_weight    616.487 
_chem_comp.id                HEM 
_chem_comp.mon_nstd_flag     . 
_chem_comp.name              'PROTOPORPHYRIN IX CONTAINING FE' 
_chem_comp.type              non-polymer 
_chem_comp.pdbx_synonyms     HEME 
#
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
CHA C1A HEM sing 148 n n 
CHA C4D HEM doub 149 n n 
CHA HHA HEM sing 150 n n 
CHB C4A HEM sing 151 n n 
CHB C1B HEM doub 152 n n 
CHB HHB HEM sing 153 n n 
CHC C4B HEM sing 154 n n 
CHC C1C HEM doub 155 n n 
CHC HHC HEM sing 156 n n 
CHD C4C HEM doub 157 n n 
CHD C1D HEM sing 158 n n 
CHD HHD HEM sing 159 n n 
C1A C2A HEM doub 160 n y 
C1A NA HEM sing 161 n y 
C2A C3A HEM sing 162 n y 
C2A CAA HEM sing 163 n n 
C3A C4A HEM doub 164 n y 
C3A CMA HEM sing 165 n n 
C4A NA HEM sing 166 n y 
CMA HMA HEM sing 167 n n 
CMA HMAA HEM sing 168 n n 
CMA HMAB HEM sing 169 n n 
CAA CBA HEM sing 170 n n 
CAA HAA HEM sing 171 n n 
CAA HAAA HEM sing 172 n n 
CBA CGA HEM sing 173 n n 
CBA HBA HEM sing 174 n n 
CBA HBAA HEM sing 175 n n 
CGA O1A HEM doub 176 n n 
CGA O2A HEM sing 177 n n 
C1B C2B HEM sing 178 n n 
C1B NB HEM sing 179 n n 
C2B C3B HEM doub 180 n n 
C2B CMB HEM sing 181 n n 
C3B C4B HEM sing 182 n n 
C3B CAB HEM sing 183 n n 
C4B NB HEM doub 184 n n 
CMB HMB HEM sing 185 n n 
CMB HMBA HEM sing 186 n n 
CMB HMBB HEM sing 187 n n 
CAB CBB HEM doub 188 n n 
CAB HAB HEM sing 189 n n 
CBB HBB HEM sing 190 n n 
CBB HBBA HEM sing 191 n n 
C1C C2C HEM sing 192 n y 
C1C NC HEM sing 193 n y 
C2C C3C HEM doub 194 n y 
C2C CMC HEM sing 195 n n 
C3C C4C HEM sing 196 n y 
C3C CAC HEM sing 197 n n 
C4C NC HEM sing 198 n y 
CMC HMC HEM sing 199 n n 
CMC HMCA HEM sing 200 n n 
CMC HMCB HEM sing 201 n n 
CAC CBC HEM doub 202 n n 
CAC HAC HEM sing 203 n n 
CBC HBC HEM sing 204 n n 
CBC HBCA HEM sing 205 n n 
C1D C2D HEM sing 206 n n 
C1D ND HEM doub 207 n n 
C2D C3D HEM doub 208 n n 
C2D CMD HEM sing 209 n n 
C3D C4D HEM sing 210 n n 
C3D CAD HEM sing 211 n n 
C4D ND HEM sing 212 n n 
CMD HMD HEM sing 213 n n 
CMD HMDA HEM sing 214 n n 
CMD HMDB HEM sing 215 n n 
CAD CBD HEM sing 216 n n 
CAD HAD HEM sing 217 n n 
CAD HADA HEM sing 218 n n 
CBD CGD HEM sing 219 n n 
CBD HBD HEM sing 220 n n 
CBD HBDA HEM sing 221 n n 
CGD O1D HEM doub 222 n n 
CGD O2D HEM sing 223 n n 
O2A H2A HEM sing 224 n n 
O2D H2D HEM sing 225 n n 
FE NA HEM sing 226 n n 
FE NB HEM sing 227 n n 
FE NC HEM sing 228 n n 
FE ND HEM sing 229 n n 
#
_atom_sites.entry_id                     8Q2F 
_atom_sites.fract_transf_matrix[1][1]    0.005972 
_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]    0.005972 
_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]    0.002742 
_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
G 2 HEM A 1 501 500 HEM HEM . 
H 3 GOL A 1 502 503 GOL GOL . 
I 3 GOL A 1 503 504 GOL GOL . 
J 4 ACT A 1 504 505 ACT ACT . 
K 4 ACT A 1 505 506 ACT ACT . 
L 3 GOL A 1 506 507 GOL GOL . 
M 5 SO4 A 1 507 508 SO4 SO4 . 
N 5 SO4 A 1 508 509 SO4 SO4 . 
O 5 SO4 A 1 509 510 SO4 SO4 . 
P 2 HEM B 1 501 500 HEM HEM . 
Q 3 GOL B 1 502 502 GOL GOL . 
R 3 GOL B 1 503 503 GOL GOL . 
S 3 GOL B 1 504 505 GOL GOL . 
T 4 ACT B 1 505 506 ACT ACT . 
U 4 ACT B 1 506 507 ACT ACT . 
V 4 ACT B 1 507 508 ACT ACT . 
W 4 ACT B 1 508 509 ACT ACT . 
X 5 SO4 B 1 509 510 SO4 SO4 . 
Y 2 HEM C 1 501 500 HEM HEM . 
Z 5 SO4 C 1 505 501 SO4 SO4 . 
AA 5 SO4 C 1 502 502 SO4 SO4 . 
BA 5 SO4 C 1 503 503 SO4 SO4 . 
CA 5 SO4 C 1 504 504 SO4 SO4 . 
DA 2 HEM D 1 501 500 HEM HEM . 
EA 3 GOL D 1 502 502 GOL GOL . 
FA 4 ACT D 1 503 505 ACT ACT . 
GA 4 ACT D 1 504 506 ACT ACT . 
HA 4 ACT D 1 505 507 ACT ACT . 
IA 5 SO4 D 1 506 508 SO4 SO4 . 
JA 5 SO4 D 1 507 509 SO4 SO4 . 
KA 5 SO4 D 1 508 510 SO4 SO4 . 
LA 2 HEM E 1 501 500 HEM HEM . 
MA 3 GOL E 1 502 503 GOL GOL . 
NA 3 GOL E 1 503 504 GOL GOL . 
OA 4 ACT E 1 504 505 ACT ACT . 
PA 3 GOL E 1 505 506 GOL GOL . 
QA 3 GOL E 1 506 507 GOL GOL . 
RA 3 GOL E 1 507 508 GOL GOL . 
SA 4 ACT E 1 508 509 ACT ACT . 
TA 5 SO4 E 1 509 511 SO4 SO4 . 
UA 5 SO4 E 1 510 512 SO4 SO4 . 
VA 2 HEM F 1 501 500 HEM HEM . 
WA 3 GOL F 1 502 503 GOL GOL . 
XA 4 ACT F 1 503 504 ACT ACT . 
YA 4 ACT F 1 504 505 ACT ACT . 
ZA 4 ACT F 1 505 506 ACT ACT . 
AB 5 SO4 F 1 506 507 SO4 SO4 . 
#
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 C CHA HEM . . . VA 2 93.714 59.8 -2.637 1 114.36 ? CHA HEM 501 F 1 
HETATM 2 C CHB HEM . . . VA 2 97.544 57.874 -4.909 1 110.31 ? CHB HEM 501 F 1 
HETATM 3 C CHC HEM . . . VA 2 96.246 53.483 -3.339 1 106.94 ? CHC HEM 501 F 1 
HETATM 4 C CHD HEM . . . VA 2 92.019 55.304 -1.818 1 99.56 ? CHD HEM 501 F 1 
HETATM 5 C C1A HEM . . . VA 2 94.912 59.689 -3.312 1 112.46 ? C1A HEM 501 F 1 
HETATM 6 C C2A HEM . . . VA 2 95.787 60.775 -3.727 1 105.35 ? C2A HEM 501 F 1 
HETATM 7 C C3A HEM . . . VA 2 96.845 60.231 -4.347 1 108.72 ? C3A HEM 501 F 1 
HETATM 8 C C4A HEM . . . VA 2 96.674 58.792 -4.359 1 116.96 ? C4A HEM 501 F 1 
HETATM 9 C CMA HEM . . . VA 2 98.053 60.972 -4.962 1 91.93 ? CMA HEM 501 F 1 
HETATM 10 C CAA HEM . . . VA 2 95.527 62.279 -3.467 1 96.8 ? CAA HEM 501 F 1 
HETATM 11 C CBA HEM . . . VA 2 95.306 63.057 -4.766 1 100.91 ? CBA HEM 501 F 1 
HETATM 12 C CGA HEM . . . VA 2 94.167 64.03 -4.583 1 112.15 ? CGA HEM 501 F 1 
HETATM 13 O O1A HEM . . . VA 2 93.261 63.716 -3.768 1 119.49 ? O1A HEM 501 F 1 
HETATM 14 O O2A HEM . . . VA 2 94.148 65.103 -5.246 1 93.11 ? O2A HEM 501 F 1 
HETATM 15 C C1B HEM . . . VA 2 97.566 56.528 -4.625 1 106.18 ? C1B HEM 501 F 1 
HETATM 16 C C2B HEM . . . VA 2 98.647 55.611 -4.927 1 92.35 ? C2B HEM 501 F 1 
HETATM 17 C C3B HEM . . . VA 2 98.285 54.394 -4.491 1 92.67 ? C3B HEM 501 F 1 
HETATM 18 C C4B HEM . . . VA 2 96.965 54.514 -3.902 1 111.31 ? C4B HEM 501 F 1 
HETATM 19 C CMB HEM . . . VA 2 99.952 56.041 -5.633 1 98.49 ? CMB HEM 501 F 1 
HETATM 20 C CAB HEM . . . VA 2 99.048 53.048 -4.551 1 84.09 ? CAB HEM 501 F 1 
HETATM 21 C CBB HEM . . . VA 2 100.273 52.894 -5.061 1 90.04 ? CBB HEM 501 F 1 
HETATM 22 C C1C HEM . . . VA 2 95.01 53.589 -2.746 1 103.58 ? C1C HEM 501 F 1 
HETATM 23 C C2C HEM . . . VA 2 94.319 52.54 -2.027 1 90.09 ? C2C HEM 501 F 1 
HETATM 24 C C3C HEM . . . VA 2 93.159 53.022 -1.603 1 91.79 ? C3C HEM 501 F 1 
HETATM 25 C C4C HEM . . . VA 2 93.053 54.413 -2.035 1 106.19 ? C4C HEM 501 F 1 
HETATM 26 C CMC HEM . . . VA 2 94.808 51.1 -1.769 1 79.59 ? CMC HEM 501 F 1 
HETATM 27 C CAC HEM . . . VA 2 92.171 52.158 -0.796 1 89.76 ? CAC HEM 501 F 1 
HETATM 28 C CBC HEM . . . VA 2 91.01 52.63 -0.348 1 111.47 ? CBC HEM 501 F 1 
HETATM 29 C C1D HEM . . . VA 2 92.11 56.684 -1.873 1 102.31 ? C1D HEM 501 F 1 
HETATM 30 C C2D HEM . . . VA 2 91.114 57.643 -1.426 1 100.33 ? C2D HEM 501 F 1 
HETATM 31 C C3D HEM . . . VA 2 91.581 58.873 -1.655 1 102.17 ? C3D HEM 501 F 1 
HETATM 32 C C4D HEM . . . VA 2 92.896 58.756 -2.251 1 105.3 ? C4D HEM 501 F 1 
HETATM 33 C CMD HEM . . . VA 2 89.744 57.305 -0.799 1 103.1 ? CMD HEM 501 F 1 
HETATM 34 C CAD HEM . . . VA 2 90.86 60.197 -1.325 1 109.2 ? CAD HEM 501 F 1 
HETATM 35 C CBD HEM . . . VA 2 91.06 60.506 0.159 1 129.13 ? CBD HEM 501 F 1 
HETATM 36 C CGD HEM . . . VA 2 90.554 61.885 0.497 1 128.37 ? CGD HEM 501 F 1 
HETATM 37 O O1D HEM . . . VA 2 90.387 62.176 1.712 1 116.43 ? O1D HEM 501 F 1 
HETATM 38 O O2D HEM . . . VA 2 90.316 62.688 -0.444 1 126.57 ? O2D HEM 501 F 1 
HETATM 39 N NA HEM . . . VA 2 95.484 58.502 -3.72 1 113.54 ? NA HEM 501 F 1 
HETATM 40 N NB HEM . . . VA 2 96.555 55.828 -4 1 118.09 ? NB HEM 501 F 1 
HETATM 41 N NC HEM . . . VA 2 94.21 54.719 -2.731 1 116.2 ? NC HEM 501 F 1 
HETATM 42 N ND HEM . . . VA 2 93.18 57.41 -2.368 1 100.38 ? ND HEM 501 F 1 
HETATM 43 FE FE HEM . . . VA 2 94.867 56.664 -3.144 1 111.3 ? FE HEM 501 F 1 
#
_model_server_stats.io_time_ms              19 
_model_server_stats.parse_time_ms           20 
_model_server_stats.create_model_time_ms    63 
_model_server_stats.query_time_ms           339 
_model_server_stats.encode_time_ms          4 
_model_server_stats.element_count           43 
#